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- Committer: Bazaar Package Importer
- Author(s): Teemu Ikonen
- Date: 2009-11-24 16:48:04 UTC
- mfrom: (3.1.4 squeeze)
- Revision ID: james.westby@ubuntu.com-20091124164804-liuvywcs6l45ibl3
Tags: 2.7.5-1
* New upstream release
* Imakefile: Use Debian versions of library dependencies
* control:
- Add build-deps to libcvector2-dev, libcqrlib2-dev, libneartree3-dev
- Update to standards-version 3.8.3
* Imakefile: Use Debian versions of library dependencies
* control:
- Add build-deps to libcvector2-dev, libcqrlib2-dev, libneartree3-dev
- Update to standards-version 3.8.3
- files added:
- doc/rasmol.man
- src/mswin/raswin.hlp
- files removed:
- src/languages/genlangsel_all
- src/mswin/raswin.exe
- src/mswin/raswin.exe.gz
- src/mswin/raswin.exe.gz.txt
- src/new_patches
- src/old_patches
- files modified:
- .symlinks
added
removed
doc/raswin.rtf
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{\rtf1\ansi
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{\fonttbl
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\f0\fswiss Arial;
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\f1\fdecor Symbol;
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\f2\fmodern Courier New;
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}\deff0\fs20
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#{\footnote rasmol}
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${\footnote RasMol V2.7.5}
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+{\footnote doc}
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{\fs8 \par }{\fs28\b RasMol V2.7.5}{\fs8 \line }
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{\fs24\b Molecular Graphics Visualisation Tool}\line\pard
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\par\par
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{\fs24\b Table of Contents}\line\pard
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\par\par
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\tx250\li250\fi-250
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{\f1\'b7}\tab
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{\uldb Notices}{\v chnotice}\line
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{\f1\'b7}\tab
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{\uldb Copying}{\v chcopying}\line
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{\f1\'b7}\tab
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{\uldb Introduction}{\v chintro}\line
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{\f1\'b7}\tab
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{\uldb Command Reference}{\v chcomref}\line
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{\f1\'b7}\tab
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{\uldb Internal Parameters}{\v chsetopt}\line
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{\f1\'b7}\tab
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{\uldb Atom Expressions}{\v chexprs}\line
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{\f1\'b7}\tab
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{\uldb Predefined Sets}{\v predefinedsets}\line
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{\f1\'b7}\tab
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{\uldb Colour Schemes}{\v chcolours}\line
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{\f1\'b7}\tab
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{\uldb File Formats}{\v chfile}\line
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{\f1\'b7}\tab
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{\uldb Machine-Specific Support}{\v chmacspec}\line
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{\f1\'b7}\tab
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{\uldb Bibliography}{\v chbib}\line
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\pard
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\par\par
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{\fs16 Based on RasMol 2.6 by Roger Sayle}\line
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{\fs16 Biomolecular Structures Group, Glaxo Wellcome Research & Development}\line
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{\fs16 Stevenage, Hertfordshire, UK}\line
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{\fs16 Version 2.6, August 1995, Version 2.6.4, December 1998}\line
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{\fs16 Copyright \'a9 Roger Sayle 1992-1999}{\fs8 \par\par }
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{\fs16 and Based on Mods by}{\fs8 \par\par }
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{\tx3400\tx5000\tx6000\tx8000
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{\b\fs16 Author\tab Version \tab Date\tab Copyright }
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{\fs8 \par\par }
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{\fs16 Arne Mueller\tab RasMol 2.6x1\tab May 98\tab \'a9 Arne Mueller 1998\ }
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{\fs8 \par\par }
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{\fs16 Gary Grossman and\tab RasMol 2.5-ucb\tab Nov 95\tab \'a9 UC Regents/ModularCHEM }\line
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{\fs16 Marco Molinaro\tab RasMol 2.5-ucb\tab Nov 96\tab Consortium 1995, 1996 }
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{\fs8 \par\par }
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{\fs16 Philippe Valadon\tab RasTop 1.3\tab Aug 00\tab
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\'a9 Philippe Valadon 2000 }
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{\fs8 \par\par }
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{\fs16 Herbert J. Bernstein\tab RasMol 2.7.0\tab Mar 99\tab \'a9 Herbert J. Bernstein }\line
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{\fs16 \tab RasMol 2.7.1 \tab Jun 99\tab 1998-2008\cell }\line
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{\fs16 \tab RasMol 2.7.1.1 \tab Jan 01 }\line
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{\fs16 \tab RasMol 2.7.2 \tab Aug 00 }\line
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{\fs16 \tab RasMol 2.7.2.1 \tab Apr 01 }\line
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{\fs16 \tab RasMol 2.7.2.1.1 \tab Jan 04 }\line
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{\fs16 \tab RasMol 2.7.3 \tab Feb 05 }\line
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{\fs16 \tab RasMol 2.7.3.1 \tab Apr 06 }\line
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{\fs16 \tab RasMol 2.7.4 \tab Nov 07 }\line
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{\fs16 \tab RasMol 2.7.4.1 \tab Jan 08 }\line
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{\fs16 \tab RasMol 2.7.4.2 \tab Mar 08 }\line
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{\fs16 \tab RasMol 2.7.5 \tab Jun 09 }\line
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{\fs16 \tab RasMol 2.7.5.1 \tab Jul 09 }
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{\fs8 \par\par }
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{\fs16 RasMol 2.7.5 incorporates changes by T. Ikonen, G. McQuillan, N. Darakev}\line
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{\fs16 and L. Andrews (via the neartree package). Work on RasMol 2.7.5}\line
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{\fs16 supported in part by grant 1R15GM078077-01 from the National Institute}\line
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{\fs16 of General Medical Sciences (NIGMS), U.S. National Institutes of Health}\line
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{\fs16 and by grant ER63601-1021466-0009501 from the Office of Biological &}\line
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{\fs16 Environmental Research (BER), Office of Science, U. S. Department of}\line
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{\fs16 Energy. RasMol 2.7.4 incorporated changes by G. Todorov, Nan Jia,}\line
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{\fs16 N. Darakev, P. Kamburov, G. McQuillan, and J. Jemilawon. Work on RasMol}\line
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{\fs16 2.7.4 supported in part by grant 1R15GM078077-01 from the NIGMS/NIH and}\line
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{\fs16 grant ER63601-1021466-0009501 from BER/DOE. RasMol 2.7.3 incorporates}\line
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{\fs16 changes by Clarice Chigbo, Ricky Chachra, and Mamoru Yamanishi. Work}\line
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{\fs16 on RasMol 2.7.3 supported in part by grants DBI-0203064, DBI-0315281}\line
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{\fs16 and EF-0312612 from the U.S. National Science Foundation and grant}\line
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{\fs16 DE-FG02-03ER63601 from BER/DOE. The content is solely the responsibility}\line
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{\fs16 of the authors and does not necessarily represent the official views of}\line
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{\fs16 the funding organizations.}\line
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{\fs8 \par\par }
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{\fs16 The code for use of RasMol under GTK in RasMol 2.7.4.2 was written by}\line
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{\fs16 Teemu Ikonen.}\line
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{\fs8 \par\par }
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{\fs16 and Incorporating Translations by}{\fs8 \par\par }}
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{\tx3400\tx6000\tx8000
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{\b\fs16 Author \tab Item \tab Language }{\fs8 \par\par }
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{\fs16 Isabel Serv\'e1n Mart\'ednez, \tab 2.6 Manual\tab Spanish }\line
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{\fs16 Jos\'e9 Miguel Fern\'e1ndez Fern\'e1ndez\tab }\line
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{\fs16 Jos\'e9 Miguel Fern\'e1ndez Fern\'e1ndez \tab 2.7.1 Manual\tab Spanish }\line
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{\fs16 Fernando Gabriel Ranea \tab 2.7.1 menus and messages\tab Spanish }{\fs8 \par\par }
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{\fs16 Jean-Pierre Demailly \tab 2.7.1 menus and messages \tab French }{\fs8 \par\par }
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{\fs16 Giuseppe Martini, Giovanni Paolella \tab 2.7.1 menus and messages \tab}\line
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{\fs16 A. Davassi, M. Masullo, C. Liotto\tab 2.7.1 help file \tab Italian}\line
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{\fs16 G. Pozhvanov \tab 2.7.3 menus and messages \tab Russian}\line
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{\fs16 G. Todorov \tab 2.7.3 menus and messages \tab Bulgarian}\line
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{\fs16 Nan Jia, G. Todorov \tab 2.7.3 menus and messages \tab Chinese}\line
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{\fs16 Mamoru Yamanishi, Katajima Hajime \tab 2.7.3 menus and messages \tab Japanese}
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\par\pard}
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\par\par
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{\fs16
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The original RasMol manual was created by Roger Sayle. In July 1996, {}
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Dr. Margaret Wong of the Chemistry Department, Swinburne University {}
110
of Technology, Australia, made extensive revisions to the RasMol 2.5 {}
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manual to accurately reflect the operation of RasMol 2.6. Eric Martz {}
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of the University of Massachusetts made further revisions. In May {}
113
1997, William McClure of Carnegie Mellon University reorganized the {}
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HTML version of the manual into multiple sections which could be {}
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downloaded quickly and added use of frames. Portions of the 2.7.1 {}
116
version of the RasMol manual were derived with permission from {}
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William McClure's version using Roger Sayle's rasmol.doc for {}
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version 2.6.4 as the primary source. Changes have been made in {}
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August 2000 for RasMol version 2.7.2, January 2001 for RasMol {}
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version 2.7.1.1, April 2001 for RasMol version 2.7.2.1, {}
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February 2005 for RasMol version 2.7.3 and November 2007, {}
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January 2008 and March 2008 for RasMol version 2.7.4. {}
123
}
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\par\par
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{\fs16 Documentation Last Updated 17 July 2009}\line
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{\fs16 Edited by Herbert J. Bernstein and Frances C. Bernstein}
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\par\par
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{\fs16 Please read the file NOTICE for important notices which apply to this}\line
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{\fs16 package and for license terms (GPL or RASLIC).}
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\pard\par
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\par\par
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RasMol Copyright \'a9 Roger Sayle 1992-1999\par {}
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Version 2.6x1 Mods Copyright \'a9 Arne Mueller 1998\par {}
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Versions 2.5-ucb and 2.6-ucb Mods Copyright \'a9\par {}
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UC Regents/ModularCHEM Consortium 1995, 1996\par {}
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RasTop 1.3 Copyright \'a9 Philippe Valadon 2000\par {}
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Version 2.7.0, 2.7.1, 2.7.1.1, 2.7.2, 2.7.2.1, 2.7.2.1.1\par {}
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2.7.3, 2.7.3.1, 2.7.4, 2.7.4.1, 2.7.4.2, 2.7.5, 2.7.5.1 Mods\par {}
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Copyright \'a9 Herbert J. Bernstein 1998-2009\par {}
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rasmol@bernstein-plus-sons.com\par {}
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\par\par
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{\fs16
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All rights reserved. Use of copyright notice does not imply publication or {}
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disclosure. The information supplied in this document is believed to be true {}
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but no liability is assumed for its use or for the infringements of the rights {}
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of the others resulting from its use. Information in this document is subject {}
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to change without notice and does not represent a commitment on the part of {}
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the supplier. {}
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}
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\par\page\par
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+{\footnote doc}
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#{\footnote chnotice}
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${\footnote Notices}
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{\fs24\b Notices}\par\par
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\par\par
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This software has been created from several sources. Much of the code is {}
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from RasMol 2.6, as created by Roger Sayle. {}
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See: {}
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{\tx750\f2\tab http://www.dcs.ed.ac.uk/home/rasmol\par}\pard\par
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The torsion angle code, new POVRAY3 code and other features are derived from {}
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the RasMol2.6x1 revisions by Arne Mueller. {}
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{\tx750\f2\tab ftp://nexus.roko.goe.net/pub/rasmol\par}\pard\par
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The Ramachandran printer plot code was derived from fisipl created by Frances C. {}
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Bernstein. See the Protein Data Bank program tape. {}
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\par\par
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The code to display multiple molecules and to allow bond rotation is derived {}
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in large part from the UCB mods by Gary Grossman and Marco Molinaro, {}
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included with {}
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permission of Eileen Lewis of the ModularCHEM Consortium. {}
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{\tx750\f2\tab http://mc2.CCHem.Berkeley.EDU/RasMol\par}\pard\par
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\par\par
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The CIF modifications make use of a library based in part on CBFlib by {}
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Paul J. Ellis and Herbert J. Bernstein. {}
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See: {}
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{\tx750\f2\tab http://www.bernstein-plus-sons.com/software/CBF\par}\pard\par
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Parts of CBFlib is loosely based on the CIFPARSE software package from the NDB {}
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at Rutgers university. {}
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See: {}
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{\tx750\f2\tab http://www.iucr.org/iucr-top/cif/mmcif/ndb/software/CIFPARSE/\par}\pard\par
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Please type the RasMol commands {}
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'{\f2\b help copying}', {}
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'{\f2\b help general}', {}
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'{\f2\b help IUCR}', {}
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'{\f2\b help CBFlib}', {}
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and {}
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'{\f2\b help CIFPARSE}' {}
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for applicable notices. Please type {}
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'{\f2\b help copyright}' {}
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for copyright notices. If you use RasMol V2.6 {}
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or an earlier version, type the RasMol command {}
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'{\f2\b help oldnotice}'. {}
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\par\page\par
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+{\footnote doc}
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#{\footnote chcopying}
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${\footnote Copying}
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{\fs24\b Copying}\par\par
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\par\par
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This version is based directly on RasMol version 2.7.4.2, {}
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on RasMol verion 2.7.4.2, on RasMol version 2.7.4, {}
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on RasMol version 2.7.3.1, on RasMol version 2.7.3, {}
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on RasMol version 2.7.2.1.1, Rasmol version 2.7.2, RasMol {}
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version 2.7.1.1 and RasTop version 1.3 and indirectly on {}
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the RasMol 2.5-ucb and 2.6-ucb versions and version {}
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2.6_CIF.2, RasMol 2.6x1 and RasMol_2.6.4. {}
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\par\par
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RasMol 2.7.5 may be distributed under the terms of the GNU {}
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General Public License (the GPL), see {}
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\par\par
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http://www.gnu.org/licenses/gpl.txt {}
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\par\par
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or the file GPL or type the command {}
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'{\uldb help GPL}{\v GPL}' {}
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\par\par
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or RasMol 2.7.5 may be distributed under the RASMOL license. {}
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See the file NOTICE {}
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or type the command {}
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'{\uldb help RASLIC}{\v RASLIC}' {}
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\par\page\par
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+{\footnote doc}
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#{\footnote gpl}
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${\footnote GPL}
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K{\footnote gpl}
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{\b GPL}\par\par
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\pard{\f2 \fs20\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~GNU\~GENERAL\~PUBLIC\~LICENSE\par}
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\pard{\f2 \fs20\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~Version\~2,\~June\~1991\par}
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\par\par
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\pard{\f2 \fs20\~Copyright\~(C)\~1989,\~1991\~Free\~Software\~Foundation,\~Inc.\par}
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\pard{\f2 \fs20\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~59\~Temple\~Place,\~Suite\~330,\~Boston,\~MA\~\~02111-1307\~\~USA\par}
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\pard{\f2 \fs20\~Everyone\~is\~permitted\~to\~copy\~and\~distribute\~verbatim\~copies\par}
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\pard{\f2 \fs20\~of\~this\~license\~document,\~but\~changing\~it\~is\~not\~allowed.\par}
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\par\par
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\pard{\f2 \fs20\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~Preamble\par}
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\par\par
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\pard{\f2 \fs20\~\~The\~licenses\~for\~most\~software\~are\~designed\~to\~take\~away\~your\par}
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\pard{\f2 \fs20freedom\~to\~share\~and\~change\~it.\~\~By\~contrast,\~the\~GNU\~General\~Public\par}
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\pard{\f2 \fs20License\~is\~intended\~to\~guarantee\~your\~freedom\~to\~share\~and\~change\~free\par}
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\pard{\f2 \fs20software--to\~make\~sure\~the\~software\~is\~free\~for\~all\~its\~users.\~\~This\par}
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\pard{\f2 \fs20General\~Public\~License\~applies\~to\~most\~of\~the\~Free\~Software\par}
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\pard{\f2 \fs20Foundation's\~software\~and\~to\~any\~other\~program\~whose\~authors\~commit\~to\par}
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\pard{\f2 \fs20using\~it.\~\~(Some\~other\~Free\~Software\~Foundation\~software\~is\~covered\~by\par}
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\pard{\f2 \fs20the\~GNU\~Library\~General\~Public\~License\~instead.)\~\~You\~can\~apply\~it\~to\par}
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\pard{\f2 \fs20your\~programs,\~too.\par}
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\par\par
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\pard{\f2 \fs20\~\~When\~we\~speak\~of\~free\~software,\~we\~are\~referring\~to\~freedom,\~not\par}
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\pard{\f2 \fs20price.\~\~Our\~General\~Public\~Licenses\~are\~designed\~to\~make\~sure\~that\~you\par}
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\pard{\f2 \fs20have\~the\~freedom\~to\~distribute\~copies\~of\~free\~software\~(and\~charge\~for\par}
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\pard{\f2 \fs20this\~service\~if\~you\~wish),\~that\~you\~receive\~source\~code\~or\~can\~get\~it\par}
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\pard{\f2 \fs20if\~you\~want\~it,\~that\~you\~can\~change\~the\~software\~or\~use\~pieces\~of\~it\par}
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\pard{\f2 \fs20in\~new\~free\~programs;\~and\~that\~you\~know\~you\~can\~do\~these\~things.\par}
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\par\par
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\pard{\f2 \fs20\~\~To\~protect\~your\~rights,\~we\~need\~to\~make\~restrictions\~that\~forbid\par}
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\pard{\f2 \fs20anyone\~to\~deny\~you\~these\~rights\~or\~to\~ask\~you\~to\~surrender\~the\~rights.\par}
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\pard{\f2 \fs20These\~restrictions\~translate\~to\~certain\~responsibilities\~for\~you\~if\~you\par}
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\pard{\f2 \fs20distribute\~copies\~of\~the\~software,\~or\~if\~you\~modify\~it.\par}
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\par\par
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\pard{\f2 \fs20\~\~For\~example,\~if\~you\~distribute\~copies\~of\~such\~a\~program,\~whether\par}
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\pard{\f2 \fs20gratis\~or\~for\~a\~fee,\~you\~must\~give\~the\~recipients\~all\~the\~rights\~that\par}
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\pard{\f2 \fs20you\~have.\~\~You\~must\~make\~sure\~that\~they,\~too,\~receive\~or\~can\~get\~the\par}
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\pard{\f2 \fs20source\~code.\~\~And\~you\~must\~show\~them\~these\~terms\~so\~they\~know\~their\par}
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\pard{\f2 \fs20rights.\par}
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\par\par
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\pard{\f2 \fs20\~\~We\~protect\~your\~rights\~with\~two\~steps:\~(1)\~copyright\~the\~software,\~and\par}
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\pard{\f2 \fs20(2)\~offer\~you\~this\~license\~which\~gives\~you\~legal\~permission\~to\~copy,\par}
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\pard{\f2 \fs20distribute\~and/or\~modify\~the\~software.\par}
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\par\par
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\pard{\f2 \fs20\~\~Also,\~for\~each\~author's\~protection\~and\~ours,\~we\~want\~to\~make\~certain\par}
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\pard{\f2 \fs20that\~everyone\~understands\~that\~there\~is\~no\~warranty\~for\~this\~free\par}
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\pard{\f2 \fs20software.\~\~If\~the\~software\~is\~modified\~by\~someone\~else\~and\~passed\~on,\~we\par}
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\pard{\f2 \fs20want\~its\~recipients\~to\~know\~that\~what\~they\~have\~is\~not\~the\~original,\~so\par}
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\pard{\f2 \fs20that\~any\~problems\~introduced\~by\~others\~will\~not\~reflect\~on\~the\~original\par}
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\pard{\f2 \fs20authors'\~reputations.\par}
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\par\par
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\pard{\f2 \fs20\~\~Finally,\~any\~free\~program\~is\~threatened\~constantly\~by\~software\par}
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\pard{\f2 \fs20patents.\~\~We\~wish\~to\~avoid\~the\~danger\~that\~redistributors\~of\~a\~free\par}
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\pard{\f2 \fs20program\~will\~individually\~obtain\~patent\~licenses,\~in\~effect\~making\~the\par}
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\pard{\f2 \fs20program\~proprietary.\~\~To\~prevent\~this,\~we\~have\~made\~it\~clear\~that\~any\par}
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\pard{\f2 \fs20patent\~must\~be\~licensed\~for\~everyone's\~free\~use\~or\~not\~licensed\~at\~all.\par}
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\par\par
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\pard{\f2 \fs20\~\~The\~precise\~terms\~and\~conditions\~for\~copying,\~distribution\~and\par}
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\pard{\f2 \fs20modification\~follow.\par}
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\par\par
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\pard{\f2 \fs20\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~GNU\~GENERAL\~PUBLIC\~LICENSE\par}
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\pard{\f2 \fs20\~\~\~TERMS\~AND\~CONDITIONS\~FOR\~COPYING,\~DISTRIBUTION\~AND\~MODIFICATION\par}
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\par\par
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\pard{\f2 \fs20\~\~0.\~This\~License\~applies\~to\~any\~program\~or\~other\~work\~which\~contains\par}
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\pard{\f2 \fs20a\~notice\~placed\~by\~the\~copyright\~holder\~saying\~it\~may\~be\~distributed\par}
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\pard{\f2 \fs20under\~the\~terms\~of\~this\~General\~Public\~License.\~\~The\~"Program",\~below,\par}
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\pard{\f2 \fs20refers\~to\~any\~such\~program\~or\~work,\~and\~a\~"work\~based\~on\~the\~Program"\par}
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\pard{\f2 \fs20means\~either\~the\~Program\~or\~any\~derivative\~work\~under\~copyright\~law:\par}
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\pard{\f2 \fs20that\~is\~to\~say,\~a\~work\~containing\~the\~Program\~or\~a\~portion\~of\~it,\par}
291
\pard{\f2 \fs20either\~verbatim\~or\~with\~modifications\~and/or\~translated\~into\~another\par}
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\pard{\f2 \fs20language.\~\~(Hereinafter,\~translation\~is\~included\~without\~limitation\~in\par}
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\pard{\f2 \fs20the\~term\~"modification".)\~\~Each\~licensee\~is\~addressed\~as\~"you".\par}
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\par\par
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\pard{\f2 \fs20Activities\~other\~than\~copying,\~distribution\~and\~modification\~are\~not\par}
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\pard{\f2 \fs20covered\~by\~this\~License;\~they\~are\~outside\~its\~scope.\~\~The\~act\~of\par}
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\pard{\f2 \fs20running\~the\~Program\~is\~not\~restricted,\~and\~the\~output\~from\~the\~Program\par}
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\pard{\f2 \fs20is\~covered\~only\~if\~its\~contents\~constitute\~a\~work\~based\~on\~the\par}
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\pard{\f2 \fs20Program\~(independent\~of\~having\~been\~made\~by\~running\~the\~Program).\par}
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\pard{\f2 \fs20Whether\~that\~is\~true\~depends\~on\~what\~the\~Program\~does.\par}
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\par\par
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\pard{\f2 \fs20\~\~1.\~You\~may\~copy\~and\~distribute\~verbatim\~copies\~of\~the\~Program's\par}
303
\pard{\f2 \fs20source\~code\~as\~you\~receive\~it,\~in\~any\~medium,\~provided\~that\~you\par}
304
\pard{\f2 \fs20conspicuously\~and\~appropriately\~publish\~on\~each\~copy\~an\~appropriate\par}
305
\pard{\f2 \fs20copyright\~notice\~and\~disclaimer\~of\~warranty;\~keep\~intact\~all\~the\par}
306
\pard{\f2 \fs20notices\~that\~refer\~to\~this\~License\~and\~to\~the\~absence\~of\~any\~warranty;\par}
307
\pard{\f2 \fs20and\~give\~any\~other\~recipients\~of\~the\~Program\~a\~copy\~of\~this\~License\par}
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\pard{\f2 \fs20along\~with\~the\~Program.\par}
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\par\par
310
\pard{\f2 \fs20You\~may\~charge\~a\~fee\~for\~the\~physical\~act\~of\~transferring\~a\~copy,\~and\par}
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\pard{\f2 \fs20you\~may\~at\~your\~option\~offer\~warranty\~protection\~in\~exchange\~for\~a\~fee.\par}
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\par\par
313
\pard{\f2 \fs20\~\~2.\~You\~may\~modify\~your\~copy\~or\~copies\~of\~the\~Program\~or\~any\~portion\par}
314
\pard{\f2 \fs20of\~it,\~thus\~forming\~a\~work\~based\~on\~the\~Program,\~and\~copy\~and\par}
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\pard{\f2 \fs20distribute\~such\~modifications\~or\~work\~under\~the\~terms\~of\~Section\~1\par}
316
\pard{\f2 \fs20above,\~provided\~that\~you\~also\~meet\~all\~of\~these\~conditions:\par}
317
\par\par
318
\pard{\f2 \fs20\~\~\~\~a)\~You\~must\~cause\~the\~modified\~files\~to\~carry\~prominent\~notices\par}
319
\pard{\f2 \fs20\~\~\~\~stating\~that\~you\~changed\~the\~files\~and\~the\~date\~of\~any\~change.\par}
320
\par\par
321
\pard{\f2 \fs20\~\~\~\~b)\~You\~must\~cause\~any\~work\~that\~you\~distribute\~or\~publish,\~that\~in\par}
322
\pard{\f2 \fs20\~\~\~\~whole\~or\~in\~part\~contains\~or\~is\~derived\~from\~the\~Program\~or\~any\par}
323
\pard{\f2 \fs20\~\~\~\~part\~thereof,\~to\~be\~licensed\~as\~a\~whole\~at\~no\~charge\~to\~all\~third\par}
324
\pard{\f2 \fs20\~\~\~\~parties\~under\~the\~terms\~of\~this\~License.\par}
325
\par\par
326
\pard{\f2 \fs20\~\~\~\~c)\~If\~the\~modified\~program\~normally\~reads\~commands\~interactively\par}
327
\pard{\f2 \fs20\~\~\~\~when\~run,\~you\~must\~cause\~it,\~when\~started\~running\~for\~such\par}
328
\pard{\f2 \fs20\~\~\~\~interactive\~use\~in\~the\~most\~ordinary\~way,\~to\~print\~or\~display\~an\par}
329
\pard{\f2 \fs20\~\~\~\~announcement\~including\~an\~appropriate\~copyright\~notice\~and\~a\par}
330
\pard{\f2 \fs20\~\~\~\~notice\~that\~there\~is\~no\~warranty\~(or\~else,\~saying\~that\~you\~provide\par}
331
\pard{\f2 \fs20\~\~\~\~a\~warranty)\~and\~that\~users\~may\~redistribute\~the\~program\~under\par}
332
\pard{\f2 \fs20\~\~\~\~these\~conditions,\~and\~telling\~the\~user\~how\~to\~view\~a\~copy\~of\~this\par}
333
\pard{\f2 \fs20\~\~\~\~License.\~\~(Exception:\~if\~the\~Program\~itself\~is\~interactive\~but\par}
334
\pard{\f2 \fs20\~\~\~\~does\~not\~normally\~print\~such\~an\~announcement,\~your\~work\~based\~on\par}
335
\pard{\f2 \fs20\~\~\~\~the\~Program\~is\~not\~required\~to\~print\~an\~announcement.)\par}
336
\par\par
337
\pard{\f2 \fs20These\~requirements\~apply\~to\~the\~modified\~work\~as\~a\~whole.\~\~If\par}
338
\pard{\f2 \fs20identifiable\~sections\~of\~that\~work\~are\~not\~derived\~from\~the\~Program,\par}
339
\pard{\f2 \fs20and\~can\~be\~reasonably\~considered\~independent\~and\~separate\~works\~in\par}
340
\pard{\f2 \fs20themselves,\~then\~this\~License,\~and\~its\~terms,\~do\~not\~apply\~to\~those\par}
341
\pard{\f2 \fs20sections\~when\~you\~distribute\~them\~as\~separate\~works.\~\~But\~when\~you\par}
342
\pard{\f2 \fs20distribute\~the\~same\~sections\~as\~part\~of\~a\~whole\~which\~is\~a\~work\~based\par}
343
\pard{\f2 \fs20on\~the\~Program,\~the\~distribution\~of\~the\~whole\~must\~be\~on\~the\~terms\~of\par}
344
\pard{\f2 \fs20this\~License,\~whose\~permissions\~for\~other\~licensees\~extend\~to\~the\par}
345
\pard{\f2 \fs20entire\~whole,\~and\~thus\~to\~each\~and\~every\~part\~regardless\~of\~who\~wrote\~it.\par}
346
\par\par
347
\pard{\f2 \fs20Thus,\~it\~is\~not\~the\~intent\~of\~this\~section\~to\~claim\~rights\~or\~contest\par}
348
\pard{\f2 \fs20your\~rights\~to\~work\~written\~entirely\~by\~you;\~rather,\~the\~intent\~is\~to\par}
349
\pard{\f2 \fs20exercise\~the\~right\~to\~control\~the\~distribution\~of\~derivative\~or\par}
350
\pard{\f2 \fs20collective\~works\~based\~on\~the\~Program.\par}
351
\par\par
352
\pard{\f2 \fs20In\~addition,\~mere\~aggregation\~of\~another\~work\~not\~based\~on\~the\~Program\par}
353
\pard{\f2 \fs20with\~the\~Program\~(or\~with\~a\~work\~based\~on\~the\~Program)\~on\~a\~volume\~of\par}
354
\pard{\f2 \fs20a\~storage\~or\~distribution\~medium\~does\~not\~bring\~the\~other\~work\~under\par}
355
\pard{\f2 \fs20the\~scope\~of\~this\~License.\par}
356
\par\par
357
\pard{\f2 \fs20\~\~3.\~You\~may\~copy\~and\~distribute\~the\~Program\~(or\~a\~work\~based\~on\~it,\par}
358
\pard{\f2 \fs20under\~Section\~2)\~in\~object\~code\~or\~executable\~form\~under\~the\~terms\~of\par}
359
\pard{\f2 \fs20Sections\~1\~and\~2\~above\~provided\~that\~you\~also\~do\~one\~of\~the\~following:\par}
360
\par\par
361
\pard{\f2 \fs20\~\~\~\~a)\~Accompany\~it\~with\~the\~complete\~corresponding\~machine-readable\par}
362
\pard{\f2 \fs20\~\~\~\~source\~code,\~which\~must\~be\~distributed\~under\~the\~terms\~of\~Sections\par}
363
\pard{\f2 \fs20\~\~\~\~1\~and\~2\~above\~on\~a\~medium\~customarily\~used\~for\~software\~interchange;\~or,\par}
364
\par\par
365
\pard{\f2 \fs20\~\~\~\~b)\~Accompany\~it\~with\~a\~written\~offer,\~valid\~for\~at\~least\~three\par}
366
\pard{\f2 \fs20\~\~\~\~years,\~to\~give\~any\~third\~party,\~for\~a\~charge\~no\~more\~than\~your\par}
367
\pard{\f2 \fs20\~\~\~\~cost\~of\~physically\~performing\~source\~distribution,\~a\~complete\par}
368
\pard{\f2 \fs20\~\~\~\~machine-readable\~copy\~of\~the\~corresponding\~source\~code,\~to\~be\par}
369
\pard{\f2 \fs20\~\~\~\~distributed\~under\~the\~terms\~of\~Sections\~1\~and\~2\~above\~on\~a\~medium\par}
370
\pard{\f2 \fs20\~\~\~\~customarily\~used\~for\~software\~interchange;\~or,\par}
371
\par\par
372
\pard{\f2 \fs20\~\~\~\~c)\~Accompany\~it\~with\~the\~information\~you\~received\~as\~to\~the\~offer\par}
373
\pard{\f2 \fs20\~\~\~\~to\~distribute\~corresponding\~source\~code.\~\~(This\~alternative\~is\par}
374
\pard{\f2 \fs20\~\~\~\~allowed\~only\~for\~noncommercial\~distribution\~and\~only\~if\~you\par}
375
\pard{\f2 \fs20\~\~\~\~received\~the\~program\~in\~object\~code\~or\~executable\~form\~with\~such\par}
376
\pard{\f2 \fs20\~\~\~\~an\~offer,\~in\~accord\~with\~Subsection\~b\~above.)\par}
377
\par\par
378
\pard{\f2 \fs20The\~source\~code\~for\~a\~work\~means\~the\~preferred\~form\~of\~the\~work\~for\par}
379
\pard{\f2 \fs20making\~modifications\~to\~it.\~\~For\~an\~executable\~work,\~complete\~source\par}
380
\pard{\f2 \fs20code\~means\~all\~the\~source\~code\~for\~all\~modules\~it\~contains,\~plus\~any\par}
381
\pard{\f2 \fs20associated\~interface\~definition\~files,\~plus\~the\~scripts\~used\~to\par}
382
\pard{\f2 \fs20control\~compilation\~and\~installation\~of\~the\~executable.\~\~However,\~as\~a\par}
383
\pard{\f2 \fs20special\~exception,\~the\~source\~code\~distributed\~need\~not\~include\par}
384
\pard{\f2 \fs20anything\~that\~is\~normally\~distributed\~(in\~either\~source\~or\~binary\par}
385
\pard{\f2 \fs20form)\~with\~the\~major\~components\~(compiler,\~kernel,\~and\~so\~on)\~of\~the\par}
386
\pard{\f2 \fs20operating\~system\~on\~which\~the\~executable\~runs,\~unless\~that\~component\par}
387
\pard{\f2 \fs20itself\~accompanies\~the\~executable.\par}
388
\par\par
389
\pard{\f2 \fs20If\~distribution\~of\~executable\~or\~object\~code\~is\~made\~by\~offering\par}
390
\pard{\f2 \fs20access\~to\~copy\~from\~a\~designated\~place,\~then\~offering\~equivalent\par}
391
\pard{\f2 \fs20access\~to\~copy\~the\~source\~code\~from\~the\~same\~place\~counts\~as\par}
392
\pard{\f2 \fs20distribution\~of\~the\~source\~code,\~even\~though\~third\~parties\~are\~not\par}
393
\pard{\f2 \fs20compelled\~to\~copy\~the\~source\~along\~with\~the\~object\~code.\par}
394
\par\par
395
\pard{\f2 \fs20\~\~4.\~You\~may\~not\~copy,\~modify,\~sublicense,\~or\~distribute\~the\~Program\par}
396
\pard{\f2 \fs20except\~as\~expressly\~provided\~under\~this\~License.\~\~Any\~attempt\par}
397
\pard{\f2 \fs20otherwise\~to\~copy,\~modify,\~sublicense\~or\~distribute\~the\~Program\~is\par}
398
\pard{\f2 \fs20void,\~and\~will\~automatically\~terminate\~your\~rights\~under\~this\~License.\par}
399
\pard{\f2 \fs20However,\~parties\~who\~have\~received\~copies,\~or\~rights,\~from\~you\~under\par}
400
\pard{\f2 \fs20this\~License\~will\~not\~have\~their\~licenses\~terminated\~so\~long\~as\~such\par}
401
\pard{\f2 \fs20parties\~remain\~in\~full\~compliance.\par}
402
\par\par
403
\pard{\f2 \fs20\~\~5.\~You\~are\~not\~required\~to\~accept\~this\~License,\~since\~you\~have\~not\par}
404
\pard{\f2 \fs20signed\~it.\~\~However,\~nothing\~else\~grants\~you\~permission\~to\~modify\~or\par}
405
\pard{\f2 \fs20distribute\~the\~Program\~or\~its\~derivative\~works.\~\~These\~actions\~are\par}
406
\pard{\f2 \fs20prohibited\~by\~law\~if\~you\~do\~not\~accept\~this\~License.\~\~Therefore,\~by\par}
407
\pard{\f2 \fs20modifying\~or\~distributing\~the\~Program\~(or\~any\~work\~based\~on\~the\par}
408
\pard{\f2 \fs20Program),\~you\~indicate\~your\~acceptance\~of\~this\~License\~to\~do\~so,\~and\par}
409
\pard{\f2 \fs20all\~its\~terms\~and\~conditions\~for\~copying,\~distributing\~or\~modifying\par}
410
\pard{\f2 \fs20the\~Program\~or\~works\~based\~on\~it.\par}
411
\par\par
412
\pard{\f2 \fs20\~\~6.\~Each\~time\~you\~redistribute\~the\~Program\~(or\~any\~work\~based\~on\~the\par}
413
\pard{\f2 \fs20Program),\~the\~recipient\~automatically\~receives\~a\~license\~from\~the\par}
414
\pard{\f2 \fs20original\~licensor\~to\~copy,\~distribute\~or\~modify\~the\~Program\~subject\~to\par}
415
\pard{\f2 \fs20these\~terms\~and\~conditions.\~\~You\~may\~not\~impose\~any\~further\par}
416
\pard{\f2 \fs20restrictions\~on\~the\~recipients'\~exercise\~of\~the\~rights\~granted\~herein.\par}
417
\pard{\f2 \fs20You\~are\~not\~responsible\~for\~enforcing\~compliance\~by\~third\~parties\~to\par}
418
\pard{\f2 \fs20this\~License.\par}
419
\par\par
420
\pard{\f2 \fs20\~\~7.\~If,\~as\~a\~consequence\~of\~a\~court\~judgment\~or\~allegation\~of\~patent\par}
421
\pard{\f2 \fs20infringement\~or\~for\~any\~other\~reason\~(not\~limited\~to\~patent\~issues),\par}
422
\pard{\f2 \fs20conditions\~are\~imposed\~on\~you\~(whether\~by\~court\~order,\~agreement\~or\par}
423
\pard{\f2 \fs20otherwise)\~that\~contradict\~the\~conditions\~of\~this\~License,\~they\~do\~not\par}
424
\pard{\f2 \fs20excuse\~you\~from\~the\~conditions\~of\~this\~License.\~\~If\~you\~cannot\par}
425
\pard{\f2 \fs20distribute\~so\~as\~to\~satisfy\~simultaneously\~your\~obligations\~under\~this\par}
426
\pard{\f2 \fs20License\~and\~any\~other\~pertinent\~obligations,\~then\~as\~a\~consequence\~you\par}
427
\pard{\f2 \fs20may\~not\~distribute\~the\~Program\~at\~all.\~\~For\~example,\~if\~a\~patent\par}
428
\pard{\f2 \fs20license\~would\~not\~permit\~royalty-free\~redistribution\~of\~the\~Program\~by\par}
429
\pard{\f2 \fs20all\~those\~who\~receive\~copies\~directly\~or\~indirectly\~through\~you,\~then\par}
430
\pard{\f2 \fs20the\~only\~way\~you\~could\~satisfy\~both\~it\~and\~this\~License\~would\~be\~to\par}
431
\pard{\f2 \fs20refrain\~entirely\~from\~distribution\~of\~the\~Program.\par}
432
\par\par
433
\pard{\f2 \fs20If\~any\~portion\~of\~this\~section\~is\~held\~invalid\~or\~unenforceable\~under\par}
434
\pard{\f2 \fs20any\~particular\~circumstance,\~the\~balance\~of\~the\~section\~is\~intended\~to\par}
435
\pard{\f2 \fs20apply\~and\~the\~section\~as\~a\~whole\~is\~intended\~to\~apply\~in\~other\par}
436
\pard{\f2 \fs20circumstances.\par}
437
\par\par
438
\pard{\f2 \fs20It\~is\~not\~the\~purpose\~of\~this\~section\~to\~induce\~you\~to\~infringe\~any\par}
439
\pard{\f2 \fs20patents\~or\~other\~property\~right\~claims\~or\~to\~contest\~validity\~of\~any\par}
440
\pard{\f2 \fs20such\~claims;\~this\~section\~has\~the\~sole\~purpose\~of\~protecting\~the\par}
441
\pard{\f2 \fs20integrity\~of\~the\~free\~software\~distribution\~system,\~which\~is\par}
442
\pard{\f2 \fs20implemented\~by\~public\~license\~practices.\~\~Many\~people\~have\~made\par}
443
\pard{\f2 \fs20generous\~contributions\~to\~the\~wide\~range\~of\~software\~distributed\par}
444
\pard{\f2 \fs20through\~that\~system\~in\~reliance\~on\~consistent\~application\~of\~that\par}
445
\pard{\f2 \fs20system;\~it\~is\~up\~to\~the\~author/donor\~to\~decide\~if\~he\~or\~she\~is\~willing\par}
446
\pard{\f2 \fs20to\~distribute\~software\~through\~any\~other\~system\~and\~a\~licensee\~cannot\par}
447
\pard{\f2 \fs20impose\~that\~choice.\par}
448
\par\par
449
\pard{\f2 \fs20This\~section\~is\~intended\~to\~make\~thoroughly\~clear\~what\~is\~believed\~to\par}
450
\pard{\f2 \fs20be\~a\~consequence\~of\~the\~rest\~of\~this\~License.\par}
451
\par\par
452
\pard{\f2 \fs20\~\~8.\~If\~the\~distribution\~and/or\~use\~of\~the\~Program\~is\~restricted\~in\par}
453
\pard{\f2 \fs20certain\~countries\~either\~by\~patents\~or\~by\~copyrighted\~interfaces,\~the\par}
454
\pard{\f2 \fs20original\~copyright\~holder\~who\~places\~the\~Program\~under\~this\~License\par}
455
\pard{\f2 \fs20may\~add\~an\~explicit\~geographical\~distribution\~limitation\~excluding\par}
456
\pard{\f2 \fs20those\~countries,\~so\~that\~distribution\~is\~permitted\~only\~in\~or\~among\par}
457
\pard{\f2 \fs20countries\~not\~thus\~excluded.\~\~In\~such\~case,\~this\~License\~incorporates\par}
458
\pard{\f2 \fs20the\~limitation\~as\~if\~written\~in\~the\~body\~of\~this\~License.\par}
459
\par\par
460
\pard{\f2 \fs20\~\~9.\~The\~Free\~Software\~Foundation\~may\~publish\~revised\~and/or\~new\~versions\par}
461
\pard{\f2 \fs20of\~the\~General\~Public\~License\~from\~time\~to\~time.\~\~Such\~new\~versions\~will\par}
462
\pard{\f2 \fs20be\~similar\~in\~spirit\~to\~the\~present\~version,\~but\~may\~differ\~in\~detail\~to\par}
463
\pard{\f2 \fs20address\~new\~problems\~or\~concerns.\par}
464
\par\par
465
\pard{\f2 \fs20Each\~version\~is\~given\~a\~distinguishing\~version\~number.\~\~If\~the\~Program\par}
466
\pard{\f2 \fs20specifies\~a\~version\~number\~of\~this\~License\~which\~applies\~to\~it\~and\~"any\par}
467
\pard{\f2 \fs20later\~version",\~you\~have\~the\~option\~of\~following\~the\~terms\~and\~conditions\par}
468
\pard{\f2 \fs20either\~of\~that\~version\~or\~of\~any\~later\~version\~published\~by\~the\~Free\par}
469
\pard{\f2 \fs20Software\~Foundation.\~\~If\~the\~Program\~does\~not\~specify\~a\~version\~number\~of\par}
470
\pard{\f2 \fs20this\~License,\~you\~may\~choose\~any\~version\~ever\~published\~by\~the\~Free\~Software\par}
471
\pard{\f2 \fs20Foundation.\par}
472
\par\par
473
\pard{\f2 \fs20\~\~10.\~If\~you\~wish\~to\~incorporate\~parts\~of\~the\~Program\~into\~other\~free\par}
474
\pard{\f2 \fs20programs\~whose\~distribution\~conditions\~are\~different,\~write\~to\~the\~author\par}
475
\pard{\f2 \fs20to\~ask\~for\~permission.\~\~For\~software\~which\~is\~copyrighted\~by\~the\~Free\par}
476
\pard{\f2 \fs20Software\~Foundation,\~write\~to\~the\~Free\~Software\~Foundation;\~we\~sometimes\par}
477
\pard{\f2 \fs20make\~exceptions\~for\~this.\~\~Our\~decision\~will\~be\~guided\~by\~the\~two\~goals\par}
478
\pard{\f2 \fs20of\~preserving\~the\~free\~status\~of\~all\~derivatives\~of\~our\~free\~software\~and\par}
479
\pard{\f2 \fs20of\~promoting\~the\~sharing\~and\~reuse\~of\~software\~generally.\par}
480
\par\par
481
\pard{\f2 \fs20\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~NO\~WARRANTY\par}
482
\par\par
483
\pard{\f2 \fs20\~\~11.\~BECAUSE\~THE\~PROGRAM\~IS\~LICENSED\~FREE\~OF\~CHARGE,\~THERE\~IS\~NO\~WARRANTY\par}
484
\pard{\f2 \fs20FOR\~THE\~PROGRAM,\~TO\~THE\~EXTENT\~PERMITTED\~BY\~APPLICABLE\~LAW.\~\~EXCEPT\~WHEN\par}
485
\pard{\f2 \fs20OTHERWISE\~STATED\~IN\~WRITING\~THE\~COPYRIGHT\~HOLDERS\~AND/OR\~OTHER\~PARTIES\par}
486
\pard{\f2 \fs20PROVIDE\~THE\~PROGRAM\~"AS\~IS"\~WITHOUT\~WARRANTY\~OF\~ANY\~KIND,\~EITHER\~EXPRESSED\par}
487
\pard{\f2 \fs20OR\~IMPLIED,\~INCLUDING,\~BUT\~NOT\~LIMITED\~TO,\~THE\~IMPLIED\~WARRANTIES\~OF\par}
488
\pard{\f2 \fs20MERCHANTABILITY\~AND\~FITNESS\~FOR\~A\~PARTICULAR\~PURPOSE.\~\~THE\~ENTIRE\~RISK\~AS\par}
489
\pard{\f2 \fs20TO\~THE\~QUALITY\~AND\~PERFORMANCE\~OF\~THE\~PROGRAM\~IS\~WITH\~YOU.\~\~SHOULD\~THE\par}
490
\pard{\f2 \fs20PROGRAM\~PROVE\~DEFECTIVE,\~YOU\~ASSUME\~THE\~COST\~OF\~ALL\~NECESSARY\~SERVICING,\par}
491
\pard{\f2 \fs20REPAIR\~OR\~CORRECTION.\par}
492
\par\par
493
\pard{\f2 \fs20\~\~12.\~IN\~NO\~EVENT\~UNLESS\~REQUIRED\~BY\~APPLICABLE\~LAW\~OR\~AGREED\~TO\~IN\~WRITING\par}
494
\pard{\f2 \fs20WILL\~ANY\~COPYRIGHT\~HOLDER,\~OR\~ANY\~OTHER\~PARTY\~WHO\~MAY\~MODIFY\~AND/OR\par}
495
\pard{\f2 \fs20REDISTRIBUTE\~THE\~PROGRAM\~AS\~PERMITTED\~ABOVE,\~BE\~LIABLE\~TO\~YOU\~FOR\~DAMAGES,\par}
496
\pard{\f2 \fs20INCLUDING\~ANY\~GENERAL,\~SPECIAL,\~INCIDENTAL\~OR\~CONSEQUENTIAL\~DAMAGES\~ARISING\par}
497
\pard{\f2 \fs20OUT\~OF\~THE\~USE\~OR\~INABILITY\~TO\~USE\~THE\~PROGRAM\~(INCLUDING\~BUT\~NOT\~LIMITED\par}
498
\pard{\f2 \fs20TO\~LOSS\~OF\~DATA\~OR\~DATA\~BEING\~RENDERED\~INACCURATE\~OR\~LOSSES\~SUSTAINED\~BY\par}
499
\pard{\f2 \fs20YOU\~OR\~THIRD\~PARTIES\~OR\~A\~FAILURE\~OF\~THE\~PROGRAM\~TO\~OPERATE\~WITH\~ANY\~OTHER\par}
500
\pard{\f2 \fs20PROGRAMS),\~EVEN\~IF\~SUCH\~HOLDER\~OR\~OTHER\~PARTY\~HAS\~BEEN\~ADVISED\~OF\~THE\par}
501
\pard{\f2 \fs20POSSIBILITY\~OF\~SUCH\~DAMAGES.\par}
502
\par\par
503
\pard{\f2 \fs20\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~END\~OF\~TERMS\~AND\~CONDITIONS\par}
504
\par\par
505
\pard{\f2 \fs20\~\~\~\~\~\~\~\~\~\~\~\~How\~to\~Apply\~These\~Terms\~to\~Your\~New\~Programs\par}
506
\par\par
507
\pard{\f2 \fs20\~\~If\~you\~develop\~a\~new\~program,\~and\~you\~want\~it\~to\~be\~of\~the\~greatest\par}
508
\pard{\f2 \fs20possible\~use\~to\~the\~public,\~the\~best\~way\~to\~achieve\~this\~is\~to\~make\~it\par}
509
\pard{\f2 \fs20free\~software\~which\~everyone\~can\~redistribute\~and\~change\~under\~these\~terms.\par}
510
\par\par
511
\pard{\f2 \fs20\~\~To\~do\~so,\~attach\~the\~following\~notices\~to\~the\~program.\~\~It\~is\~safest\par}
512
\pard{\f2 \fs20to\~attach\~them\~to\~the\~start\~of\~each\~source\~file\~to\~most\~effectively\par}
513
\pard{\f2 \fs20convey\~the\~exclusion\~of\~warranty;\~and\~each\~file\~should\~have\~at\~least\par}
514
\pard{\f2 \fs20the\~"copyright"\~line\~and\~a\~pointer\~to\~where\~the\~full\~notice\~is\~found.\par}
515
\par\par
516
\pard{\f2 \fs20\~\~\~\~<one\~line\~to\~give\~the\~program's\~name\~and\~a\~brief\~idea\~of\~what\~it\~does.>\par}
517
\pard{\f2 \fs20\~\~\~\~Copyright\~(C)\~<year>\~\~<name\~of\~author>\par}
518
\par\par
519
\pard{\f2 \fs20\~\~\~\~This\~program\~is\~free\~software;\~you\~can\~redistribute\~it\~and/or\~modify\par}
520
\pard{\f2 \fs20\~\~\~\~it\~under\~the\~terms\~of\~the\~GNU\~General\~Public\~License\~as\~published\~by\par}
521
\pard{\f2 \fs20\~\~\~\~the\~Free\~Software\~Foundation;\~either\~version\~2\~of\~the\~License,\~or\par}
522
\pard{\f2 \fs20\~\~\~\~(at\~your\~option)\~any\~later\~version.\par}
523
\par\par
524
\pard{\f2 \fs20\~\~\~\~This\~program\~is\~distributed\~in\~the\~hope\~that\~it\~will\~be\~useful,\par}
525
\pard{\f2 \fs20\~\~\~\~but\~WITHOUT\~ANY\~WARRANTY;\~without\~even\~the\~implied\~warranty\~of\par}
526
\pard{\f2 \fs20\~\~\~\~MERCHANTABILITY\~or\~FITNESS\~FOR\~A\~PARTICULAR\~PURPOSE.\~\~See\~the\par}
527
\pard{\f2 \fs20\~\~\~\~GNU\~General\~Public\~License\~for\~more\~details.\par}
528
\par\par
529
\pard{\f2 \fs20\~\~\~\~You\~should\~have\~received\~a\~copy\~of\~the\~GNU\~General\~Public\~License\par}
530
\pard{\f2 \fs20\~\~\~\~along\~with\~this\~program;\~if\~not,\~write\~to\~the\~Free\~Software\par}
531
\pard{\f2 \fs20\~\~\~\~Foundation,\~Inc.,\~59\~Temple\~Place,\~Suite\~330,\~Boston,\~MA\~\~02111-1307\~\~USA\par}
532
\par\par
533
\pard{\f2 \fs20Also\~add\~information\~on\~how\~to\~contact\~you\~by\~electronic\~and\~paper\~mail.\par}
534
\par\par
535
\pard{\f2 \fs20If\~the\~program\~is\~interactive,\~make\~it\~output\~a\~short\~notice\~like\~this\par}
536
\pard{\f2 \fs20when\~it\~starts\~in\~an\~interactive\~mode:\par}
537
\par\par
538
\pard{\f2 \fs20\~\~\~\~Gnomovision\~version\~69,\~Copyright\~(C)\~year\~name\~of\~author\par}
539
\pard{\f2 \fs20\~\~\~\~Gnomovision\~comes\~with\~ABSOLUTELY\~NO\~WARRANTY;\~for\~details\~type\~`show\~w'.\par}
540
\pard{\f2 \fs20\~\~\~\~This\~is\~free\~software,\~and\~you\~are\~welcome\~to\~redistribute\~it\par}
541
\pard{\f2 \fs20\~\~\~\~under\~certain\~conditions;\~type\~`show\~c'\~for\~details.\par}
542
\par\par
543
\pard{\f2 \fs20The\~hypothetical\~commands\~`show\~w'\~and\~`show\~c'\~should\~show\~the\~appropriate\par}
544
\pard{\f2 \fs20parts\~of\~the\~General\~Public\~License.\~\~Of\~course,\~the\~commands\~you\~use\~may\par}
545
\pard{\f2 \fs20be\~called\~something\~other\~than\~`show\~w'\~and\~`show\~c';\~they\~could\~even\~be\par}
546
\pard{\f2 \fs20mouse-clicks\~or\~menu\~items--whatever\~suits\~your\~program.\par}
547
\par\par
548
\pard{\f2 \fs20You\~should\~also\~get\~your\~employer\~(if\~you\~work\~as\~a\~programmer)\~or\~your\par}
549
\pard{\f2 \fs20school,\~if\~any,\~to\~sign\~a\~"copyright\~disclaimer"\~for\~the\~program,\~if\par}
550
\pard{\f2 \fs20necessary.\~\~Here\~is\~a\~sample;\~alter\~the\~names:\par}
551
\par\par
552
\pard{\f2 \fs20\~\~Yoyodyne,\~Inc.,\~hereby\~disclaims\~all\~copyright\~interest\~in\~the\~program\par}
553
\pard{\f2 \fs20\~\~`Gnomovision'\~(which\~makes\~passes\~at\~compilers)\~written\~by\~James\~Hacker.\par}
554
\par\par
555
\pard{\f2 \fs20\~\~<signature\~of\~Ty\~Coon>,\~1\~April\~1989\par}
556
\pard{\f2 \fs20\~\~Ty\~Coon,\~President\~of\~Vice\par}
557
\par\par
558
\pard{\f2 \fs20This\~General\~Public\~License\~does\~not\~permit\~incorporating\~your\~program\~into\par}
559
\pard{\f2 \fs20proprietary\~programs.\~\~If\~your\~program\~is\~a\~subroutine\~library,\~you\~may\par}
560
\pard{\f2 \fs20consider\~it\~more\~useful\~to\~permit\~linking\~proprietary\~applications\~with\~the\par}
561
\pard{\f2 \fs20library.\~\~If\~this\~is\~what\~you\~want\~to\~do,\~use\~the\~GNU\~Library\~General\par}
562
\pard{\f2 \fs20Public\~License\~instead\~of\~this\~License.\par}
563
\par\page\par
564
+{\footnote doc}
565
#{\footnote raslic}
566
${\footnote RASLIC}
567
K{\footnote raslic}
568
{\b RASLIC}\par\par
569
If you do not use the GPL, the following license terms apply: {}
570
\par\par
571
RasMol License {}
572
\par\par
573
Even though the authors of the various documents and software found here {}
574
have made a good faith effort to ensure that the documents are correct and {}
575
that the software performs according to its documentation, and we would {}
576
greatly appreciate hearing of any problems you may encounter, the programs {}
577
and documents any files created by the programs are provided **AS IS** {}
578
without any warranty as to correctness, merchantability or fitness for any {}
579
particular or general use. {}
580
\par\par
581
THE RESPONSIBILITY FOR ANY ADVERSE CONSEQUENCES FROM THE USE OF PROGRAMS OR {}
582
DOCUMENTS OR ANY FILE OR FILES CREATED BY USE OF THE PROGRAMS OR DOCUMENTS {}
583
LIES SOLELY WITH THE USERS OF THE PROGRAMS OR DOCUMENTS OR FILE OR FILES AND {}
584
NOT WITH AUTHORS OF THE PROGRAMS OR DOCUMENTS. {}
585
\par\par
586
Subject to your acceptance of the conditions stated above, and your respect {}
587
for the terms and conditions stated in the notices below, if you are not {}
588
going to make any modifications or create derived works, you are given {}
589
permission to freely copy and distribute this package, provided you do the {}
590
following: {}
591
\par\par
592
1. Either include the complete documentation, especially the file {}
593
NOTICE, with what you distribute or provide a clear indication where {}
594
people can get a copy of the documentation; and {}
595
\par\par
596
2. Please give credit where credit is due citing the version and {}
597
original authors properly; and {}
598
\par\par
599
3. Please do not give anyone the impression that the original {}
600
authors are providing a warranty of any kind. {}
601
\par\par
602
If you would like to use major pieces of RasMol in some other program, {}
603
make modifications to RasMol, or in some other way make what a lawyer {}
604
would call a "derived work", you are not only permitted to do so, you {}
605
are encouraged to do so. In addition to the things we discussed above, {}
606
please do the following: {}
607
\par\par
608
4. Please explain in your documentation how what you did differs {}
609
from this version of RasMol; and {}
610
\par\par
611
5. Please make your modified source code available. {}
612
\par\par
613
This version of RasMol is _not_ in the public domain, but it is given {}
614
freely to the community in the hopes of advancing science. If you make {}
615
changes, please make them in a responsible manner, and please offer us {}
616
the opportunity to include those changes in future versions of RasMol. {}
617
\par\page\par
618
+{\footnote doc}
619
#{\footnote generalnotice}
620
${\footnote General Notice}
621
K{\footnote general notice}
622
{\b General Notice}\par\par
623
The following notice applies to this work as a whole and to the works {}
624
included within it: {}
625
\par\par
626
* Creative endeavors depend on the lively exchange of ideas. There are laws {}
627
and customs which establish rights and responsibilities for authors and the {}
628
users of what authors create. This notice is not intended to prevent you {}
629
from using the software and documents in this package, but to ensure that {}
630
there are no misunderstandings about terms and conditions of such use. {}
631
\par\par
632
* Please read the following notice carefully. If you do not understand any {}
633
portion of this notice, please seek appropriate professional legal advice {}
634
before making use of the software and documents included in this software {}
635
package. In addition to whatever other steps you may be obliged to take {}
636
to respect the intellectual property rights of the various parties {}
637
involved, if you do make use of the software and documents in this package, {}
638
please give credit where credit is due by citing this package, its authors {}
639
and the URL or other source from which you obtained it, or equivalent {}
640
primary references in the literature with the same authors. {}
641
\par\par
642
* Some of the software and documents included within this software package {}
643
are the intellectual property of various parties, and placement in this {}
644
package does not in any way imply that any such rights have in any way been {}
645
waived or diminished. {}
646
\par\par
647
* With respect to any software or documents for which a copyright exists, {}
648
ALL RIGHTS ARE RESERVED TO THE OWNERS OF SUCH COPYRIGHT. {}
649
\par\par
650
* Even though the authors of the various documents and software found here {}
651
have made a good faith effort to ensure that the documents are correct and {}
652
that the software performs according to its documentation, and we would {}
653
greatly appreciate hearing of any problems you may encounter, the programs {}
654
and documents and any files created by the programs are provided **AS IS** {}
655
without any warranty as to correctness, merchantability or fitness for any {}
656
particular or general use. {}
657
\par\par
658
* THE RESPONSIBILITY FOR ANY ADVERSE CONSEQUENCES FROM THE USE OF PROGRAMS {}
659
OR DOCUMENTS OR ANY FILE OR FILES CREATED BY USE OF THE PROGRAMS OR {}
660
DOCUMENTS LIES SOLELY WITH THE USERS OF THE PROGRAMS OR DOCUMENTS OR FILE {}
661
OR FILES AND NOT WITH AUTHORS OF THE PROGRAMS OR DOCUMENTS. {}
662
\par\par
663
See the files GPL and RASLIC for two alternate ways to license this {}
664
package. {}
665
\par\page\par
666
+{\footnote doc}
667
#{\footnote rasmolv26notice}
668
${\footnote RasMol V2.6 Notice}
669
K{\footnote rasmol v2.6 notice}
670
{\b RasMol V2.6 Notice}\par\par
671
The following notice applies to RasMol V 2.6 and older RasMol versions. {}
672
\par\par
673
Information in this document is subject to change without notice and {}
674
does not represent a commitment on the part of the supplier. This package {}
675
is sold/distributed subject to the condition that it shall not, by way {}
676
of trade or otherwise, be lent, re-sold, hired out or otherwise {}
677
circulated without the supplier's prior consent, in any form of {}
678
packaging or cover other than that in which it was produced. No {}
679
part of this manual or accompanying software may be reproduced, {}
680
stored in a retrieval system on optical or magnetic disk, tape or {}
681
any other medium, or transmitted in any form or by any means, {}
682
electronic, mechanical, photocopying, recording or otherwise for {}
683
any purpose other than the purchaser's personal use. {}
684
\par\par
685
This product is not to be used in the planning, construction, {}
686
maintenance, operation or use of any nuclear facility nor the {}
687
flight, navigation or communication of aircraft or ground support {}
688
equipment. The author shall not be liable, in whole or in part, for {}
689
any claims or damages arising from such use, including death, {}
690
bankruptcy or outbreak of war. {}
691
\par\page\par
692
+{\footnote doc}
693
#{\footnote iucrpolicy}
694
${\footnote IUCR Policy}
695
K{\footnote iucr policy}
696
{\b IUCR Policy}\par\par
697
{\f2\b The IUCr Policy for the Protection and the Promotion of the STAR File and} {}
698
{\f2\b CIF Standards for Exchanging and Archiving Electronic Data}. {}
699
\par\par
700
{\f2\b Overview} {}
701
\par\par
702
The Crystallographic Information File (CIF)[1] is a standard for information {}
703
interchange promulgated by the International Union of Crystallography {}
704
(IUCr). CIF (Hall, Allen & Brown, 1991) is the recommended method for {}
705
submitting publications to Acta Crystallographica Section C and reports of {}
706
crystal structure determinations to other sections of Acta Crystallographica {}
707
and many other journals. The syntax of a CIF is a subset of the more general {}
708
STAR File[2] format. The CIF and STAR File approaches are used increasingly {}
709
in the structural sciences for data exchange and archiving, and are having a {}
710
significant influence on these activities in other fields. {}
711
\par\par
712
{\f2\b Statement of intent} {}
713
\par\par
714
The IUCr's interest in the STAR File is as a general data interchange {}
715
standard for science, and its interest in the CIF, a conformant derivative {}
716
of the STAR File, is as a concise data exchange and archival standard for {}
717
crystallography and structural science. {}
718
\par\par
719
{\f2\b Protection of the standards} {}
720
\par\par
721
To protect the STAR File and the CIF as standards for interchanging and {}
722
archiving electronic data, the IUCr, on behalf of the scientific community, {}
723
\par\par
724
* holds the copyrights on the standards themselves, {}
725
\par\par
726
* owns the associated trademarks and service marks, and {}
727
\par\par
728
* holds a patent on the STAR File. {}
729
\par\par
730
These intellectual property rights relate solely to the interchange formats, {}
731
not to the data contained therein, nor to the software used in the {}
732
generation, access or manipulation of the data. {}
733
\par\par
734
{\f2\b Promotion of the standards} {}
735
\par\par
736
The sole requirement that the IUCr, in its protective role, imposes on {}
737
software purporting to process STAR File or CIF data is that the following {}
738
conditions be met prior to sale or distribution. {}
739
\par\par
740
* Software claiming to read files written to either the STAR File or the {}
741
CIF standard must be able to extract the pertinent data from a file {}
742
conformant to the STAR File syntax, or the CIF syntax, respectively. {}
743
\par\par
744
* Software claiming to write files in either the STAR File, or the CIF, {}
745
standard must produce files that are conformant to the STAR File {}
746
syntax, or the CIF syntax, respectively. {}
747
\par\par
748
* Software claiming to read definitions from a specific data dictionary {}
749
approved by the IUCr must be able to extract any pertinent definition {}
750
which is conformant to the dictionary definition language (DDL)[3] {}
751
associated with that dictionary. {}
752
\par\par
753
The IUCr, through its Committee on CIF Standards, will assist any developer {}
754
to verify that software meets these conformance conditions. {}
755
\par\par
756
{\f2\b Glossary of terms} {}
757
\par\par
758
[1] CIF: {}
759
\par\par
760
is a data file conformant to the file syntax defined at {}
761
http://www.iucr.org/iucr-top/cif/spec/index.html {}
762
\par\par
763
[2] STAR File: {}
764
\par\par
765
is a data file conformant to the file syntax defined at {}
766
http://www.iucr.org/iucr-top/cif/spec/star/index.html {}
767
\par\par
768
[3] DDL: {}
769
\par\par
770
is a language used in a data dictionary to define data items in terms {}
771
of "attributes". Dictionaries currently approved by the IUCr, and the {}
772
DDL versions used to construct these dictionaries, are listed at {}
773
http://www.iucr.org/iucr-top/cif/spec/ddl/index.html {}
774
\par\par
775
Last modified: 30 September 2000 {}
776
\par\par
777
IUCr Policy Copyright (C) 2000 International Union of Crystallography {}
778
\par\page\par
779
+{\footnote doc}
780
#{\footnote cbflib}
781
${\footnote CBFLIB}
782
K{\footnote cbflib}
783
{\b CBFLIB}\par\par
784
The following Disclaimer Notice applies to CBFlib V0.1, from which this code {}
785
in part is derived. {}
786
\par\par
787
* The items furnished herewith were developed under the sponsorship of the {}
788
U.S. Government. Neither the U.S., nor the U.S. D.O.E., nor the Leland {}
789
Stanford Junior University, nor their employees, makes any warranty, {}
790
express or implied, or assumes any liability or responsibility for {}
791
accuracy, completeness or usefulness of any information, apparatus, product {}
792
or process disclosed, or represents that its use will not infringe {}
793
privately-owned rights. Mention of any product, its manufacturer, or {}
794
suppliers shall not, nor is it intended to, imply approval, disapproval, {}
795
or fitness for any particular use. The U.S. and the University at all times {}
796
retain the right to use and disseminate the furnished items for any purpose {}
797
whatsoever. {}
798
\par\par
799
Notice 91 02 01 {}
800
\par\page\par
801
+{\footnote doc}
802
#{\footnote cifparse}
803
${\footnote CIFPARSE}
804
K{\footnote cifparse}
805
{\b CIFPARSE}\par\par
806
Portions of this software are loosely based on the CIFPARSE software package {}
807
from the NDB at Rutgers University. See {}
808
\par\par
809
http://ndbserver.rutgers.edu/NDB/mmcif/software {}
810
\par\par
811
CIFPARSE is part of the NDBQUERY application, a program component of the {}
812
Nucleic Acid Database Project [ H. M. Berman, W. K. Olson, D. L. Beveridge, {}
813
J. K. Westbrook, A. Gelbin, T. Demeny, S. H. Shieh, A. R. Srinivasan, and B. {}
814
Schneider. (1992). The Nucleic Acid Database: A Comprehensive Relational {}
815
Database of Three-Dimensional Structures of Nucleic Acids. Biophys J., 63, {}
816
751-759.], whose cooperation is gratefully acknowledged, especially in the {}
817
form of design concepts created by J. Westbrook. {}
818
\par\par
819
Please be aware of the following notice in the CIFPARSE API: {}
820
\par\par
821
This software is provided WITHOUT WARRANTY OF MERCHANTABILITY OR FITNESS {}
822
FOR A PARTICULAR PURPOSE OR ANY OTHER WARRANTY, EXPRESS OR IMPLIED. RUTGERS {}
823
MAKE NO REPRESENTATION OR WARRANTY THAT THE SOFTWARE WILL NOT INFRINGE ANY {}
824
PATENT, COPYRIGHT OR OTHER PROPRIETARY RIGHT. {}
825
\par\page\par
826
+{\footnote doc}
827
#{\footnote chintro}
828
${\footnote Introduction}
829
{\fs24\b Introduction}\par\par
830
RasMol is a molecular graphics program intended for the visualisation of {}
831
proteins, nucleic acids and small molecules. {}
832
The program is aimed at display, teaching and generation of {}
833
publication quality images. RasMol runs on wide range of architectures {}
834
and operating systems including Microsoft Windows, Apple {}
835
Macintosh, UNIX and VMS systems. UNIX and VMS versions require an 8, 24 or {}
836
32 bit colour X Windows display (X11R4 or later). The X Windows version of {}
837
RasMol provides optional support for a hardware dials box and accelerated {}
838
shared memory communication (via the XInput and MIT-SHM extensions) {}
839
if available on the current X Server. {}
840
\par\par
841
The program reads in a {}
842
molecule coordinate file and interactively displays the molecule on the {}
843
screen in a variety of colour schemes and molecule representations. Currently {}
844
available representations include depth-cued wireframes, 'Dreiding' sticks, {}
845
spacefilling (CPK) spheres, ball and stick, solid and strand biomolecular {}
846
ribbons, atom labels and dot surfaces. {}
847
\par\par
848
Up to 5 molecules may be loaded and displayed at once. Any one or all of {}
849
the molecules may be rotated and translated. {}
850
\par\par
851
The RasMol help facility can be accessed by typing "help <topic>" or "help {}
852
<topic> <subtopic>" from the command line. A complete list of RasMol commands {}
853
may be displayed by typing "help commands". A single question mark may also {}
854
be used to abbreviate the keyword "help". Please type "help notices" for {}
855
important notices. {}
856
\par\page\par
857
+{\footnote doc}
858
#{\footnote chcomref}
859
${\footnote Command Reference}
860
{\fs24\b Command Reference}\par\par
861
RasMol allows the execution of interactive commands typed at the {}
862
'{\f2\b RasMol>}' {}
863
prompt in the terminal window. Each command must be given on {}
864
a separate line. Keywords are case insensitive and may be entered in {}
865
either upper or lower case letters. All whitespace characters are {}
866
ignored except to separate keywords and their arguments. {}
867
\par\par
868
All commands may be prefixed by a parenthesized {}
869
'{\uldb atom expression}{\v chexprs}' {}
870
to temporarily select certain atoms just for the execution {}
871
of that one command. After execution of the command, the {}
872
previous selection is restored except for the commands {}
873
'{\uldb select}{\v select}' {}
874
, {}
875
'{\uldb restrict}{\v restrict}' {}
876
and {}
877
'{\uldb script}{\v script}'. {}
878
\par\par
879
The commands/keywords currently recognised by RasMol are given below. {}
880
\par\par
881
{\cellx1200\cellx2400\cellx3600\cellx4800
882
\intbl
883
{\uldb backbone}{\v backbone}\cell
884
{\uldb background}{\v background}\cell
885
{\uldb bond}{\v bond}\cell
886
{\uldb bulgarian}{\v bulgarian}\cell
887
\row\intbl
888
{\uldb cartoon}{\v cartoon}\cell
889
{\uldb centre}{\v centre}\cell
890
{\uldb chinese}{\v chinese}\cell
891
{\uldb clipboard}{\v clipboard}\cell
892
\row\intbl
893
{\uldb colour}{\v colour}\cell
894
{\uldb colourmode}{\v colourmode}\cell
895
{\uldb connect}{\v connect}\cell
896
{\uldb cpk}{\v cpk}\cell
897
\row\intbl
898
{\uldb cpknew}{\v cpknew}\cell
899
{\uldb defer}{\v defer}\cell
900
{\uldb define}{\v define}\cell
901
{\uldb depth}{\v depth}\cell
902
\row\intbl
903
{\uldb dots}{\v dots}\cell
904
{\uldb echo}{\v echo}\cell
905
{\uldb english}{\v english}\cell
906
{\uldb execute}{\v execute}\cell
907
\row\intbl
908
{\uldb exit}{\v exit}\cell
909
{\uldb french}{\v french}\cell
910
{\uldb hbonds}{\v hbonds}\cell
911
{\uldb help}{\v help}\cell
912
\row\intbl
913
{\uldb italian}{\v italian}\cell
914
{\uldb japanese}{\v japanese}\cell
915
{\uldb label}{\v label}\cell
916
{\uldb load}{\v load}\cell
917
\row\intbl
918
{\uldb map}{\v map}\cell
919
{\uldb molecule}{\v molecule}\cell
920
{\uldb monitor}{\v pause}\cell
921
{\uldb notoggle}{\v notoggle}\cell
922
\row\intbl
923
{\uldb pause}{\v pause}\cell
924
{\uldb pause}{\v play}\cell
925
{\uldb print}{\v print}\cell
926
{\uldb quit}{\v quit}\cell
927
\row\intbl
928
{\uldb record}{\v record}\cell
929
{\uldb refresh}{\v refresh}\cell
930
{\uldb renumber}{\v renumber}\cell
931
{\uldb reset}{\v reset}\cell
932
\row\intbl
933
{\uldb restrict}{\v restrict}\cell
934
{\uldb ribbons}{\v ribbons}\cell
935
{\uldb rotate}{\v rotate}\cell
936
{\uldb save}{\v save}\cell
937
\row\intbl
938
{\uldb script}{\v script}\cell
939
{\uldb select}{\v select}\cell
940
{\uldb set}{\v set}\cell
941
{\uldb show}{\v show}\cell
942
\row\intbl
943
{\uldb slab}{\v slab}\cell
944
{\uldb source}{\v source}\cell
945
{\uldb spacefill}{\v spacefill}\cell
946
{\uldb spanish}{\v spanish}\cell
947
\row\intbl
948
{\uldb ssbonds}{\v ssbonds}\cell
949
{\uldb star}{\v star}\cell
950
{\uldb stereo}{\v stereo}\cell
951
{\uldb strands}{\v strands}\cell
952
\row\intbl
953
{\uldb structure}{\v structure}\cell
954
{\uldb surface}{\v surface}\cell
955
{\uldb trace}{\v trace}\cell
956
{\uldb translate}{\v translate}\cell
957
\row\intbl
958
{\uldb unbond}{\v unbond}\cell
959
{\uldb wireframe}{\v wireframe}\cell
960
{\uldb write}{\v write}\cell
961
{\uldb zap}{\v zap}\cell
962
\row\intbl
963
{\uldb zoom}{\v zoom}\cell\cell
964
\row\pard\par\trowd}
965
\par\page\par
966
+{\footnote doc}
967
#{\footnote backbone}
968
${\footnote Backbone}
969
K{\footnote backbone}
970
{\b Backbone}\par\par
971
\tx1200
972
{\f2\b Syntax:\tab
973
backbone \{<boolean>\}\line\tab
974
backbone <value>\par
975
}\pard\par
976
The RasMol {}
977
'{\f2\b backbone}' {}
978
command permits the representation of a polypeptide {}
979
backbone as a series of bonds connecting the adjacent alpha carbons of {}
980
each amino acid in a chain. The display of these backbone 'bonds' is {}
981
turned on and off by the command parameter in the same way as with the {}
982
'{\uldb wireframe}{\v wireframe}' {}
983
command. The command {}
984
'{\f2\b backbone off}' {}
985
turns off the selected 'bonds', and {}
986
'{\f2\b backbone on}' {}
987
or with a number turns them on. The number can be used {}
988
to specify the cylinder radius of the representation in either Angstrom {}
989
or RasMol units. A parameter value of 500 (2.0 Angstroms) or above {}
990
results in a "Parameter value too large" error. Backbone objects may be {}
991
coloured using the RasMol {}
992
'{\uldb colour backbone}{\v colour}' {}
993
command. {}
994
\par\par
995
The reserved word backbone is also used as a predefined set ("help sets") {}
996
and as a parameter to the {}
997
'{\uldb set hbond}{\v sethbonds}' {}
998
and {}
999
'{\uldb set ssbond}{\v setssbonds}' {}
1000
commands. The {}
1001
RasMol command {}
1002
'{\f2\b trace}' {}
1003
renders a smoothed backbone, in contrast to {}
1004
'{\f2\b backbone}' {}
1005
which connects alpha carbons with straight lines. {}
1006
\par\par
1007
The backbone may be displayed with dashed lines by use of the {}
1008
'{\f2\b backbone dash}' {}
1009
command. {}
1010
\par\page\par
1011
+{\footnote doc}
1012
#{\footnote background}
1013
${\footnote Background}
1014
K{\footnote background}
1015
{\b Background}\par\par
1016
\tx1200
1017
{\f2\b Syntax:\tab
1018
background <colour>\par
1019
}\pard\par
1020
The RasMol {}
1021
'{\f2\b background}' {}
1022
command is used to set the colour of the "canvas" background. The {}
1023
colour may be given as either a colour name or a comma separated {}
1024
triple of Red, Green and Blue (RGB) components enclosed in square {}
1025
brackets. Typing the command {}
1026
'{\uldb help colours}{\v help}' {}
1027
will give a list of the predefined colour names recognised by RasMol. {}
1028
When running under X Windows, RasMol also recognises colours in the {}
1029
X server's colour name database. {}
1030
\par\par
1031
The {}
1032
'{\f2\b background}' {}
1033
command is synonymous with the RasMol {}
1034
'{\uldb set background}{\v setbackground}' {}
1035
command. {}
1036
\par\page\par
1037
+{\footnote doc}
1038
#{\footnote bond}
1039
${\footnote Bond}
1040
K{\footnote bond}
1041
{\b Bond}\par\par
1042
\tx1200
1043
{\f2\b Syntax:\tab
1044
bond <number> <number> +\line\tab
1045
bond <number> <number> pick\line\tab
1046
bond rotate \{<boolean>\}\par
1047
}\pard\par
1048
The RasMol command {}
1049
'{\f2\b bond <number> <number> +}' {}
1050
adds the designated bond to the drawing, increasing the bond order {}
1051
if the bond already exists. The command {}
1052
'{\f2\b bond <number> <number> pick}' {}
1053
selects the two atoms specified by the atom serial numbers {}
1054
as the two ends of a bond around which the {}
1055
'{\uldb rotate bond <angle>}{\v rotate}' {}
1056
command will be applied. If no bond exists, it is created. {}
1057
\par\par
1058
Rotation around a previously picked bond may be specified by the {}
1059
'{\uldb rotate bond <angle>}{\v rotate}' {}
1060
command, or may also be controlled with the mouse, using the {}
1061
'{\f2\b bond rotate on/off}' {}
1062
or the equivalent {}
1063
'{\uldb rotate bond on/off}{\v rotate}' {}
1064
commands. {}
1065
\par\page\par
1066
+{\footnote doc}
1067
#{\footnote bulgarian}
1068
${\footnote Bulgarian}
1069
K{\footnote bulgarian}
1070
{\b Bulgarian}\par\par
1071
\tx1200
1072
{\f2\b Syntax:\tab
1073
Bulgarian \par
1074
}\pard\par
1075
The RasMol {}
1076
'{\f2\b Bulgarian}' {}
1077
command sets the menus and messages to the Bulgarian versions. {}
1078
\par\par
1079
This command may not work correctly unless appropriate fonts {}
1080
have been installed. The commands {}
1081
'{\uldb Bulgarian}{\v bulgarian}', {}
1082
'{\uldb Chinese}{\v chinese}', {}
1083
'{\uldb English}{\v english}', {}
1084
'{\uldb French}{\v french}', {}
1085
'{\uldb Italian}{\v italian}', {}
1086
'{\uldb Russian}{\v russian}' {}
1087
and {}
1088
'{\uldb Spanish}{\v spanish}' {}
1089
may be used to select Bulgarian, Chinese, English, French, {}
1090
Italian, Japanese, Russian and Spanish menus and messages if the {}
1091
appropriate fonts have been installed. {}
1092
\par\page\par
1093
+{\footnote doc}
1094
#{\footnote cartoon}
1095
${\footnote Cartoon}
1096
K{\footnote cartoon}
1097
{\b Cartoon}\par\par
1098
\tx1200
1099
{\f2\b Syntax:\tab
1100
cartoon \{<number>\}\par
1101
}\pard\par
1102
The RasMol {}
1103
'{\f2\b cartoon}' {}
1104
command does a display of a molecule {}
1105
'{\uldb ribbons}{\v ribbons}' {}
1106
as Richardson (MolScript) style protein {}
1107
'{\f2\b cartoons}', {}
1108
implemented as thick (deep) ribbons. The {}
1109
easiest way to obtain a cartoon representation of a protein is {}
1110
to use the {}
1111
'{\f2\b Cartoons}' {}
1112
option on the {}
1113
'{\f2\b Display}' {}
1114
menu. The {}
1115
'{\f2\b cartoon}' {}
1116
command represents the currently selected residues {}
1117
as a deep ribbon with width specified by the command's argument. {}
1118
Using the command without a parameter results in the ribbon's {}
1119
width being taken from the protein's secondary structure, {}
1120
as described in the {}
1121
'{\uldb ribbons}{\v ribbons}' {}
1122
command. By default, the C-termini of beta-sheets are displayed {}
1123
as arrow heads. This may be enabled and disabled using the {}
1124
'{\uldb set cartoons}{\v setcartoon}' {}
1125
command. {}
1126
The depth of the cartoon may be adjusted using the {}
1127
'{\uldb set cartoons <number>}{\v setcartoon}' {}
1128
command. The {}
1129
'{\uldb set cartoons}{\v setcartoon}' {}
1130
command without any parameters returns these two options {}
1131
to their default values. {}
1132
\par\page\par
1133
+{\footnote doc}
1134
#{\footnote center}
1135
#{\footnote centre}
1136
${\footnote Centre}
1137
K{\footnote centre}
1138
{\b Centre}\par\par
1139
\tx1200
1140
{\f2\b Syntax:\tab
1141
centre \{<expression>\} \{translate|center\}\line\tab
1142
center \{<expression>\} \{translate|center\}\par
1143
}\pard\par
1144
The RasMol {}
1145
'{\f2\b centre}' {}
1146
command defines the point about which the {}
1147
'{\uldb rotate}{\v rotate}' {}
1148
command and the scroll bars rotate the current molecule. Without a {}
1149
parameter the centre command resets the centre of rotation to be the {}
1150
centre of gravity of the molecule. If an atom expression is specified, {}
1151
RasMol rotates the molecule about the centre of gravity of the set of {}
1152
atoms specified by the expression. Hence, if a single atom is specified {}
1153
by the expression, that atom will remain 'stationary' during rotations. {}
1154
\par\par
1155
Type {}
1156
'{\uldb help expression}{\v help}' {}
1157
for more information on RasMol atom expressions. {}
1158
\par\par
1159
Alternatively the centring may be given as a comma separated triple of {}
1160
[CenX, CenY, CenZ] offsets in RasMol units (1/250 of an Angstrom) from {}
1161
the centre of gravity. The triple must be enclosed in square brackets. {}
1162
\par\par
1163
The optional forms {}
1164
'{\f2\b centre ... translate}' {}
1165
and {}
1166
'{\f2\b centre ... center}' {}
1167
may be used to specify use of a translated centre of rotation (not {}
1168
necessarily in the centre of the canvas) or a centre of rotation {}
1169
which is placed at the centre of the canvas. Starting with {}
1170
RasMol 2.7.2, the default is {}
1171
to center the new axis on the canvas. {}
1172
\par\page\par
1173
+{\footnote doc}
1174
#{\footnote chinese}
1175
${\footnote Chinese}
1176
K{\footnote chinese}
1177
{\b Chinese}\par\par
1178
\tx1200
1179
{\f2\b Syntax:\tab
1180
Chinese \par
1181
}\pard\par
1182
The RasMol {}
1183
'{\f2\b Chinese}' {}
1184
command sets the menus and messages to the Chinese versions. {}
1185
\par\par
1186
This command may not work correctly unless appropriate fonts {}
1187
have been installed. The commands {}
1188
'{\uldb Bulgarian}{\v bulgarian}', {}
1189
'{\uldb Chinese}{\v chinese}', {}
1190
'{\uldb English}{\v english}', {}
1191
'{\uldb French}{\v french}', {}
1192
'{\uldb Italian}{\v italian}', {}
1193
'{\uldb Russian}{\v russian}' {}
1194
and {}
1195
'{\uldb Spanish}{\v spanish}' {}
1196
may be used to select Bulgarian, Chinese, English, French, {}
1197
Italian, Japanese, Russian and Spanish menus and messages if the {}
1198
appropriate fonts have been installed. {}
1199
\par\page\par
1200
+{\footnote doc}
1201
#{\footnote clipboard}
1202
${\footnote Clipboard}
1203
K{\footnote clipboard}
1204
{\b Clipboard}\par\par
1205
\tx1200
1206
{\f2\b Syntax:\tab
1207
clipboard\par
1208
}\pard\par
1209
The RasMol {}
1210
'{\f2\b clipboard}' {}
1211
command places a copy of the currently displayed image on the local {}
1212
graphics 'clipboard'. Note: this command is not yet supported on {}
1213
UNIX or VMS machines. It is intended to make transfering images {}
1214
between applications easier under Microsoft Windows or on an Apple {}
1215
Macintosh. {}
1216
\par\par
1217
When using RasMol on a UNIX or VMS system this functionality may be {}
1218
achieved by generating a raster image in a format that can be read {}
1219
by the receiving program using the RasMol {}
1220
'{\uldb write}{\v write}' {}
1221
command. {}
1222
\par\page\par
1223
+{\footnote doc}
1224
#{\footnote color}
1225
#{\footnote colour}
1226
${\footnote Colour}
1227
K{\footnote colour}
1228
{\b Colour}\par\par
1229
\tx1200
1230
{\f2\b Syntax:\tab
1231
colour \{<object>\} <colour>\line\tab
1232
color \{<object>\} <colour>\par
1233
}\pard\par
1234
Colour the atoms (or other objects) of the selected region. The colour may {}
1235
be given as either a colour name or a comma separated triple of Red, Green {}
1236
and Blue (RGB) components enclosed in square brackets. Typing the command {}
1237
'{\uldb help colours}{\v help}' {}
1238
will give a list of all the predefined colour names recognised {}
1239
by RasMol. {}
1240
\par\par
1241
Allowed objects are {}
1242
'{\f2\b atoms}', {}
1243
'{\f2\b bonds}', {}
1244
'{\uldb backbone}{\v backbone}', {}
1245
'{\uldb ribbons}{\v ribbons}', {}
1246
'{\uldb labels}{\v label}', {}
1247
'{\uldb dots}{\v dots}', {}
1248
'{\uldb hbonds}{\v hbonds}', {}
1249
'{\uldb map}{\v map}', {}
1250
and {}
1251
'{\uldb ssbonds}{\v ssbonds}'. {}
1252
If no object is specified, the default keyword {}
1253
'{\f2\b atom}' {}
1254
is assumed. {}
1255
Some colour schemes are defined for certain object types. The colour scheme {}
1256
'{\f2\b none}' {}
1257
can be applied to all objects except atoms and dots, stating that the selected {}
1258
objects have no colour of their own, but use the colour of their associated {}
1259
atoms (i.e. the atoms they connect). {}
1260
'{\f2\b Atom}' {}
1261
objects can also be coloured by {}
1262
'{\uldb alt}{\v altcolours}', {}
1263
'{\uldb amino}{\v aminocolours}', {}
1264
'{\uldb chain}{\v chaincolours}', {}
1265
'{\uldb charge}{\v chargecolours}', {}
1266
'{\uldb cpk}{\v cpkcolours}', {}
1267
'{\uldb group}{\v groupcolours}', {}
1268
'{\uldb model}{\v nmrmodelcolours}', {}
1269
'{\uldb shapely}{\v shapelycolours}', {}
1270
'{\uldb structure}{\v structurecolours}', {}
1271
'{\uldb temperature}{\v temperaturecolours}' {}
1272
or {}
1273
'{\uldb user}{\v usercolours}'. {}
1274
Hydrogen bonds can also be coloured by {}
1275
'{\uldb type}{\v hbondtypecolours}' {}
1276
and dot surfaces can also be coloured by {}
1277
'{\uldb electrostatic potential}{\v potentialcolours}'. {}
1278
For more information type {}
1279
'{\uldb help colour <colour>}{\v chcolours}'. {}
1280
Map objects may be coloured by specific color of by nearest atom. {}
1281
\par\page\par
1282
+{\footnote doc}
1283
#{\footnode colourmode}
1284
#{\footnote colourmode}
1285
${\footnote ColourMode}
1286
K{\footnote colourmode}
1287
{\b ColourMode}\par\par
1288
\tx1200
1289
{\f2\b Syntax:\tab
1290
colourmode \{<boolean>\}\line\tab
1291
colormode \{<boolean>\}\par
1292
}\pard\par
1293
ColourMode allows the user to switch between using the new {}
1294
'{\uldb colour}{\v colour}' {}
1295
method. At present, the new coloring technique is the same as {}
1296
the old one, but to preserve compatibility for older scripts {}
1297
it may be wise to add a "colormode on" near the top of your {}
1298
script somewhere, if the script was designed for version 2.7.3 {}
1299
of RasMol or earlier. The new color method, when completed, {}
1300
aims to fix a few bugs in the coloring routines. {}
1301
\par\par
1302
#{\footnote connect}
1303
${\footnote Connect}
1304
K{\footnote connect}
1305
{\b Connect}\par\par
1306
\tx1200
1307
{\f2\b Syntax:\tab
1308
connect \{<boolean>\}\par
1309
}\pard\par
1310
The RasMol {}
1311
'{\f2\b connect}' {}
1312
command is used to force RasMol to (re)calculate the connectivity {}
1313
of the current molecule. {}
1314
If the original input file contained connectivity information, this {}
1315
is discarded. The command {}
1316
'{\f2\b connect false}' {}
1317
uses a fast heuristic {}
1318
algorithm that is suitable for determining bonding in large {}
1319
bio-molecules such as proteins and nucleic acids. The command {}
1320
'{\f2\b connect true}' {}
1321
uses a slower more accurate algorithm based upon {}
1322
covalent radii that is more suitable to small molecules containing {}
1323
inorganic elements or strained rings. If no parameters are given, {}
1324
RasMol determines which algorithm to use based on the number of atoms {}
1325
in the input file. Greater than 255 atoms causes RasMol to use the {}
1326
faster implementation. This is the method used to determine bonding, {}
1327
if necessary, when a molecule is first read in using the {}
1328
'{\uldb load}{\v load}' {}
1329
command. {}
1330
\par\page\par
1331
+{\footnote doc}
1332
#{\footnote defer}
1333
${\footnote Defer}
1334
K{\footnote defer}
1335
{\b Defer}\par\par
1336
\tx1200
1337
{\f2\b Syntax:\tab
1338
defer <name> <command to defer>\par
1339
}\pard\par
1340
The RasMol {}
1341
'{\f2\b defer}' {}
1342
command adds the command given to the macro with given name, {}
1343
if no name is given, the command is added to the macro with a {}
1344
blank name. The command {}
1345
'{\f2\b zap}' {}
1346
is a special case. In that case the macro is erased. If no name is {}
1347
given the command must begin with a selection, e.g. {}
1348
'{\f2\b defer (selection).spacefill}' {}
1349
\par\par
1350
The deferred commands accumulated under the given name can be executed {}
1351
using the {}
1352
'{\uldb execute}{\v execute}' {}
1353
command {}
1354
\par\page\par
1355
+{\footnote doc}
1356
#{\footnote define}
1357
${\footnote Define}
1358
K{\footnote define}
1359
{\b Define}\par\par
1360
\tx1200
1361
{\f2\b Syntax:\tab
1362
define <identifier> <expression>\par
1363
}\pard\par
1364
The RasMol {}
1365
'{\f2\b define}' {}
1366
command allows the user to associate an arbitrary set of atoms with a {}
1367
unique identifier. This allows the definition of user-defined sets. These {}
1368
sets are declared statically, i.e. once defined the contents of the set {}
1369
do not change, even if the expression defining them depends on the {}
1370
current transformation and representation of the molecule. {}
1371
\par\page\par
1372
+{\footnote doc}
1373
#{\footnote depth}
1374
${\footnote Depth}
1375
K{\footnote depth}
1376
{\b Depth}\par\par
1377
\tx1200
1378
{\f2\b Syntax:\tab
1379
depth \{<boolean>\}\line\tab
1380
depth <value>\par
1381
}\pard\par
1382
The RasMol {}
1383
'{\f2\b depth}' {}
1384
command enables, disables or positions the back-clipping plane of the {}
1385
molecule. The program only draws those portions of the {}
1386
molecule that are closer to the viewer than the clipping plane. {}
1387
Integer values range from zero at the very back of the molecule to {}
1388
100 which is completely in front of the molecule. Intermediate values {}
1389
determine the percentage of the molecule to be drawn. {}
1390
\par\par
1391
This command interacts with the {}
1392
'{\uldb slab <value>}{\v slab}' {}
1393
command, which clips to the front of a given z-clipping plane. {}
1394
\par\page\par
1395
+{\footnote doc}
1396
#{\footnote dots}
1397
${\footnote Dots}
1398
K{\footnote dots}
1399
{\b Dots}\par\par
1400
\tx1200
1401
{\f2\b Syntax:\tab
1402
dots \{<boolean>\}\line\tab
1403
dots \{<value>\}\par
1404
}\pard\par
1405
The RasMol {}
1406
'{\f2\b dots}' {}
1407
command is used to generate a van der Waals' dot surface around the {}
1408
currently selected atoms. Dot surfaces display regularly spaced points {}
1409
on a sphere of van der Waals' radius about each selected atom. Dots that {}
1410
would are 'buried' within the van der Waals' radius of any other atom {}
1411
(selected or not) are not displayed. {}
1412
The command {}
1413
'{\f2\b dots on}' {}
1414
deletes any existing dot surface and generates a dots surface around {}
1415
the currently selected atom set with a default dot density of 100. The {}
1416
command {}
1417
'{\f2\b dots off}' {}
1418
deletes any existing dot surface. The dot density may be {}
1419
specified by providing a numeric parameter between 1 and 1000. This {}
1420
value approximately corresponds to the number of dots on the surface {}
1421
of a medium sized atom. {}
1422
\par\par
1423
By default, the colour of each point on a dot surface is the colour {}
1424
of its closest atom at the time the surface is generated. The colour {}
1425
of the whole dot surface may be changed using the {}
1426
'{\uldb colour dots}{\v colour}' {}
1427
command. {}
1428
\par\page\par
1429
+{\footnote doc}
1430
#{\footnote echo}
1431
${\footnote Echo}
1432
K{\footnote echo}
1433
{\b Echo}\par\par
1434
\tx1200
1435
{\f2\b Syntax:\tab
1436
echo \{<string>\}\par
1437
}\pard\par
1438
The RasMol {}
1439
'{\f2\b echo}' {}
1440
command is used to display a message in the RasMol command/terminal {}
1441
window. The string parameter may optionally be delimited in double {}
1442
quote characters. If no parameter is specified, the {}
1443
'{\f2\b echo}' {}
1444
command displays a blank line. This command is particularly useful {}
1445
for displaying text from within a RasMol {}
1446
'{\uldb script}{\v script}' {}
1447
file. {}
1448
\par\page\par
1449
+{\footnote doc}
1450
#{\footnote english}
1451
${\footnote English}
1452
K{\footnote english}
1453
{\b English}\par\par
1454
\tx1200
1455
{\f2\b Syntax:\tab
1456
English \par
1457
}\pard\par
1458
The RasMol {}
1459
'{\f2\b English}' {}
1460
command sets the menus and messages to the English versions. {}
1461
\par\par
1462
This command may not work correctly unless appropriate fonts {}
1463
have been installed. The commands {}
1464
'{\uldb Bulgarian}{\v bulgarian}', {}
1465
'{\uldb Chinese}{\v chinese}', {}
1466
'{\uldb English}{\v english}', {}
1467
'{\uldb French}{\v french}', {}
1468
'{\uldb Italian}{\v italian}', {}
1469
'{\uldb Russian}{\v russian}' {}
1470
and {}
1471
'{\uldb Spanish}{\v spanish}' {}
1472
may be used to select Bulgarian, Chinese, English, French, {}
1473
Italian, Japanese, Russian and Spanish menus and messages if the {}
1474
appropriate fonts have been installed. {}
1475
\par\page\par
1476
+{\footnote doc}
1477
#{\footnote execute}
1478
${\footnote Execute}
1479
K{\footnote execute}
1480
{\b Execute}\par\par
1481
\tx1200
1482
{\f2\b Syntax:\tab
1483
execute <name>\par
1484
}\pard\par
1485
The RasMol {}
1486
'{\f2\b execute}' {}
1487
command: {}
1488
\par\par
1489
1. saves the old poise of the molecule (translation, {}
1490
rotation and zoom) {}
1491
\par\par
1492
2. executes the specified macro suppressing both screen {}
1493
updates and recording {}
1494
\par\par
1495
3. animates motion of the newly rendered molecule linearly {}
1496
from the old poise to the new poise {}
1497
\par\par
1498
The macro must have been previously defined by calls to the {}
1499
'{\uldb defer}{\v defer}' {}
1500
command. {}
1501
\par\par
1502
The animation of the motion depends on the prior settings of the {}
1503
'{\uldb record}{\v record}' {}
1504
command. {}
1505
\par\page\par
1506
+{\footnote doc}
1507
#{\footnote french}
1508
${\footnote French}
1509
K{\footnote french}
1510
{\b French}\par\par
1511
\tx1200
1512
{\f2\b Syntax:\tab
1513
French \par
1514
}\pard\par
1515
The RasMol {}
1516
'{\f2\b French}' {}
1517
command sets the menus and messages to the French versions. {}
1518
\par\par
1519
This command may not work correctly unless appropriate fonts {}
1520
have been installed. The commands {}
1521
'{\uldb Bulgarian}{\v bulgarian}', {}
1522
'{\uldb Chinese}{\v chinese}', {}
1523
'{\uldb English}{\v english}', {}
1524
'{\uldb French}{\v french}', {}
1525
'{\uldb Italian}{\v italian}', {}
1526
'{\uldb Russian}{\v russian}' {}
1527
and {}
1528
'{\uldb Spanish}{\v spanish}' {}
1529
may be used to select Bulgarian, Chinese, English, French, {}
1530
Italian, Japanese, Russian and Spanish menus and messages if the {}
1531
appropriate fonts have been installed. {}
1532
\par\page\par
1533
+{\footnote doc}
1534
#{\footnote hbond}
1535
#{\footnote hbonds}
1536
${\footnote HBonds}
1537
K{\footnote hbonds}
1538
{\b HBonds}\par\par
1539
\tx1200
1540
{\f2\b Syntax:\tab
1541
hbonds \{<boolean>\}\line\tab
1542
hbonds <value>\par
1543
}\pard\par
1544
The RasMol {}
1545
'{\f2\b hbond}' {}
1546
command is used to represent the hydrogen bonding of the protein {}
1547
molecule's backbone. This information is useful in assessing the {}
1548
protein's secondary structure. Hydrogen bonds are represented as {}
1549
either dotted lines or cylinders between the donor and acceptor {}
1550
residues. The first time the {}
1551
'{\f2\b hbond}' {}
1552
command is used, the program searches the structure of the {}
1553
molecule to find hydrogen bonded residues and reports the number of bonds {}
1554
to the user. The command {}
1555
'{\f2\b hbonds on}' {}
1556
displays the selected 'bonds' as dotted lines, and the {}
1557
'{\f2\b hbonds off}' {}
1558
turns off their display. The colour of hbond objects may be changed {}
1559
by the {}
1560
'{\uldb colour hbond}{\v colour}' {}
1561
command. Initially, each hydrogen bond has the colours of its connected {}
1562
atoms. {}
1563
\par\par
1564
By default the dotted lines are drawn between the accepting oxygen and {}
1565
the donating nitrogen. By using the {}
1566
'{\uldb set hbonds}{\v sethbonds}' {}
1567
command the alpha carbon positions of the appropriate residues may be {}
1568
used instead. This is especially useful when examining proteins in {}
1569
backbone representation. {}
1570
\par\page\par
1571
+{\footnote doc}
1572
#{\footnote help}
1573
${\footnote Help}
1574
K{\footnote help}
1575
{\b Help}\par\par
1576
\tx1200
1577
{\f2\b Syntax:\tab
1578
help \{<topic> \{<subtopic>\}\}\line\tab
1579
? \{<topic> \{<subtopic>\}\}\par
1580
}\pard\par
1581
The RasMol {}
1582
'{\f2\b help}' {}
1583
command provides on-line help on the given topic. {}
1584
\par\page\par
1585
+{\footnote doc}
1586
#{\footnote italian}
1587
${\footnote Italian}
1588
K{\footnote italian}
1589
{\b Italian}\par\par
1590
\tx1200
1591
{\f2\b Syntax:\tab
1592
Italian \par
1593
}\pard\par
1594
The RasMol {}
1595
'{\f2\b Italian}' {}
1596
command sets the menus and messages to the Italian versions. {}
1597
\par\par
1598
This command may not work correctly unless appropriate fonts {}
1599
have been installed. The commands {}
1600
'{\uldb Bulgarian}{\v bulgarian}', {}
1601
'{\uldb Chinese}{\v chinese}', {}
1602
'{\uldb English}{\v english}', {}
1603
'{\uldb French}{\v french}', {}
1604
'{\uldb Italian}{\v italian}', {}
1605
'{\uldb Russian}{\v russian}' {}
1606
and {}
1607
'{\uldb Spanish}{\v spanish}' {}
1608
may be used to select Bulgarian, Chinese, English, French, {}
1609
Italian, Japanese, Russian and Spanish menus and messages if the {}
1610
appropriate fonts have been installed. {}
1611
\par\page\par
1612
+{\footnote doc}
1613
#{\footnote japanese}
1614
${\footnote Japanese}
1615
K{\footnote japanese}
1616
{\b Japanese}\par\par
1617
\tx1200
1618
{\f2\b Syntax:\tab
1619
Japanese \par
1620
}\pard\par
1621
The RasMol {}
1622
'{\f2\b Japanese}' {}
1623
command sets the menus and messages to the Japanese versions. {}
1624
\par\par
1625
This command may not work correctly unless appropriate fonts {}
1626
have been installed. The commands {}
1627
'{\uldb Bulgarian}{\v bulgarian}', {}
1628
'{\uldb Chinese}{\v chinese}', {}
1629
'{\uldb English}{\v english}', {}
1630
'{\uldb French}{\v french}', {}
1631
'{\uldb Italian}{\v italian}', {}
1632
'{\uldb Russian}{\v russian}' {}
1633
and {}
1634
'{\uldb Spanish}{\v spanish}' {}
1635
may be used to select Bulgarian, Chinese, English, French, {}
1636
Italian, Japanese, Russian and Spanish menus and messages if the {}
1637
appropriate fonts have been installed. {}
1638
\par\page\par
1639
+{\footnote doc}
1640
#{\footnote labels}
1641
#{\footnote label}
1642
${\footnote Label}
1643
K{\footnote label}
1644
{\b Label}\par\par
1645
\tx1200
1646
{\f2\b Syntax:\tab
1647
label \{<string>\}\line\tab
1648
label <boolean>\par
1649
}\pard\par
1650
The RasMol {}
1651
'{\f2\b label}' {}
1652
command allows an arbitrary formatted text string to be {}
1653
associated with each currently selected atom. This string may contain {}
1654
embedded 'expansion specifiers' which display properties of the atom {}
1655
being labelled. An expansion specifier consists of a '%' character {}
1656
followed by a single alphabetic character specifying the property to be {}
1657
displayed (similar to C's printf syntax). {}
1658
An actual '%' character may be displayed by using the expansion {}
1659
specifier '%%'. {}
1660
\par\par
1661
Atom labelling for the currently selected atoms may be turned off with {}
1662
the command {}
1663
'{\f2\b label off}'. {}
1664
By default, if no string is given as a parameter, RasMol uses labels {}
1665
appropriate for the current molecule. {}
1666
RasMol uses the label '%n%r:%c.%a' if the molecule contains more than {}
1667
one chain, '%e%i' if the molecule has only a single residue (a small {}
1668
molecule) and '%n%r.%a' otherwise. {}
1669
\par\par
1670
The colour of each label may be changed using the {}
1671
'{\uldb colour label}{\v colour}' {}
1672
command. By default, each label is drawn in the same colour as the atom {}
1673
to which it is attached. The size and spacing of the displayed text {}
1674
may be changed using the {}
1675
'{\uldb set fontsize}{\v setfontsize}' {}
1676
command. The width of the strokes in the displayed text may be changed {}
1677
using the {}
1678
'{\uldb set fontstroke}{\v setfontstroke}' {}
1679
command. {}
1680
\par\par
1681
The following table lists the current expansion specifiers: {}
1682
\par\par
1683
{\cellx500\cellx1000\cellx5500
1684
\intbl
1685
%a\cell \cell Atom Name\cell\row\intbl
1686
%b\cell %t\cell B-factor/Temperature\cell\row\intbl
1687
%c\cell %s\cell Chain Identifier\cell\row\intbl
1688
%e\cell \cell Element Atomic Symbol\cell\row\intbl
1689
%i\cell \cell Atom Serial Number\cell\row\intbl
1690
%n\cell \cell Residue Name\cell\row\intbl
1691
%r\cell \cell Residue Number\cell\row\intbl
1692
%M\cell \cell NMR Model Number (with leading "/")\cell\row\intbl
1693
%A\cell \cell Alternate Conformation Identifier (with leading ";")\cell\row
1694
\pard\par\trowd}
1695
\par\page\par
1696
+{\footnote doc}
1697
#{\footnote load}
1698
${\footnote Load}
1699
K{\footnote load}
1700
{\b Load}\par\par
1701
\tx1200
1702
{\f2\b Syntax:\tab
1703
load \{<format>\} <filename>\line\tab
1704
}\pard\par
1705
Load a molecule coordinate file into RasMol. Valid molecule file {}
1706
formats are {}
1707
'{\f2\b pdb}' {}
1708
(Protein Data Bank format), {}
1709
'{\f2\b mdl}' {}
1710
(Molecular Design Limited's MOL file format), {}
1711
'{\f2\b alchemy}' {}
1712
(Tripos' Alchemy file format), {}
1713
'{\f2\b mol2}' {}
1714
(Tripos' Sybyl Mol2 file format), {}
1715
'{\f2\b charmm}' {}
1716
(CHARMm file format), {}
1717
'{\f2\b xyz}' {}
1718
(MSC's XMol XYZ file format), {}
1719
'{\f2\b mopac}' {}
1720
(J. P. Stewart's MOPAC file format) or {}
1721
'{\f2\b cif}' {}
1722
(IUCr CIF or mmCIF file format). If no file format is specified, {}
1723
'{\f2\b PDB}', {}
1724
'{\f2\b CIF}', {}
1725
or {}
1726
'{\f2\b mmCIF}' {}
1727
is assumed by default. Up to 20 molecules may be loaded at a time. {}
1728
If CHEM_COMP ligand models are included in an mmCIF file, they will be loaded {}
1729
as NMR models, first giving the all the NMR models for model {}
1730
coordinates if specified and then giving all the NMR models for {}
1731
ideal model coordinates. {}
1732
\par\par
1733
To delete a molecule prior to loading another use the RasMol {}
1734
'{\uldb zap}{\v zap}' {}
1735
command. To select a molecule for manipulation use the RasMol {}
1736
'{\uldb molecule <n>}{\v molecule}' {}
1737
command. {}
1738
\par\par
1739
The {}
1740
'{\f2\b load}' {}
1741
command selects all the atoms in the molecule, centres it on the {}
1742
screen and renders it as a CPK coloured wireframe model. If the molecule {}
1743
contains no bonds (i.e. contains only alpha carbons), it is drawn as {}
1744
an alpha carbon backbone. If the file specifies fewer bonds than atoms, {}
1745
RasMol determines connectivity using the {}
1746
'{\uldb connect}{\v connect}' {}
1747
command. {}
1748
\par\par
1749
The {}
1750
'{\f2\b load inline}' {}
1751
command also allows the storing of atom coordinates in scripts {}
1752
to allow better integration with WWW browsers. A load command {}
1753
executed inside a script file may specify the keyword {}
1754
'{\f2\b inline}' {}
1755
instead of a conventional filename. This option specifies that {}
1756
the coordinates of the molecule to load are stored in the same {}
1757
file as the currently executing commands. {}
1758
\par\page\par
1759
+{\footnote doc}
1760
#{\footnote map}
1761
${\footnote Map}
1762
K{\footnote map}
1763
{\b Map}\par\par
1764
\tx1200
1765
{\f2\b Syntax:\tab
1766
map \{<map_selector>\} \{<map_subcommand> <parameters>\}\par
1767
}\pard\par
1768
The RasMol {}
1769
'{\f2\b map}' {}
1770
commands manipulate electron density maps in coordination {}
1771
with the display of molecules. These commands are very {}
1772
memory intensive and may not work on machines with {}
1773
limited memory. Each molecule may have as many maps {}
1774
as available memory permits. Maps may be read from {}
1775
files or generated from Gaussian density distributions {}
1776
around atoms. {}
1777
\par\par
1778
'{\uldb map colour}{\v mapcolour}', {}
1779
to colour a map according to a given colour scheme, {}
1780
'{\uldb map generate}{\v mapgenerate}', {}
1781
to generate a map from selected atoms based on pseudo-Gaussians, {}
1782
'{\uldb map level}{\v maplevel}', {}
1783
to set the contouring level for selected maps, {}
1784
'{\uldb map load}{\v mapload}', {}
1785
to load a map from a file, {}
1786
'{\uldb map mask}{\v mapmask}' {}
1787
to designate a mask for the selected maps, {}
1788
'{\uldb map resolution}{\v mapresolution}', {}
1789
to set the resolution for contouring selected maps, {}
1790
'{\uldb map restrict}{\v maprestrict}', {}
1791
to select one or more maps and to disable all others, {}
1792
'{\uldb map save}{\v mapsave}', {}
1793
to save map information to a file, {}
1794
'{\uldb map scale}{\v mapscale}', {}
1795
'{\uldb control the scaling of pseudo-Gaussians when generating maps}{\v to}', {}
1796
'{\uldb map select}{\v mapselect}', {}
1797
to select one or more maps, {}
1798
'{\uldb map show}{\v mapshow}', {}
1799
to display information about one or more maps or about the {}
1800
parameters to be used in generating or loading the next map, {}
1801
'{\uldb map spacing}{\v mapspacing}', {}
1802
to set the spacing betwen contour lines of selected maps, {}
1803
'{\uldb map spread}{\v mapspread}', {}
1804
to set the variance of the Gaussians for map generation as a fraction {}
1805
of the atomic radius, and {}
1806
'{\uldb map zap}{\v mapzap}' {}
1807
to delete previously generated or loaded maps. {}
1808
\par\par
1809
The effect of {}
1810
'{\uldb map generate}{\v mapgenerate}' {}
1811
and {}
1812
'{\uldb map load}{\v mapload}' {}
1813
commands is modified by the {}
1814
'{\uldb map mask}{\v mapmask}' {}
1815
command which limits the portion of the display space {}
1816
that can be considered for display of maps. {}
1817
\par\page\par
1818
+{\footnote doc}
1819
#{\footnote mapcolour}
1820
${\footnote Map colour}
1821
K{\footnote map colour}
1822
{\b Map colour}\par\par
1823
\tx1200
1824
{\f2\b Syntax:\tab
1825
map \{<map_selector>\} colour <colour_scheme>
1826
}\pard\par
1827
The RasMol {}
1828
'{\f2\b map colour}' {}
1829
command colours the selected maps according to the specified {}
1830
colour scheme. The colour scheme may be a colour name or {}
1831
and RBG triple in brackets, or the keyword {}
1832
'{\f2\b atom}' {}
1833
to cause the map points to be coloured by the color of the {}
1834
nearest atom. {}
1835
\par\page\par
1836
+{\footnote doc}
1837
#{\footnote mapgenerate}
1838
${\footnote Map generate}
1839
K{\footnote map generate}
1840
{\b Map generate}\par\par
1841
\tx1200
1842
{\f2\b Syntax:\tab
1843
map \{<map_selector>\} generate \{LRsurf\} dots\line\tab
1844
map \{<map_selector>\} generate \{LRsurf\} mesh\line\tab
1845
map \{<map_selector>\} generate \{LRsurf\} surface
1846
}\pard\par
1847
The RasMol {}
1848
'{\f2\b map generate}' {}
1849
command generates a map from whatever atoms are currently selected, {}
1850
by summing electron densities approximated by Gaussian distributions. {}
1851
The height of each Gaussian is determined by the setting of the {}
1852
'{\uldb map scale}{\v mapscale}' {}
1853
command. {}
1854
In the default of map scale true, each Gaussian has a height proportional {}
1855
element type of the atom. {}
1856
If the optional 'LRSurf' parameter is given or if map scale false {}
1857
has been executed, each Gaussian is scaled so that {}
1858
the Gaussian contour level 1 is at the van der Waals radius. {}
1859
In either case a standard deviation determined by the {}
1860
most recently specified spread or resolution is used. If a non-zero spread has been {}
1861
given the radius of the atom is multiplied by the spread to find the {}
1862
standard deviation. The default is 2/3rds. If a resolution {}
1863
has been given, the spread is inferred as 2/3rds of the resolution. {}
1864
\par\par
1865
For example, if the resolution is given as 1., and the atom in question {}
1866
is a Carbon with a van der Waals radius of 468 RasMol units (1.87 Angstroms), {}
1867
the inferred spead is .6667, and the standard deviation of the Gaussian {}
1868
is taken as 1.25 Angstroms. {}
1869
\par\par
1870
If the spread has been set to zero, the spread for each atom is determined {}
1871
from the van der Waals radius and the probe atom radius to simulate the {}
1872
effect of a Lee-Richards surface. {}
1873
\par\par
1874
If no specific map was given by the map selector, the new map is {}
1875
given the next available map number. {}
1876
\par\par
1877
If a specific map was given by the map selector, the new map replaces {}
1878
that map. If more than one map was given by the map selector, the {}
1879
new map replaces the lowest numbered of the selected maps. In any {}
1880
case the new map becomes the currently selected map. {}
1881
\par\par
1882
The map is displayed as dots, mesh or a surface, depending on the last {}
1883
map rendering mode selected or the mode selected on the command itself. {}
1884
\par\page\par
1885
+{\footnote doc}
1886
#{\footnote maplevel}
1887
${\footnote Map level}
1888
K{\footnote map level}
1889
{\b Map level}\par\par
1890
\tx1200
1891
{\f2\b Syntax:\tab
1892
map \{<map_selector>\} level \{MEAN\} <number>
1893
}\pard\par
1894
The RasMol {}
1895
'{\f2\b map level}' {}
1896
command sets the contour level to be used in creating subsequent {}
1897
representations of generated or loaded maps. If the keyword MEAN {}
1898
in used the level is relative to the mean of the map data. Otherwise {}
1899
the level is absolute. {}
1900
\par\par
1901
In general, a lower level results in a map containing more of the {}
1902
displayed volume, while a higher level results in a map containing {}
1903
less of the displayed volume. {}
1904
\par\page\par
1905
+{\footnote doc}
1906
#{\footnote mapload}
1907
${\footnote Map load}
1908
K{\footnote map load}
1909
{\b Map load}\par\par
1910
\tx1200
1911
{\f2\b Syntax:\tab
1912
map \{<map_selector>\} load <filename>
1913
}\pard\par
1914
The RasMol {}
1915
'{\f2\b map load}' {}
1916
command loads a map file into RasMol. The valid formats are {}
1917
CCP4 map format and imgCIF format. {}
1918
\par\par
1919
If no specific map was given by the map selector, the new map is {}
1920
given the next available map number. {}
1921
\par\par
1922
If a specific map was given by the map selector, the new map replaces {}
1923
that map. If more than one map was given by the map selector, the {}
1924
new map replaces the lowest numbered of the selected maps. In any {}
1925
case the new map becomes the currently selected map. {}
1926
\par\par
1927
The map is displayed as dots, mesh or a surface depending on the {}
1928
last map rendering mode selected. {}
1929
\par\page\par
1930
+{\footnote doc}
1931
#{\footnote mapmask}
1932
${\footnote Map mask}
1933
K{\footnote map mask}
1934
{\b Map mask}\par\par
1935
\tx1200
1936
{\f2\b Syntax:\tab
1937
map \{<map_selector>\} mask selected\line\tab
1938
map \{<map_selector>\} mask <number>\line\tab
1939
map \{<map_selector>\} mask none
1940
}\pard\par
1941
The RasMol {}
1942
'{\f2\b map mask}' {}
1943
command specifies a mask to be used to limit the display space {}
1944
to be used for making representations of other maps or removes {}
1945
an earlier mask specification. {}
1946
\par\par
1947
The 'selected' option indicates that the mask is to be created {}
1948
from the currently selected atoms. The '<number>' option indicates {}
1949
that the mask is to be copied from the map of the number specified. {}
1950
The 'none' option removes the previously specified mask, if any. {}
1951
\par\par
1952
The map selector specifies the map or maps to which the specified mask {}
1953
will the applied. For example, 'map next mask selected' specifies {}
1954
that the currently selected atoms are to be used to generate a {}
1955
mask to be applied to any maps created by subsequent 'map load' {}
1956
or 'map generate' commands. {}
1957
\par\par
1958
Any map may be used as a mask. The portions of the mask map greater than {}
1959
than or equal to the average value of the mask map allow the values of the {}
1960
map being masked to be used as given. The portions of the mask {}
1961
map lower than the average value of the mask map cause the values of {}
1962
the map being masked to be treated as if they were equal to the {}
1963
lowest data value of the map being masked. {}
1964
\par\page\par
1965
+{\footnote doc}
1966
#{\footnote mapresolution}
1967
${\footnote Map resolution}
1968
K{\footnote map resolution}
1969
{\b Map resolution}\par\par
1970
\tx1200
1971
{\f2\b Syntax:\tab
1972
map \{<map_selector>\} resolution <number>
1973
}\pard\par
1974
The RasMol {}
1975
'{\f2\b map resolution}' {}
1976
command specifies the resolution in RasMol units or, {}
1977
if a number containing a decimal point is given, the {}
1978
resolution in Angstroms to be used in generating and {}
1979
in representing maps. {}
1980
\par\par
1981
The resolution is used at the map spacing for {}
1982
representations of maps, indicating the separation {}
1983
between contour levels (see the {}
1984
'{\uldb map spacing}{\v mapspacing}' {}
1985
command) and to infer the map spread to be used in {}
1986
generated maps from selected atoms (see the {}
1987
'{\uldb map spread}{\v mapspread}' {}
1988
command). The map spread is set to two thirds of {}
1989
the specified resolution. {}
1990
\par\page\par
1991
+{\footnote doc}
1992
#{\footnote maprestrict}
1993
${\footnote Map restrict}
1994
K{\footnote map restrict}
1995
{\b Map restrict}\par\par
1996
\tx1200
1997
{\f2\b Syntax:\tab
1998
map \{<map_selector>\} restrict
1999
}\pard\par
2000
The RasMol {}
2001
'{\f2\b map restrict}' {}
2002
command selects particular maps to make them active for {}
2003
subsequent map commands. This is similar to the {}
2004
'{\uldb map select}{\v mapselect}' {}
2005
command, but does disables the display of the {}
2006
maps that were not selected. {}
2007
\par\page\par
2008
+{\footnote doc}
2009
#{\footnote mapsave}
2010
${\footnote Map save}
2011
K{\footnote map save}
2012
{\b Map save}\par\par
2013
\tx1200
2014
{\f2\b Syntax:\tab
2015
map \{<map_selector>\} save <filename>
2016
}\pard\par
2017
The RasMol {}
2018
'{\f2\b map save}' {}
2019
command saves an imgCIF map file. {}
2020
\par\par
2021
If no specific map was given by the map selector, the currently {}
2022
selected maps and their masks are written to the file, one {}
2023
map and mask pair per data block. {}
2024
\par\page\par
2025
+{\footnote doc}
2026
#{\footnote mapscale}
2027
${\footnote Map scale}
2028
K{\footnote map scale}
2029
{\b Map scale}\par\par
2030
\tx1200
2031
{\f2\b Syntax:\tab
2032
map \{<map_selector>\} scale <boolean>
2033
}\pard\par
2034
The RasMol {}
2035
'{\f2\b map scale}' {}
2036
command selects the scaling of pseudo-Gaussians in the {}
2037
'{\uldb map generate}{\v mapgenerate}' {}
2038
commands. {}
2039
In the default of map scale true, each Gaussian has a height proportional {}
2040
element type of the atom. {}
2041
If map scale false has been executed, each Gaussian is scaled so that {}
2042
the Gaussian contour level 1 is at the van der Waals radius. {}
2043
In either case a standard deviation determined by the {}
2044
most recently specified spread or resolution is used. {}
2045
\par\page\par
2046
+{\footnote doc}
2047
#{\footnote mapselect}
2048
${\footnote Map select}
2049
K{\footnote map select}
2050
{\b Map select}\par\par
2051
\tx1200
2052
{\f2\b Syntax:\tab
2053
map \{<map_selector>\} select \{atom \{within\} \{add\} \{search_radius\}\}
2054
}\pard\par
2055
The RasMol {}
2056
'{\f2\b map select}' {}
2057
command selects particular maps to make them active for {}
2058
subsequent map commands. This is similar to the {}
2059
'{\uldb map restrict}{\v maprestrict}' {}
2060
command, but does not disable the display of the {}
2061
maps that were not selected. {}
2062
\par\par
2063
If the optional {}
2064
'{\f2\b atom}' {}
2065
parameter is given, the command selects the atoms with centres closest to the {}
2066
map points. The radius of the search may be specified by the parameter {}
2067
'{\f2\b search_radius}'. {}
2068
The default is to look for atoms within 4 Angstroms plus the probe radius. {}
2069
If the optional {}
2070
'{\f2\b within}' {}
2071
parameter is given, the new selection is taken from within the currently {}
2072
selected atoms. If the options {}
2073
'{\f2\b add}' {}
2074
parameter is given, the new selection is added to the currently selected atoms. {}
2075
The default is to search within all atoms. {}
2076
\par\page\par
2077
+{\footnote doc}
2078
#{\footnote mapshow}
2079
${\footnote Map show}
2080
K{\footnote map show}
2081
{\b Map show}\par\par
2082
\tx1200
2083
{\f2\b Syntax:\tab
2084
map \{<map_selector>\} show
2085
}\pard\par
2086
The RasMol {}
2087
'{\f2\b map show}' {}
2088
command causes information about the maps specified by {}
2089
the map selector to be written to the command window. {}
2090
\par\page\par
2091
+{\footnote doc}
2092
#{\footnote mapspacing}
2093
${\footnote Map spacing}
2094
K{\footnote map spacing}
2095
{\b Map spacing}\par\par
2096
\tx1200
2097
{\f2\b Syntax:\tab
2098
map \{<map_selector>\} spacing <number>
2099
}\pard\par
2100
The RasMol {}
2101
'{\f2\b map spacing}' {}
2102
command specifies the spacing to be used between contour lines {}
2103
in creating representations of maps. The spacing is typically {}
2104
given in Angstroms with a decimal point, but may also be {}
2105
specified in RasMol units (250ths of an Angstom) as an {}
2106
integer. For maps loaded in grid coordinates that spacing {}
2107
is parallel to the cell edges. The default spacing is {}
2108
one half Angstrom. {}
2109
\par\page\par
2110
+{\footnote doc}
2111
#{\footnote mapspread}
2112
${\footnote Map spread}
2113
K{\footnote map spread}
2114
{\b Map spread}\par\par
2115
\tx1200
2116
{\f2\b Syntax:\tab
2117
map \{<map_selector>\} spread <number>
2118
}\pard\par
2119
The RasMol {}
2120
'{\f2\b map spread}' {}
2121
command specifies the reciprocal of the number of {}
2122
standard deviations per radius to be used in {}
2123
generating maps as sums of Gaussians centered {}
2124
on atomic positions. The default spread is one {}
2125
two thirds (i.e. each radius covers 1.5 standard deviations). {}
2126
\par\par
2127
If the spread has been set to zero, the spread for each atom is determined {}
2128
from the van der Waals radius and the probe atom radius to simulate the {}
2129
effect of a Lee-Richards surface. {}
2130
\par\page\par
2131
+{\footnote doc}
2132
#{\footnote mapzap}
2133
${\footnote Map zap}
2134
K{\footnote map zap}
2135
{\b Map zap}\par\par
2136
\tx1200
2137
{\f2\b Syntax:\tab
2138
map \{<map_selector>\} zap
2139
}\pard\par
2140
The RasMol {}
2141
'{\f2\b map zap}' {}
2142
command removes the data and representations of the {}
2143
maps specified by the map selector. The map numbers {}
2144
of maps that have not been removed are not changed. {}
2145
\par\page\par
2146
+{\footnote doc}
2147
#{\footnote molecule}
2148
${\footnote Molecule}
2149
K{\footnote molecule}
2150
{\b Molecule}\par\par
2151
\tx1200
2152
{\f2\b Syntax:\tab
2153
molecule <number>\par
2154
}\pard\par
2155
The RasMol {}
2156
'{\f2\b molecule}' {}
2157
command selects one of up to 5 previously loaded molecules {}
2158
for active manipulation. While all the molcules are displayed {}
2159
and may be rotated collectively (see the {}
2160
'{\uldb rotate all}{\v rotate}' {}
2161
command), only one molecule at a time {}
2162
time is active for manipulation by the commands which {}
2163
control the details of rendering. {}
2164
\par\page\par
2165
+{\footnote doc}
2166
#{\footnote monitor}
2167
${\footnote Monitor}
2168
K{\footnote monitor}
2169
{\b Monitor}\par\par
2170
\tx1200
2171
{\f2\b Syntax:\tab
2172
monitor <number> <number>\line\tab
2173
monitor \{<boolean>\}\par
2174
}\pard\par
2175
The RasMol {}
2176
'{\f2\b monitor}' {}
2177
command allows the display of distance monitors. A distance {}
2178
monitor is a dashed (dotted) line between an arbitrary pair {}
2179
of atoms, optionally labelled by the distance between them. {}
2180
The RasMol command {}
2181
'{\f2\b monitor <number> <number>}' {}
2182
adds such a distance monitor between the two atoms specified by the atom {}
2183
serial numbers given as parameters {}
2184
\par\par
2185
Distance monitors are turned off with the command {}
2186
'{\f2\b monitors off}'. {}
2187
By default, monitors display the {}
2188
distance between its two end points as a label at the centre of {}
2189
the monitor. These distance labels may be turned off with the {}
2190
command {}
2191
'{\uldb set monitors off}{\v setmonitor}', {}
2192
and re-enabled with the command {}
2193
'{\uldb set monitors on}{\v setmonitor}'. {}
2194
Like most other representations, {}
2195
the colour of a monitor is taken from the colour of its end points unless {}
2196
specified by the {}
2197
'{\uldb colour monitors}{\v colour}' {}
2198
command. {}
2199
\par\par
2200
Distance monitors may also be added to a molecule interactively with {}
2201
the mouse, using the {}
2202
'{\uldb set picking monitor}{\v setpicking}' {}
2203
command. Clicking on an atom results {}
2204
in its being identified on the rasmol command line. In addition {}
2205
every atom picked increments a modulo counter such that, in monitor {}
2206
mode, every second atom displays the distance between this atom and {}
2207
the previous one. The shift key may be used to form distance monitors {}
2208
between a fixed atom and several consecutive positions. A distance {}
2209
monitor may also be removed (toggled) by selecting the appropriate {}
2210
pair of atom end points a second time. {}
2211
\par\page\par
2212
+{\footnote doc}
2213
#{\footnote notoggle}
2214
${\footnote Notoggle}
2215
K{\footnote notoggle}
2216
{\b Notoggle}\par\par
2217
\tx1200
2218
{\f2\b Syntax:\tab
2219
notoggle \{<boolean>\}\par
2220
}\pard\par
2221
The RasMol {}
2222
'{\f2\b NoToggle}' {}
2223
command enables or disables the use of the toggle ability {}
2224
that is used by some of the other RasMol commands. {}
2225
When no boolean value is specified, NoToggle mode is ENABLED. {}
2226
When NoToggle mode is ENABLED, all toggle functionality is {}
2227
DISABLED. To turn it off, one must explicitly set {}
2228
'{\f2\b notoggle off}'. {}
2229
\par\par
2230
Some commands which use the toggle feature are: {}
2231
'{\uldb ColourMode}{\v colourmode}'. {}
2232
More functions that utilize this capability may be added {}
2233
at a later date. {}
2234
\par\page\par
2235
+{\footnote doc}
2236
#{\footnote pause}
2237
${\footnote Pause}
2238
K{\footnote pause}
2239
{\b Pause}\par\par
2240
\tx1200
2241
{\f2\b Syntax:\tab
2242
pause\par\tab
2243
wait\par
2244
}\pard\par
2245
The RasMol {}
2246
'{\f2\b pause}' {}
2247
command is used in script files to stop the script file for local {}
2248
manipulation by a mouse, until any key is pushed to restart the {}
2249
script file. {}
2250
'{\f2\b Wait}' {}
2251
is synonymous with {}
2252
'{\f2\b pause}'. {}
2253
This command may be executed in RasMol script files to suspend {}
2254
the sequential execution of commands and allow the user to examine {}
2255
the current image. When RasMol executes a {}
2256
'{\f2\b pause}' {}
2257
command in a script file, it suspends execution of the rest {}
2258
of the file, refreshes the image on the screen and allows the {}
2259
manipulation of the image using the mouse and scroll bars, or {}
2260
resizing of the graphics window. Once a key is pressed, control {}
2261
returns to the script file at the line following the {}
2262
'{\f2\b pause}' {}
2263
command. While a script is suspended the molecule may be rotated, {}
2264
translated, scaled, slabbed and picked as usual, but all menu {}
2265
commands are disabled. {}
2266
\par\page\par
2267
+{\footnote doc}
2268
#{\footnote play}
2269
${\footnote Play}
2270
K{\footnote play}
2271
{\b Play}\par\par
2272
\tx1200
2273
{\f2\b Syntax:\tab
2274
print play \{from <time>\} \{until <time>\} \{\{on|off|eject\} \{<type>\} <medium>\}\par
2275
}\pard\par
2276
The RasMol {}
2277
'{\f2\b play}' {}
2278
command specifies the recording medium from which to play back a movie. {}
2279
The playback frame start time is given in seconds to millisecond precision. {}
2280
Since we are working on computers, the medium is specified as a set of files, {}
2281
each marked with the playback frame start time in milliseconds as part of the {}
2282
name. The place in the name at which to look for the playback frame start {}
2283
time in milliseconds is marked by the characters "ssssss" with an {}
2284
appropriate number of digits. RasMol accepts either upper or lower case {}
2285
s's or decimal digits to mark the place for the time. The play off and play {}
2286
eject commands effectively remove the specified medium from use. If no medium {}
2287
is specified, play off suspends playing and play on resumes playing. {}
2288
Normally play starts immediately and runs to the end of the medium. However, {}
2289
if play off and/or or some combination of play from and play until is entered {}
2290
before {}
2291
'{\f2\b play type medium}', {}
2292
those settings will be used. {}
2293
\par\par
2294
As of release 2.7.5, RasMol support play from scripts and data files. {}
2295
\par\page\par
2296
+{\footnote doc}
2297
#{\footnote print}
2298
${\footnote Print}
2299
K{\footnote print}
2300
{\b Print}\par\par
2301
\tx1200
2302
{\f2\b Syntax:\tab
2303
print\par
2304
}\pard\par
2305
The RasMol {}
2306
'{\f2\b print}' {}
2307
command sends the currently displayed image to the local default printer {}
2308
using the operating system's native printer driver. Note: this command {}
2309
is not yet supported under UNIX or VMS. It is intended to take advantage {}
2310
of Microsoft Windows and Apple Macintosh printer drivers. For example, {}
2311
this allows images to be printed directly on a dot matrix printer. {}
2312
\par\par
2313
When using RasMol on a UNIX or VMS system this functionality may be {}
2314
achieved by either generating a PostScript file using the RasMol {}
2315
'{\uldb write ps}{\v write}' {}
2316
or {}
2317
'{\uldb write vectps}{\v write}' {}
2318
commands and printing that or generating a raster image file and using a {}
2319
utility to dump that to the local printer. {}
2320
\par\page\par
2321
+{\footnote doc}
2322
#{\footnote exit}
2323
#{\footnote quit}
2324
${\footnote Quit}
2325
K{\footnote quit}
2326
{\b Quit}\par\par
2327
\tx1200
2328
{\f2\b Syntax:\tab
2329
quit\line\tab
2330
exit\par
2331
}\pard\par
2332
Exit from the RasMol program. The RasMol commands {}
2333
'{\f2\b exit}' {}
2334
and {}
2335
'{\f2\b quit}' {}
2336
are synonymous, except within nested scripts. In that case, {}
2337
'{\f2\b exit}' {}
2338
terminates only the current level, while {}
2339
'{\f2\b quit}' {}
2340
terminates all nested levels of scripts. {}
2341
\par\page\par
2342
+{\footnote doc}
2343
#{\footnote record}
2344
${\footnote Record}
2345
K{\footnote record}
2346
{\b Record}\par\par
2347
\tx1200
2348
{\f2\b Syntax:\tab
2349
print record \{from <time>\} \{until <time>\} \{\{on|off\} \{<type>\} <medium>\}\par
2350
\tab record \{mouse|motion|appearance\} \{on|off\}
2351
}\pard\par
2352
The RasMol {}
2353
'{\f2\b record}' {}
2354
command specifies the recording medium to hold the movie. Since we are {}
2355
working on computers, the medium is specified as a template for a set of {}
2356
files, each marked with the playback frame start time in milliseconds {}
2357
(rather than as seconds to avoid embedding a decimal point) as part of {}
2358
the name. The place in the name to be replaced with the playback frame {}
2359
start time in milliseconds is marked by the characters "ssssss" with {}
2360
an appropriate number of digits. RasMol accepts either upper or lower case {}
2361
s's or decimal digits to mark the place for the time. The record off {}
2362
commands remove the specified medium from use. If no medium is specified, {}
2363
record off suspends recording and record on resumes recording with the {}
2364
next available time on the same medium. The screen is the default medium {}
2365
and is, by default, on. Writing to disk must be explicitly specified so {}
2366
that the disk does not get filled up unintentionally. The type of a {}
2367
recording medium may be an image type such as gif, pict or png to record {}
2368
the actual screen images or script to record the RasMol commands used to {}
2369
generate the frames. {}
2370
\par\par
2371
Normally recording starts at playback frame start time 0 seconds. {}
2372
A non-zero starting time in seconds can be specified with the {}
2373
'{\f2\b record from}' {}
2374
command as in {}
2375
'{\f2\b record from 25}' {}
2376
or {}
2377
'{\f2\b record from 37.25}' {}
2378
to help in organizing scenes of movies to be assembled later in an {}
2379
appropriate order. {}
2380
The {}
2381
'{\f2\b record until}' {}
2382
command allows an upper limit to be set on recording time in seconds. {}
2383
The default is to have no limit. Issuing the commands {}
2384
\par\par
2385
'{\f2\b record from 600}' {}
2386
\par\par
2387
'{\f2\b record until 1800}' {}
2388
\par\par
2389
would result in a 20 minute movie segment intended to start 10 {}
2390
minutes into a longer movie. {}
2391
These commands allow control over rewriting selected time segments. {}
2392
\par\page\par
2393
+{\footnote doc}
2394
#{\footnote refresh}
2395
${\footnote Refresh}
2396
K{\footnote refresh}
2397
{\b Refresh}\par\par
2398
\tx1200
2399
{\f2\b Syntax:\tab
2400
refresh
2401
}\pard\par
2402
The RasMol {}
2403
'{\f2\b refresh}' {}
2404
command redraws the current image. This is useful in scripts {}
2405
to ensure application of a complex list of parameter changes. {}
2406
\par\page\par
2407
+{\footnote doc}
2408
#{\footnote renum}
2409
#{\footnote renumber}
2410
${\footnote Renumber}
2411
K{\footnote renumber}
2412
{\b Renumber}\par\par
2413
\tx1200
2414
{\f2\b Syntax:\tab
2415
renumber \{\{-\} <value>\}\par
2416
}\pard\par
2417
The RasMol {}
2418
'{\f2\b renumber}' {}
2419
command sequentially numbers the residues in a macromolecular chain. {}
2420
The optional parameter specifies the value of the first residue in the {}
2421
sequence. By default, this value is one. For proteins, {}
2422
each amino acid is numbered consecutively from the N terminus to the C {}
2423
terminus. For nucleic acids, each base is numbered from the 5' terminus {}
2424
to the 3' terminus. All chains in the current database are renumbered and gaps {}
2425
in the original sequence are ignored. The starting value for numbering may {}
2426
be negative. {}
2427
\par\page\par
2428
+{\footnote doc}
2429
#{\footnote reset}
2430
${\footnote Reset}
2431
K{\footnote reset}
2432
{\b Reset}\par\par
2433
\tx1200
2434
{\f2\b Syntax:\tab
2435
reset\par
2436
}\pard\par
2437
The RasMol {}
2438
'{\f2\b reset}' {}
2439
command restores the original viewing transformation {}
2440
and centre of rotation. The scale is set to its default value, {}
2441
'{\uldb zoom 100}{\v zoom}', {}
2442
the centre of rotation is set to the geometric centre of the currently {}
2443
loaded molecule, {}
2444
'{\uldb centre all}{\v centre}', {}
2445
this centre is translated to the middle of the screen and {}
2446
the viewpoint set to the default orientation. {}
2447
\par\par
2448
This command should not be mistaken for the RasMol {}
2449
'{\uldb zap}{\v zap}' {}
2450
command which deletes the currently stored molecule, returning the {}
2451
program to its initial state. {}
2452
\par\page\par
2453
+{\footnote doc}
2454
#{\footnote restrict}
2455
${\footnote Restrict}
2456
K{\footnote restrict}
2457
{\b Restrict}\par\par
2458
\tx1200
2459
{\f2\b Syntax:\tab
2460
restrict \{<expression>\}\par
2461
}\pard\par
2462
The RasMol {}
2463
'{\f2\b restrict}' {}
2464
command both defines the currently selected region of the {}
2465
molecule and disables the representation of (most of) those parts of the {}
2466
molecule no longer selected. All subsequent RasMol commands that modify {}
2467
a molecule's colour or representation affect only the currently selected {}
2468
region. The parameter of a {}
2469
'{\f2\b restrict}' {}
2470
command is a RasMol atom expression that is evaluated for every atom {}
2471
of the current molecule. This command is very similar to the RasMol {}
2472
'{\uldb select}{\v select}' {}
2473
command, except {}
2474
'{\f2\b restrict}' {}
2475
disables the {}
2476
'{\uldb wireframe}{\v wireframe}', {}
2477
'{\uldb spacefill}{\v spacefill}' {}
2478
and {}
2479
'{\uldb backbone}{\v backbone}' {}
2480
representations in the non-selected region. {}
2481
\par\par
2482
Type "help expression" for more information on RasMol atom expressions or {}
2483
see section {}
2484
'{\uldb Atom Expressions}{\v chexprs}'. {}
2485
\par\page\par
2486
+{\footnote doc}
2487
#{\footnote ribbon}
2488
#{\footnote ribbons}
2489
${\footnote Ribbons}
2490
K{\footnote ribbons}
2491
{\b Ribbons}\par\par
2492
\tx1200
2493
{\f2\b Syntax:\tab
2494
ribbons \{<boolean>\}\line\tab
2495
ribbons <value>\par
2496
}\pard\par
2497
The RasMol {}
2498
'{\f2\b ribbons}' {}
2499
command displays the currently loaded protein or nucleic acid as a {}
2500
smooth solid "ribbon" surface passing along the backbone of the protein. {}
2501
The ribbon is drawn between each amino acid whose alpha carbon is {}
2502
currently selected. The colour of the ribbon is changed by the RasMol {}
2503
'{\uldb colour ribbon}{\v colour}' {}
2504
command. If the current ribbon colour is {}
2505
'{\f2\b none}' {}
2506
(the default), the colour is taken from the alpha carbon at each {}
2507
position along its length. {}
2508
\par\par
2509
The width of the ribbon at each position is determined by the optional {}
2510
parameter in the usual RasMol units. By default the width of the ribbon {}
2511
is taken from the secondary structure of the protein or a constant value {}
2512
of 720 (2.88 Angstroms) for nucleic acids. {}
2513
The default width of protein alpha helices and beta sheets is 380 (1.52 {}
2514
Angstroms) and 100 (0.4 Angstroms) for turns and random coil. The {}
2515
secondary structure assignment is either from the PDB file or calculated {}
2516
using the DSSP algorithm as used by the {}
2517
'{\uldb structure}{\v structure}' {}
2518
command. This command is similar to the RasMol command {}
2519
'{\uldb strands}{\v strands}' {}
2520
which renders the biomolecular ribbon as parallel depth-cued curves. {}
2521
\par\page\par
2522
+{\footnote doc}
2523
#{\footnote rotate}
2524
${\footnote Rotate}
2525
K{\footnote rotate}
2526
{\b Rotate}\par\par
2527
\tx1200
2528
{\f2\b Syntax:\tab
2529
rotate <axis> \{-\} <value>\line\tab
2530
rotate bond \{<boolean>\}\line\tab
2531
rotate molecule \{<boolean>\}\line\tab
2532
rotate all \{<boolean>\}\par
2533
}\pard\par
2534
Rotate the molecule about the specified axis. {}
2535
Permitted values for the axis parameter are {}
2536
"{\f2\b x}", "{\f2\b y}", "{\f2\b z}" and "{\f2b bond}". {}
2537
The integer parameter states the angle in degrees for the structure to {}
2538
be rotated. For the X and Y axes, positive values move the closest point {}
2539
up and right, and negative values move it down and left, respectively. For {}
2540
the Z axis, a positive rotation acts clockwise and a negative angle {}
2541
anti-clockwise. {}
2542
\par\par
2543
Alternatively, this command may be used to specify which rotations {}
2544
the mouse or dials will control. If {}
2545
'{\f2\b rotate bond true}' {}
2546
is selected, the horizontal scroll bar will control rotation around {}
2547
the axis selected by the {}
2548
'{\uldb bond src dst pick}{\v bond}' {}
2549
command. If {}
2550
'{\f2\b rotate all true}' {}
2551
is selected, and multiple molecules have been loaded, then all molecules {}
2552
will rotate together. In all other cases, the mouseand dials control the {}
2553
the rotation of the molecule selected by the {}
2554
'{\uldb molecule n}{\v molecule}' {}
2555
command. {}
2556
\par\page\par
2557
+{\footnote doc}
2558
#{\footnote russian}
2559
${\footnote Russian}
2560
K{\footnote russian}
2561
{\b Russian}\par\par
2562
\tx1200
2563
{\f2\b Syntax:\tab
2564
Russian \par
2565
}\pard\par
2566
The RasMol {}
2567
'{\f2\b Russian}' {}
2568
command sets the menus and messages to the Russian versions. {}
2569
\par\par
2570
This command may not work correctly unless appropriate fonts {}
2571
have been installed. The commands {}
2572
'{\uldb Bulgarian}{\v bulgarian}', {}
2573
'{\uldb Chinese}{\v chinese}', {}
2574
'{\uldb English}{\v english}', {}
2575
'{\uldb French}{\v french}', {}
2576
'{\uldb Italian}{\v italian}', {}
2577
'{\uldb Russian}{\v russian}' {}
2578
and {}
2579
'{\uldb Spanish}{\v spanish}' {}
2580
may be used to select Bulgarian, Chinese, English, French, {}
2581
Italian, Japanese, Russian and Spanish menus and messages if the {}
2582
appropriate fonts have been installed. {}
2583
\par\page\par
2584
+{\footnote doc}
2585
#{\footnote save}
2586
${\footnote Save}
2587
K{\footnote save}
2588
{\b Save}\par\par
2589
\tx1200
2590
{\f2\b Syntax:\tab
2591
save \{pdb\} <filename>\line\tab
2592
save mdl <filename>\line\tab
2593
save alchemy <filename>\line\tab
2594
save xyz <filename>\par
2595
}\pard\par
2596
Save the currently selected set of atoms in a Protein {}
2597
Data Bank (PDB), MDL, Alchemy(tm) or XYZ format file. {}
2598
The distinction between this command and the RasMol {}
2599
'{\uldb write}{\v write}' {}
2600
command has been dropped. The only difference is that without a format {}
2601
specifier the {}
2602
'{\f2\b save}' {}
2603
command generates a {}
2604
'{\f2\b PDB}' {}
2605
file and the {}
2606
'{\uldb write}{\v write}' {}
2607
command generates a {}
2608
'{\f2\b GIF}' {}
2609
image. {}
2610
\par\page\par
2611
+{\footnote doc}
2612
#{\footnote script}
2613
${\footnote Script}
2614
K{\footnote script}
2615
{\b Script}\par\par
2616
#{\footnote source}
2617
\tx1200
2618
{\f2\b Syntax:\tab
2619
script <filename>\par
2620
}\pard\par
2621
The RasMol {}
2622
'{\f2\b script}' {}
2623
command reads a set of RasMol commands sequentially from a {}
2624
text file and executes them. This allows sequences of commonly used {}
2625
commands to be stored and performed by single command. A RasMol script {}
2626
file may contain a further script command up to a maximum "depth" of 10, {}
2627
allowing complicated sequences of actions to be executed. RasMol {}
2628
ignores all characters after the first '#' character on each line {}
2629
allowing the scripts to be annotated. Script files are often also {}
2630
annotated using the RasMol {}
2631
'{\uldb echo}{\v echo}' {}
2632
command. {}
2633
\par\par
2634
The most common way to generate a RasMol script file is to use the {}
2635
'{\uldb write script}{\v write}' {}
2636
or {}
2637
'{\uldb write rasmol}{\v write}' {}
2638
commands to output the sequence of commands that are needed to {}
2639
regenerate the current view, representation and colouring of the {}
2640
currently displayed molecule. {}
2641
\par\par
2642
The RasMol command {}
2643
'{\f2\b source}' {}
2644
is synonymous with the {}
2645
'{\f2\b script}' {}
2646
command. {}
2647
\par\page\par
2648
+{\footnote doc}
2649
#{\footnote select}
2650
${\footnote Select}
2651
K{\footnote select}
2652
{\b Select}\par\par
2653
\tx1200
2654
{\f2\b Syntax:\tab
2655
select \{<expression>\}\par
2656
}\pard\par
2657
Define the currently selected region of the molecule. All subsequent RasMol {}
2658
commands that manipulate a molecule or modify its colour or representation {}
2659
only affect the currently selected region. The parameter of a {}
2660
'{\f2\b select}' {}
2661
command is a RasMol expression that is evaluated for every atom of the {}
2662
current molecule. The currently selected (active) region of the molecule {}
2663
are those atoms that cause the expression to evaluate true. To select {}
2664
the whole molecule use the RasMol command {}
2665
'{\f2\b select all}'. {}
2666
The behaviour of the {}
2667
'{\f2\b select}' {}
2668
command without any parameters is determined by the RasMol {}
2669
'{\uldb hetero}{\v sethetero}' {}
2670
and {}
2671
'{\uldb hydrogen}{\v set}' {}
2672
parameters. {}
2673
\par\par
2674
Type "help expression" for more information on RasMol atom expressions or {}
2675
see section {}
2676
'{\uldb Atom Expressions}{\v chexprs}'. {}
2677
\par\page\par
2678
+{\footnote doc}
2679
#{\footnote set}
2680
${\footnote Set}
2681
K{\footnote set}
2682
{\b Set}\par\par
2683
\tx1200
2684
{\f2\b Syntax:\tab
2685
set <parameter> \{<option>\}\par
2686
}\pard\par
2687
The RasMol {}
2688
'{\f2\b set}' {}
2689
command allows the user to alter various internal program parameters {}
2690
such as those controlling rendering options. Each parameter has its {}
2691
own set or permissible parameter options. Typically, omitting the {}
2692
paramter option resets that parameter to its default value. A list of {}
2693
valid parameter names is given below. {}
2694
\par\par
2695
{\cellx1200\cellx2400\cellx3600\cellx4800
2696
\intbl
2697
{\uldb ambient}{\v setambient}\cell
2698
{\uldb axes}{\v setaxes}\cell
2699
{\uldb background}{\v setbackground}\cell
2700
{\uldb backfade}{\v setbackfade}\cell
2701
\row\intbl
2702
{\uldb bondmode}{\v setbondmode}\cell
2703
{\uldb bonds}{\v setbonds}\cell
2704
{\uldb booundbox}{\v setboundbox}\cell
2705
{\uldb cartoons}{\v setcartoon}\cell
2706
\row\intbl
2707
{\uldb cisangle}{\v setcisangle}\cell
2708
{\uldb display}{\v setdisplay}\cell
2709
{\uldb fontsize}{\v setfontsize}\cell
2710
{\uldb fontstroke}{\v setfontstroke}\cell
2711
\row\intbl
2712
{\uldb hbonds}{\v sethbonds}\cell
2713
{\uldb hetero}{\v sethetero}\cell
2714
{\uldb hourglass}{\v sethourglass}\cell
2715
{\uldb hydrogen}{\v sethydrogen}\cell
2716
\row\intbl
2717
{\uldb kinemage}{\v setkinemage}\cell
2718
{\uldb menus}{\v setmenus}\cell
2719
{\uldb monitor}{\v setmonitor}\cell
2720
{\uldb mouse}{\v setmouse}\cell
2721
\row\intbl
2722
{\uldb picking}{\v setpicking}\cell
2723
{\uldb play...}{\v setplay}\cell
2724
{\uldb radius}{\v setradius}\cell
2725
{\uldb record...}{\v setrecord}\cell
2726
\row\intbl
2727
{\uldb shadepower}{\v setshadepower}\cell
2728
{\uldb shadow}{\v setshadow}\cell
2729
{\uldb slabmode}{\v setslabmode}\cell
2730
{\uldb solvent}{\v setsolvent}\cell
2731
\row\intbl
2732
{\uldb specular}{\v setspecular}\cell
2733
{\uldb specpower}{\v setspecpower}\cell
2734
{\uldb ssbonds}{\v setssbonds}\cell
2735
{\uldb stereo}{\v setstereo}\cell
2736
\row\intbl
2737
{\uldb strands}{\v setstrands}\cell
2738
{\uldb transparent}{\v settransparent}\cell
2739
{\uldb unitcell}{\v setunitcell}\cell
2740
{\uldb vectps}{\v setvectps}\cell
2741
\row\intbl
2742
{\uldb write}{\v setwrite}\cell
2743
\cell
2744
\cell
2745
\cell
2746
\row}
2747
\pard\par\trowd
2748
\par\page\par
2749
+{\footnote doc}
2750
#{\footnote show}
2751
${\footnote Show}
2752
K{\footnote show}
2753
{\b Show}\par\par
2754
\tx1200
2755
{\f2\b Syntax:\tab
2756
show information\line\tab
2757
show centre\line\tab
2758
show phipsi\line\tab
2759
show RamPrint\line\tab
2760
show rotation\line\tab
2761
show selected \{ group | chain | atom \}\line\tab
2762
show sequence\line\tab
2763
show symmetry\line\tab
2764
show translation\line\tab
2765
show zoom\par
2766
}\pard\par
2767
The RasMol {}
2768
'{\f2\b show}' {}
2769
command display details of the status of the currently {}
2770
loaded molecule. The command {}
2771
'{\f2\b show information}' {}
2772
lists the molecule's name, {}
2773
classification, PDB code and the number of atoms, chains, groups it contains. {}
2774
If hydrogen bonding, disulphide bridges or secondary structure have been {}
2775
determined, the number of hbonds, ssbonds, helices, ladders and turns {}
2776
are also displayed, respectively. The command {}
2777
'{\f2\b show centre}' {}
2778
shows any non-zero centering values selected by the {}
2779
'{\uldb centre [CenX, CenY, CenZ]}{\v centre}' {}
2780
command. The command {}
2781
'{\f2\b show phipsi}' {}
2782
shows the phi and psi angles of the currently selected residues and {}
2783
the omega angles of cis peptide bonds. The command {}
2784
'{\f2\b show RamPrint}' {}
2785
(or 'show RPP' or 'show RamachandranPrinterPlot') shows a simple {}
2786
Ramachandran printer plot in the style of Frances Bernstein's fisipl {}
2787
program. The command {}
2788
'{\f2\b show rotation}' {}
2789
(or 'show rot' or 'show 'rotate') shows the currently selected values {}
2790
of z, y, x and bond rotations, if any. {}
2791
The command {}
2792
'{\f2\b show selected}' {}
2793
(or 'show selected group' or 'show selected chain' or 'show selected atom' ) {}
2794
shows the groups (default), chains or atoms of the current selection. {}
2795
The command {}
2796
'{\f2\b show sequence}' {}
2797
lists the residues that comprise each chain of the molecule. The command {}
2798
'{\f2\b show symmetry}' {}
2799
shows the space group and unit cell of the molecule. The command {}
2800
'{\f2\b show translation}' {}
2801
shows any non-zero translation values selected by the {}
2802
'{\uldb translate <axis> <value>}{\v translate}' {}
2803
command. The command {}
2804
'{\f2\b show zoom}' {}
2805
shows any non-zero zoom value selected by the {}
2806
'{\uldb zoom <value>}{\v zoom}' {}
2807
command. {}
2808
\par\page\par
2809
+{\footnote doc}
2810
#{\footnote slab}
2811
${\footnote Slab}
2812
K{\footnote slab}
2813
{\b Slab}\par\par
2814
\tx1200
2815
{\f2\b Syntax:\tab
2816
slab \{<boolean>\}\line\tab
2817
slab <value>\par
2818
}\pard\par
2819
The RasMol {}
2820
'{\f2\b slab}' {}
2821
command enables, disables or positions the z-clipping plane of the {}
2822
molecule. The program only draws those portions of the {}
2823
molecule that are further from the viewer than the slabbing plane. {}
2824
Integer values range from zero at the very back of the molecule to {}
2825
100 which is completely in front of the molecule. Intermediate values {}
2826
determine the percentage of the molecule to be drawn. {}
2827
\par\par
2828
This command interacts with the {}
2829
'{\uldb depth <value>}{\v depth}' {}
2830
command, which clips to the rear of a given z-clipping plane. {}
2831
\par\page\par
2832
+{\footnote doc}
2833
#{\footnote cpk}
2834
#{\footnote cpknew}
2835
#{\footnote spacefill}
2836
${\footnote Spacefill}
2837
K{\footnote spacefill}
2838
{\b Spacefill}\par\par
2839
\tx1200
2840
{\f2\b Syntax:\tab
2841
spacefill \{<boolean>\}\line\tab
2842
spacefill temperature\line\tab
2843
spacefill user\line\tab
2844
spacefill <value>\par
2845
}\pard\par
2846
The RasMol {}
2847
'{\f2\b spacefill}' {}
2848
command is used to represent all of the currently selected atoms as solid {}
2849
spheres. This command is used to produce both union-of-spheres and {}
2850
ball-and-stick models of a molecule. The command, {}
2851
'{\f2\b spacefill true}', {}
2852
the default, represents each atom as a sphere of van der Waals radius. {}
2853
The command {}
2854
'{\f2\b spacefill off}' {}
2855
turns off the representation of the selected atom as spheres. A sphere {}
2856
radius may be specified as an integer in RasMol units (1/250th Angstrom) {}
2857
or a value containing a decimal point. A value of 500 (2.0 {}
2858
Angstroms) or greater results in a "Parameter value too large" error. {}
2859
\par\par
2860
The {}
2861
'{\f2\b temperature}' {}
2862
option sets the radius of each sphere to the value stored in its temperature {}
2863
field. Zero or negative values have no effect and values greater than {}
2864
2.0 are truncated to 2.0. The {}
2865
'{\f2\b user}' {}
2866
option allows the radius of each sphere to be specified by additional lines {}
2867
in the molecule's PDB file using Raster 3D's COLOUR record extension. {}
2868
\par\par
2869
The RasMol command {}
2870
'{\f2\b cpk}' {}
2871
is synonymous with the {}
2872
'{\f2\b spacefill}' {}
2873
command. {}
2874
\par\par
2875
The RasMol command {}
2876
'{\f2\b cpknew}' {}
2877
is synonymous with the {}
2878
'{\f2\b spacefill}' {}
2879
command, except that a slightly different set of colours is used. {}
2880
\par\page\par
2881
+{\footnote doc}
2882
#{\footnote spanish}
2883
${\footnote Spanish}
2884
K{\footnote spanish}
2885
{\b Spanish}\par\par
2886
\tx1200
2887
{\f2\b Syntax:\tab
2888
Spanish \par
2889
}\pard\par
2890
The RasMol {}
2891
'{\f2\b Spanish}' {}
2892
command sets the menus and messages to the Spanish versions. {}
2893
\par\par
2894
This command may not work correctly unless appropriate fonts {}
2895
have been installed. The commands {}
2896
'{\uldb Bulgarian}{\v bulgarian}', {}
2897
'{\uldb Chinese}{\v chinese}', {}
2898
'{\uldb English}{\v english}', {}
2899
'{\uldb French}{\v french}', {}
2900
'{\uldb Italian}{\v italian}', {}
2901
'{\uldb Russian}{\v russian}' {}
2902
and {}
2903
'{\uldb Spanish}{\v spanish}' {}
2904
may be used to select Bulgarian, Chinese, English, French, {}
2905
Italian, Japanese, Russian and Spanish menus and messages if the {}
2906
appropriate fonts have been installed. {}
2907
\par\page\par
2908
+{\footnote doc}
2909
#{\footnote ssbond}
2910
#{\footnote ssbonds}
2911
${\footnote SSBonds}
2912
K{\footnote ssbonds}
2913
{\b SSBonds}\par\par
2914
\tx1200
2915
{\f2\b Syntax:\tab
2916
ssbonds \{<boolean>\}\line\tab
2917
ssbonds <value>\par
2918
}\pard\par
2919
The RasMol {}
2920
'{\f2\b ssbonds}' {}
2921
command is used to represent the disulphide bridges of the protein {}
2922
molecule as either dotted lines or cylinders between the connected {}
2923
cysteines. The first time that the {}
2924
'{\f2\b ssbonds}' {}
2925
command is used, the program searches the structure of the protein to {}
2926
find half-cysteine pairs (cysteines whose sulphurs are within 3 Angstroms {}
2927
of each other) and reports the number of bridges to the user. The command {}
2928
'{\f2\b ssbonds on}' {}
2929
displays the selected "bonds" as dotted lines, and the command {}
2930
'{\f2\b ssbonds off}' {}
2931
disables the display of ssbonds in the currently selected area. Selection {}
2932
of disulphide bridges is identical to normal bonds, and may be adjusted {}
2933
using the RasMol {}
2934
'{\uldb set bondmode}{\v setbondmode}' {}
2935
command. The colour of disulphide bonds may be changed using the {}
2936
'{\uldb colour ssbonds}{\v colour}' {}
2937
command. By default, each disulphide bond has the colours of its connected {}
2938
atoms. {}
2939
\par\par
2940
By default disulphide bonds are drawn between the sulphur atoms within {}
2941
the cysteine groups. By using the {}
2942
'{\uldb set ssbonds}{\v setssbonds}' {}
2943
command the position of the cysteine's alpha carbons may be used instead. {}
2944
\par\page\par
2945
+{\footnote doc}
2946
#{\footnote star}
2947
${\footnote Star}
2948
K{\footnote star}
2949
{\b Star}\par\par
2950
\tx1200
2951
{\f2\b Syntax:\tab
2952
star \{<boolean>\}\line\tab
2953
star temperature\line\tab
2954
star user\line\tab
2955
star <value>\par
2956
}\pard\par
2957
The RasMol {}
2958
'{\f2\b star}' {}
2959
command is used to represent all of the currently selected atoms as {}
2960
stars (six strokes, one each in the x, -x, y, -y, z and -z directions). {}
2961
The commands {}
2962
'{\f2\b select not bonded}' {}
2963
followed by {}
2964
'{\f2\b star 75}' {}
2965
are useful to mark unbonded atoms in a {}
2966
'{\uldb wireframe}{\v wireframe}' {}
2967
display with less overhead than provided by {}
2968
'{\uldb spacefill 75}{\v spacefill}'. {}
2969
This can be done automatically for all subsequent wireframe {}
2970
displays with the command {}
2971
'{\uldb set bondmode not bonded}{\v setbondmode}'. {}
2972
\par\par
2973
The command {}
2974
'{\f2\b star true}', {}
2975
the default, represents each atom as a star with strokes {}
2976
length equal to van der Waals radius. {}
2977
The command {}
2978
'{\f2\b star off}' {}
2979
turns off the representation of the selected atom as stars. A star {}
2980
stroke length may be specified as an integer in RasMol units {}
2981
(1/250th Angstrom) {}
2982
or a value containing a decimal point. A value of 500 (2.0 {}
2983
Angstroms) or greater results in a "Parameter value too large" error. {}
2984
\par\par
2985
The {}
2986
'{\f2\b temperature}' {}
2987
option sets the stroke length of each star to the value stored {}
2988
in its temperature {}
2989
field. Zero or negative values have no effect and values greater than {}
2990
2.0 are truncated to 2.0. The {}
2991
'{\f2\b user}' {}
2992
option allows the stroke length of each star to be specified by {}
2993
additional lines {}
2994
in the molecule's PDB file using Raster 3D's COLOUR record extension. {}
2995
\par\par
2996
The RasMol {}
2997
'{\uldb spacefill}{\v spacefill}' {}
2998
command can be used for more artistic rendering of atoms as spheres. {}
2999
\par\page\par
3000
+{\footnote doc}
3001
#{\footnote stereo}
3002
${\footnote Stereo}
3003
K{\footnote stereo}
3004
{\b Stereo}\par\par
3005
\tx1200
3006
{\f2\b Syntax:\tab
3007
stereo on\line\tab
3008
stereo [-] <number>\line\tab
3009
stereo off\par
3010
}\pard\par
3011
The RasMol {}
3012
'{\f2\b stereo}' {}
3013
command provides side-by-side stereo display of images. Stereo {}
3014
viewing of a molecule may be turned on (and off) either by {}
3015
selecting {}
3016
'{\f2\b Stereo}' {}
3017
from the {}
3018
'{\f2\b Options}' {}
3019
menu, or by {}
3020
typing the commands {}
3021
'{\f2\b stereo on}' {}
3022
or {}
3023
'{\f2\b stereo off}'. {}
3024
\par\par
3025
Starting with RasMol version 2.7.2.1, the {}
3026
'{\f2\b Stereo}' {}
3027
menu selection and the command {}
3028
'{\f2\b stereo}' {}
3029
without arguments cycle from the initial state of {}
3030
'{\f2\b stereo off}' {}
3031
to {}
3032
'{\f2\b stereo on}' {}
3033
in cross-eyed mode to {}
3034
'{\f2\b stereo on}' {}
3035
in wall-eyed mode and then back to {}
3036
'{\f2\b stereo off}'. {}
3037
\par\par
3038
The separation angle between {}
3039
the two views may be adjusted with the {}
3040
'{\uldb set stereo [-] <number>}{\v setstereo}' {}
3041
command, where positive values result in crossed eye {}
3042
viewing and negative values in relaxed (wall-eyed) viewing. {}
3043
The inclusion of {}
3044
'{\f2\b [-] <number>}' {}
3045
in the {}
3046
'{\f2\b stereo}' {}
3047
command, as for example in {}
3048
'{\f2\b stereo 3}' {}
3049
or {}
3050
'{\f2\b stereo -5}', {}
3051
also controls angle and direction. {}
3052
\par\par
3053
The stereo command is only partially {}
3054
implemented. When stereo is turned on, the image is not properly {}
3055
recentred. (This can be done with a {}
3056
'{\uldb translate x -<number>}{\v translate}' {}
3057
command.) {}
3058
It is not supported in vector PostScript output files, is not {}
3059
saved by the {}
3060
'{\f2\b write script}' {}
3061
command, and in {}
3062
general is not yet properly interfaced with several other {}
3063
features of the program. {}
3064
\par\page\par
3065
+{\footnote doc}
3066
#{\footnote strands}
3067
${\footnote Strands}
3068
K{\footnote strands}
3069
{\b Strands}\par\par
3070
\tx1200
3071
{\f2\b Syntax:\tab
3072
strands \{<boolean>\}\line\tab
3073
strands <value>\par
3074
}\pard\par
3075
The RasMol {}
3076
'{\f2\b strands}' {}
3077
command displays the currently loaded protein or nucleic acid as a {}
3078
smooth "ribbon" of depth-cued curves passing along the backbone of the {}
3079
protein. The ribbon is composed of a number of strands that run parallel {}
3080
to one another along the peptide plane of each residue. The ribbon is {}
3081
drawn between each amino acid whose alpha carbon is currently selected. {}
3082
The colour of the ribbon is changed by the RasMol {}
3083
'{\uldb colour ribbon}{\v colour}' {}
3084
command. If the current ribbon colour is {}
3085
'{\f2\b none}' {}
3086
(the default), the colour is taken from the alpha carbon at each {}
3087
position along its length. The central and outermost {}
3088
strands may be coloured independently using the {}
3089
'{\uldb colour ribbon1}{\v colour}' {}
3090
and {}
3091
'{\uldb colour ribbon2}{\v colour}' {}
3092
commands, respectively. The number of strands in the ribbon may be {}
3093
altered using the RasMol {}
3094
'{\uldb set strands}{\v setstrands}' {}
3095
command. {}
3096
\par\par
3097
The width of the ribbon at each position is determined by the optional {}
3098
parameter in the usual RasMol units. By default the width of the ribbon {}
3099
is taken from the secondary structure of the protein or a constant value {}
3100
of 720 for nucleic acids (which produces a ribbon 2.88 Angstroms wide). {}
3101
The default width of protein alpha helices and beta sheets is 380 (1.52 {}
3102
Angstroms) and 100 (0.4 Angstroms) for turns and random coil. The {}
3103
secondary structure assignment is either from the PDB file or calculated {}
3104
using the DSSP algorithm as used by the {}
3105
'{\uldb structure}{\v structure}' {}
3106
command. This command is similar to the RasMol command {}
3107
'{\uldb ribbons}{\v ribbons}' {}
3108
which renders the biomolecular ribbon as a smooth shaded surface. {}
3109
\par\page\par
3110
+{\footnote doc}
3111
#{\footnote structure}
3112
${\footnote Structure}
3113
K{\footnote structure}
3114
{\b Structure}\par\par
3115
\tx1200
3116
{\f2\b Syntax:\tab
3117
structure\par
3118
}\pard\par
3119
The RasMol {}
3120
'{\f2\b structure}' {}
3121
command calculates secondary structure assignments {}
3122
for the currently loaded protein. If the original PDB file contained {}
3123
structural assignment records (HELIX, SHEET and TURN) these are discarded. {}
3124
Initially, the hydrogen bonds of the current molecule are found, if this {}
3125
hasn't been done already. The secondary structure is then determined using {}
3126
Kabsch and Sander's DSSP algorithm. Once finished the program reports the {}
3127
number of helices, strands and turns found. {}
3128
\par\page\par
3129
+{\footnote doc}
3130
#{\footnote surface}
3131
${\footnote Surface}
3132
K{\footnote surface}
3133
{\b Surface}\par\par
3134
\tx1200
3135
{\f2\b Syntax:\tab
3136
structure molecule <value>\line\tab
3137
structure solvent <value>\par
3138
}\pard\par
3139
The RasMol {}
3140
'{\f2\b surface}' {}
3141
command renders a Lee-Richards molecular surface resulting {}
3142
from rolling a probe atom on the selected atoms. {}
3143
The value given specifies the radius of the probe. {}
3144
If given in the first form, the evolute of the surface {}
3145
of the probe is shown (the solvent excluded surface). {}
3146
If given in the second form, the envelope of the {}
3147
positions of the center of the probe is shown {}
3148
(the solvent accessible surface). {}
3149
\par\page\par
3150
+{\footnote doc}
3151
#{\footnote trace}
3152
${\footnote Trace}
3153
K{\footnote trace}
3154
{\b Trace}\par\par
3155
\tx1200
3156
{\f2\b Syntax:\tab
3157
trace \{<boolean>\}\line\tab
3158
trace <value>\line\tab
3159
trace temperature\par
3160
}\pard\par
3161
The RasMol {}
3162
'{\f2\b trace}' {}
3163
command displays a smooth spline between consecutive alpha {}
3164
carbon positions. This spline does not pass exactly through {}
3165
the alpha carbon position of each residue, but follows the {}
3166
same path as {}
3167
'{\uldb ribbons}{\v ribbons}', {}
3168
'{\uldb strands}{\v strands}' {}
3169
and {}
3170
'{\uldb cartoons}{\v cartoon}'. {}
3171
Note that residues may be displayed as {}
3172
'{\uldb ribbons}{\v ribbons}', {}
3173
'{\uldb strands}{\v strands}', {}
3174
'{\uldb cartoons}{\v cartoon}' {}
3175
or as a {}
3176
'{\f2\b trace}'. {}
3177
Enabling one of these {}
3178
representations disables the others. However, a residue {}
3179
may be displayed simultaneously as backbone and as one of {}
3180
the above representations. This may change in future {}
3181
versions of RasMol. Prior to version 2.6, {}
3182
'{\f2\b trace}' {}
3183
was synonymous with {}
3184
'{\f2\b backbone}'. {}
3185
\par\par
3186
'{\f2\b Trace temperature}' {}
3187
displays the backbone as a wider cylinder {}
3188
at high temperature factors and thinner at lower. This {}
3189
representation is useful to X-ray crystallographers and NMR spectroscopists. {}
3190
\par\page\par
3191
+{\footnote doc}
3192
#{\footnote translate}
3193
${\footnote Translate}
3194
K{\footnote translate}
3195
{\b Translate}\par\par
3196
\tx1200
3197
{\f2\b Syntax:\tab
3198
translate <axis> \{-\} <value>\par
3199
}\pard\par
3200
The RasMol {}
3201
'{\f2\b translate}' {}
3202
command moves the position of the centre of the molecule on the {}
3203
screen. The axis parameter specifies along which axis the molecule {}
3204
is to be moved and the integer parameter specifies the absolute {}
3205
position of the molecule centre from the middle of the screen. {}
3206
Permitted values for the axis parameter are {}
3207
"{\f2\b x}", "{\f2\b y}" and "{\f2\b z}". {}
3208
Displacement values must be between -100 and 100 which correspond to {}
3209
moving the current molecule just off the screen. A positive {}
3210
"{\f2\b x}" {}
3211
displacement moves the molecule to the right, and a positive {}
3212
"{\f2\b y}" {}
3213
displacement moves the molecule down the screen. The pair of commands {}
3214
'{\f2\b translate x 0}' {}
3215
and {}
3216
'{\f2\b translate y 0}' {}
3217
centres the molecule on the screen. {}
3218
\par\page\par
3219
+{\footnote doc}
3220
#{\footnote unbond}
3221
${\footnote UnBond}
3222
K{\footnote unbond}
3223
{\b UnBond}\par\par
3224
\tx1200
3225
{\f2\b Syntax:\tab
3226
unbond <number> <number>\line\tab
3227
unbond\par
3228
}\pard\par
3229
The RasMol command {}
3230
'{\f2\b unbond <number> <number>}' {}
3231
removes the designated bond from the drawing. {}
3232
\par\par
3233
The command {}
3234
'{\f2\b unbond}' {}
3235
without arguments removes a bond previously picked by the {}
3236
'{\uldb bond <number> <number> pick}{\v bond}' {}
3237
command. {}
3238
\par\page\par
3239
+{\footnote doc}
3240
#{\footnote wireframe}
3241
${\footnote Wireframe}
3242
K{\footnote wireframe}
3243
{\b Wireframe}\par\par
3244
\tx1200
3245
{\f2\b Syntax:\tab
3246
wireframe \{<boolean>\}\line\tab
3247
wireframe <value> \{<value>\}\par
3248
}\pard\par
3249
The RasMol {}
3250
'{\f2\b wireframe}' {}
3251
command represents each bond within the selected region of the molecule {}
3252
as a cylinder, a line or a depth-cued vector. The display of bonds {}
3253
as depth-cued vectors (drawn darker the further away from the viewer) {}
3254
is turned on by the command {}
3255
'{\f2\b wireframe}' {}
3256
or {}
3257
'{\f2\b wireframe on}'. {}
3258
The selected bonds are displayed as cylinders by specifying a radius {}
3259
either as an integer in RasMol units or containing a decimal point as {}
3260
a value in Angstroms. A parameter value of 500 (2.0 Angstroms) or {}
3261
above results in an "Parameter value too large" error. Bonds may be {}
3262
coloured using the {}
3263
'{\uldb colour bonds}{\v colour}' {}
3264
command. {}
3265
{}
3266
If the selected bonds involved atoms of alternate conformers then {}
3267
the bonds are narrowed in the middle to a radius of .8 of the specified {}
3268
radius (or to the radius specifed as the optional second parameter). {}
3269
\par\par
3270
Non-bonded atoms, which could become invisible in an {}
3271
ordinary {}
3272
'{\f2\b wireframe}' {}
3273
display can be marked by a preceding {}
3274
'{\uldb set bondmode not bonded}{\v setbondmode}' {}
3275
command. If nearly co-linear bonds to atoms cause them to be {}
3276
difficult to see in a wireframe display, the {}
3277
'{\uldb set bondmode all}{\v setbondmode}' {}
3278
command will add markers for {}
3279
'{\f2\b all}' {}
3280
atoms in subsequent {}
3281
'{\f2\b wireframe}' {}
3282
command executions. {}
3283
\par\page\par
3284
+{\footnote doc}
3285
#{\footnote write}
3286
${\footnote Write}
3287
K{\footnote write}
3288
{\b Write}\par\par
3289
\tx1200
3290
{\f2\b Syntax:\tab
3291
write \{<format>\} <filename>\par
3292
}\pard\par
3293
Write the current image to a file in a standard format. Currently {}
3294
supported image file formats include {}
3295
'{\f2\b bmp}' {}
3296
(Microsoft bitmap) and {}
3297
'{\f2\b gif}' {}
3298
(Compuserve GIF), {}
3299
'{\f2\b iris}' {}
3300
(IRIS RGB), {}
3301
'{\f2\b ppm}' {}
3302
(Portable Pixmap), {}
3303
'{\f2\b ras}' {}
3304
(Sun rasterfile), {}
3305
'{\f2\b ps}' {}
3306
and {}
3307
'{\f2\b epsf}' {}
3308
(Encapsulated PostScript), {}
3309
'{\f2\b monops}' {}
3310
(Monochrome Encapsulated PostScript), {}
3311
'{\f2\b pict}' {}
3312
(Apple PICT), {}
3313
'{\f2\b vectps}' {}
3314
(Vector Postscript). The {}
3315
'{\f2\b write}' {}
3316
command may also be used to generate command scripts for other graphics {}
3317
programs. The format {}
3318
'{\f2\b script}' {}
3319
writes out a file containing the RasMol {}
3320
'{\uldb script}{\v script}' {}
3321
commands to reproduce the current image. The format {}
3322
'{\f2\b molscript}' {}
3323
writes out the commands required to render the current view of the {}
3324
molecule as ribbons in Per Kraulis' Molscript program and the format {}
3325
'{\f2\b kinemage}' {}
3326
the commands for David Richardson's program Mage. The following {}
3327
formats are useful for further processing: {}
3328
'{\f2\b povray}' {}
3329
(POVRay 2), {}
3330
'{\f2\b povray3}' {}
3331
(POVRay 3 -- under development), {}
3332
'{\f2\b vrml}' {}
3333
(VRML file). {}
3334
Finally, several {}
3335
formats are provided to provide phi-psi data for listing or for {}
3336
'{\f2\b phipsi}' {}
3337
(phi-psi data as an annotated list with cis omegas), {}
3338
'{\f2\b ramachan}' {}
3339
and {}
3340
'{\f2\b RDF}' {}
3341
and {}
3342
'{\f2\b RamachandranDataFile}' {}
3343
(phi-psi data as columns of numbers for gnuplot), {}
3344
'{\f2\b RPP}' {}
3345
and {}
3346
'{\f2\b RamachandranPrinterPlot}' {}
3347
(phi-psi data as a printer plot). {}
3348
\par\par
3349
The distinction between this command and the RasMol {}
3350
'{\uldb save}{\v save}' {}
3351
command has been dropped. The only difference is that without a format {}
3352
specifier the {}
3353
'{\uldb save}{\v save}' {}
3354
command generates a {}
3355
'{\f2\b PDB}' {}
3356
file and the {}
3357
'{\f2\b write}' {}
3358
command generates a {}
3359
'{\f2\b GIF}' {}
3360
image. {}
3361
\par\page\par
3362
+{\footnote doc}
3363
#{\footnote zap}
3364
${\footnote Zap}
3365
K{\footnote zap}
3366
{\b Zap}\par\par
3367
\tx1200
3368
{\f2\b Syntax:\tab
3369
zap\par
3370
}\pard\par
3371
Deletes the contents of the current database and resets parameter {}
3372
variables to their initial default state. {}
3373
\par\page\par
3374
+{\footnote doc}
3375
#{\footnote zoom}
3376
${\footnote Zoom}
3377
K{\footnote zoom}
3378
{\b Zoom}\par\par
3379
\tx1200
3380
{\f2\b Syntax:\tab
3381
zoom \{<boolean>\}\line\tab
3382
zoom <value>\par
3383
}\pard\par
3384
Change the magnification of the currently displayed image. Boolean {}
3385
parameters either magnify or reset the scale of current molecule. An {}
3386
integer parameter specifies the desired magnification as a percentage {}
3387
of the default scale. The minimum parameter value is 10; the maximum {}
3388
parameter value is dependent upon the size of the molecule being {}
3389
displayed. For medium sized proteins this is about 500. {}
3390
\par\page\par
3391
+{\footnote doc}
3392
#{\footnote chsetopt}
3393
${\footnote Internal Parameters}
3394
{\fs24\b Internal Parameters}\par\par
3395
RasMol has a number of internal parameters that may be modified using the {}
3396
'{\uldb set}{\v set}' {}
3397
command. These parameters control a number of program options such as {}
3398
rendering options and mouse button mappings. {}
3399
\par\par
3400
A complete list of internal parameter names is given below. {}
3401
\par\par
3402
{\cellx1200\cellx2400\cellx3600\cellx4800
3403
\intbl
3404
{\uldb ambient}{\v setambient}\cell
3405
{\uldb axes}{\v setaxes}\cell
3406
{\uldb background}{\v setbackground}\cell
3407
{\uldb backfade}{\v setbackfade}\cell
3408
\row\intbl
3409
{\uldb bondmode}{\v setbondmode}\cell
3410
{\uldb bonds}{\v setbonds}\cell
3411
{\uldb booundbox}{\v setboundbox}\cell
3412
{\uldb cartoons}{\v setcartoon}\cell
3413
\row\intbl
3414
{\uldb cisangle}{\v setcisangle}\cell
3415
{\uldb display}{\v setdisplay}\cell
3416
{\uldb fontsize}{\v setfontsize}\cell
3417
{\uldb fontstroke}{\v setfontstroke}\cell
3418
\row\intbl
3419
{\uldb hbonds}{\v sethbonds}\cell
3420
{\uldb hetero}{\v sethetero}\cell
3421
{\uldb hourglass}{\v sethourglass}\cell
3422
{\uldb hydrogen}{\v sethydrogen}\cell
3423
\row\intbl
3424
{\uldb kinemage}{\v setkinemage}\cell
3425
{\uldb menus}{\v setmenus}\cell
3426
{\uldb monitor}{\v setmonitor}\cell
3427
{\uldb mouse}{\v setmouse}\cell
3428
\row\intbl
3429
{\uldb picking}{\v setpicking}\cell
3430
{\uldb play...}{\v setplay}\cell
3431
{\uldb radius}{\v setradius}\cell
3432
{\uldb record...}{\v setrecord}\cell
3433
\row\intbl
3434
{\uldb shadepower}{\v setshadepower}\cell
3435
{\uldb shadow}{\v setshadow}\cell
3436
{\uldb slabmode}{\v setslabmode}\cell
3437
{\uldb solvent}{\v setsolvent}\cell
3438
\row\intbl
3439
{\uldb specular}{\v setspecular}\cell
3440
{\uldb specpower}{\v setspecpower}\cell
3441
{\uldb ssbonds}{\v setssbonds}\cell
3442
{\uldb stereo}{\v setstereo}\cell
3443
\row\intbl
3444
{\uldb strands}{\v setstrands}\cell
3445
{\uldb transparent}{\v settransparent}\cell
3446
{\uldb unitcell}{\v setunitcell}\cell
3447
{\uldb vectps}{\v setvectps}\cell
3448
\row\intbl
3449
{\uldb write}{\v setwrite}\cell
3450
\cell
3451
\cell
3452
\cell
3453
\row}
3454
\pard\par\trowd
3455
\par\page\par
3456
+{\footnote doc}
3457
#{\footnote setambient}
3458
${\footnote Set Ambient}
3459
K{\footnote set ambient}
3460
{\b Set Ambient}\par\par
3461
K{\footnote ambient}
3462
\tx1200
3463
{\f2\b Syntax:\tab
3464
set ambient \{<value>\}\par
3465
}\pard\par
3466
The RasMol {}
3467
'{\f2\b ambient}' {}
3468
parameter is used to control the amount of ambient (or surrounding) {}
3469
light in the scene. The {}
3470
'{\f2\b ambient}' {}
3471
value must be between 0 and 100. It controls the percentage intensity {}
3472
of the darkest shade of an object. For a solid object, this is the {}
3473
intensity of surfaces facing away from the light source or in shadow. {}
3474
For depth-cued objects this is the intensity of objects furthest from {}
3475
the viewer. {}
3476
\par\par
3477
This parameter is commonly used to correct for monitors with different {}
3478
"gamma values" (brightness), to change how light or dark a hardcopy {}
3479
image appears when printed or to alter the feeling of depth for {}
3480
wireframe or ribbon representations. {}
3481
\par\page\par
3482
+{\footnote doc}
3483
#{\footnote setaxes}
3484
${\footnote Set Axes}
3485
K{\footnote set axes}
3486
{\b Set Axes}\par\par
3487
K{\footnote axes}
3488
\tx1200
3489
{\f2\b Syntax:\tab
3490
set axes <boolean>\par
3491
}\pard\par
3492
The RasMol {}
3493
'{\f2\b axes}' {}
3494
parameter controls the display of orthogonal coordinate axes on {}
3495
the current display. The coordinate axes are those used in the {}
3496
molecule data file, and the origin is the centre of the molecule's {}
3497
bounding box. The {}
3498
'{\f2\b set axes}' {}
3499
command is similar to the commands {}
3500
'{\uldb set boundbox}{\v setboundbox}' {}
3501
and {}
3502
'{\uldb set unitcell}{\v setunitcell}' {}
3503
that display the bounding box and the crystallographic unit cell, {}
3504
respectively. {}
3505
\par\page\par
3506
+{\footnote doc}
3507
#{\footnote setbackfade}
3508
${\footnote Set Backfade}
3509
K{\footnote set backfade}
3510
{\b Set Backfade}\par\par
3511
K{\footnote backfade}
3512
\tx1200
3513
{\f2\b Syntax:\tab
3514
set background <boolean>\par
3515
}\pard\par
3516
The RasMol {}
3517
'{\f2\b backfade}' {}
3518
parameter is used to control backfade to the specified background {}
3519
colour, rather than black. This is controlled by the commands {}
3520
'{\f2\b set backfade on}' {}
3521
and {}
3522
'{\f2\b set backfade off}'. {}
3523
For example, this may be used to generate depth-cued images that {}
3524
fade to white, rather than black. {}
3525
\par\page\par
3526
+{\footnote doc}
3527
#{\footnote setbackground}
3528
${\footnote Set Background}
3529
K{\footnote set background}
3530
{\b Set Background}\par\par
3531
K{\footnote background}
3532
\tx1200
3533
{\f2\b Syntax:\tab
3534
set background <colour>\par
3535
}\pard\par
3536
The RasMol {}
3537
'{\f2\b background}' {}
3538
parameter is used to set the colour of the "canvas" background. The {}
3539
colour may be given as either a colour name or a comma separated {}
3540
triple of Red, Green, Blue (RGB) components enclosed in square {}
3541
brackets. Typing the command {}
3542
'{\uldb help colours}{\v help}' {}
3543
will give a list of the predefined colour names recognised by RasMol. {}
3544
When running under X Windows, RasMol also recognises colours in the {}
3545
X server's colour name database. {}
3546
\par\par
3547
The command {}
3548
'{\f2\b set background}' {}
3549
is synonymous with the RasMol command {}
3550
'{\uldb background}{\v background}'. {}
3551
\par\page\par
3552
+{\footnote doc}
3553
#{\footnote setbondmode}
3554
${\footnote Set BondMode}
3555
K{\footnote set bondmode}
3556
{\b Set BondMode}\par\par
3557
K{\footnote bondmode}
3558
\tx1200
3559
{\f2\b Syntax:\tab
3560
set bondmode and\line\tab
3561
set bondmode or\line\tab
3562
set bondmode all\line\tab
3563
set bondmode none\line\tab
3564
set bondmode not bonded\par
3565
}\pard\par
3566
The RasMol {}
3567
'{\f2\b set bondmode}' {}
3568
command controls the mechanism used to select individual bonds {}
3569
and modifies the display of bonded and non-bonded atoms by subsequent {}
3570
'{\uldb wireframe}{\v wireframe}' {}
3571
commands. {}
3572
\par\par
3573
When using the {}
3574
'{\uldb select}{\v select}' {}
3575
and {}
3576
'{\uldb restrict}{\v restrict}' {}
3577
commands, a given bond will be selected if i) the bondmode is {}
3578
'{\f2\b or}' {}
3579
and either of the connected atoms is selected, or ii) the bondmode is {}
3580
'{\f2\b and}' {}
3581
and both atoms connected by the bond are selected. Hence an individual {}
3582
bond may be uniquely identified by using the command {}
3583
'{\f2\b set bondmode and}' {}
3584
and then uniquely selecting the atoms at both ends. {}
3585
\par\par
3586
The {}
3587
'{\f2\b bondmode [all | none | not bonded]}' {}
3588
commands add {}
3589
'{\uldb star 75}{\v star}' {}
3590
or {}
3591
'{\uldb spacefill 75}{\v spacefill}' {}
3592
markers for the designated atoms to {}
3593
'{\uldb wireframe}{\v wireframe}' {}
3594
displays. Stars are used when the specified wireframe radius is zero. {}
3595
\par\page\par
3596
+{\footnote doc}
3597
#{\footnote setbonds}
3598
${\footnote Set Bonds}
3599
K{\footnote set bonds}
3600
{\b Set Bonds}\par\par
3601
K{\footnote bonds}
3602
\tx1200
3603
{\f2\b Syntax:\tab
3604
set bonds <boolean>\par
3605
}\pard\par
3606
The RasMol {}
3607
'{\f2\b bonds}' {}
3608
parameter is used to control display of double and triple bonds as {}
3609
multiple lines or cylinders. Currently bond orders are only read {}
3610
from MDL Mol files, Sybyl Mol2 format files, Tripos Alchemy format {}
3611
files, CIF and mmCIF, and suitable PDB files. Double (and triple) bonds {}
3612
are specified in some PDB files by specifying a given bond twice (and {}
3613
three times) in CONECT records. The command {}
3614
'{\f2\b set bonds on}' {}
3615
enables the display of bond orders, and the command {}
3616
'{\f2\b set bonds off}' {}
3617
disables them. {}
3618
\par\page\par
3619
+{\footnote doc}
3620
#{\footnote setboundbox}
3621
${\footnote Set BoundBox}
3622
K{\footnote set boundbox}
3623
{\b Set BoundBox}\par\par
3624
K{\footnote boundbox}
3625
\tx1200
3626
{\f2\b Syntax:\tab
3627
set boundbox <boolean>\par
3628
}\pard\par
3629
The RasMol {}
3630
'{\f2\b boundbox}' {}
3631
parameter controls the display of the current molecule's bounding box {}
3632
on the display. The bounding box is orthogonal to the data file's {}
3633
original coordinate axes. The {}
3634
'{\f2\b set boundbox}' {}
3635
command is similar to the commands {}
3636
'{\uldb set axes}{\v setaxes}' {}
3637
and {}
3638
'{\uldb set unitcell}{\v setboundbox}' {}
3639
that display orthogonal coordinate axes and the bounding box, {}
3640
respectively. {}
3641
\par\page\par
3642
+{\footnote doc}
3643
#{\footnote setcartoon}
3644
${\footnote Set Cartoon}
3645
K{\footnote set cartoon}
3646
{\b Set Cartoon}\par\par
3647
K{\footnote bonds}
3648
\tx1200
3649
{\f2\b Syntax:\tab
3650
set cartoon \{<boolean>\}\line\tab
3651
set cartoon \{<number>\}\par
3652
}\pard\par
3653
The RasMol {}
3654
'{\f2\b cartoon}' {}
3655
parameter is used to control display of the cartoon version of the {}
3656
'{\uldb ribbons}{\v ribbons}' {}
3657
display. By default, the C-termini of beta-sheets are displayed as {}
3658
arrow heads. This may be enabled and disabled using the {}
3659
'{\f2\b set cartoons <boolean>}' {}
3660
command. The depth of the cartoon may be adjusted using the {}
3661
'{\f2\b cartoons <number>}' {}
3662
command. The {}
3663
'{\f2\b set cartoons}' {}
3664
command without any parameters returns these two options to {}
3665
their default values. {}
3666
\par\page\par
3667
+{\footnote doc}
3668
#{\footnote setcisangle}
3669
${\footnote Set CisAngle}
3670
K{\footnote set cisangle}
3671
{\b Set CisAngle}\par\par
3672
K{\footnote cisangle}
3673
\tx1200
3674
{\f2\b Syntax:\tab
3675
set cisangle \{<value>\}\par
3676
}\pard\par
3677
The RasMol {}
3678
'{\f2\b cisangle}' {}
3679
parameter controls the cutoff angle for identifying cis peptide {}
3680
bonds. If no value is given, the cutoff is set to 90 degrees. {}
3681
\par\page\par
3682
+{\footnote doc}
3683
#{\footnote setdisplay}
3684
${\footnote Set Display}
3685
K{\footnote set display}
3686
{\b Set Display}\par\par
3687
K{\footnote display}
3688
\tx1200
3689
{\f2\b Syntax:\tab
3690
set display selected\line\tab
3691
set display normal\par
3692
}\pard\par
3693
This command controls the display mode within RasMol. By default, {}
3694
'{\f2\b set display normal}', {}
3695
RasMol displays the molecule in the representation specified by the {}
3696
user. The command {}
3697
'{\f2\b set display selected}' {}
3698
changes the display mode such that the molecule is temporarily drawn {}
3699
so as to indicate currently selected portion of the molecule. The {}
3700
user specified colour scheme and representation remains unchanged. {}
3701
In this representation all selected atoms are shown in yellow and {}
3702
all non selected atoms are shown in blue. The colour of the background {}
3703
is also changed to a dark grey to indicate the change of display mode. {}
3704
This command is typically only used by external Graphical User {}
3705
Interfaces (GUIs). {}
3706
\par\page\par
3707
+{\footnote doc}
3708
#{\footnote setfontsize}
3709
${\footnote Set FontSize}
3710
K{\footnote set fontsize}
3711
{\b Set FontSize}\par\par
3712
K{\footnote fontsize}
3713
\tx1200
3714
{\f2\b Syntax:\tab
3715
set fontsize \{<value>\} \{ FS | PS \}\par
3716
}\pard\par
3717
The RasMol {}
3718
'{\f2\b set fontsize}' {}
3719
command is used to control the size of the characters that {}
3720
form atom labels. This value corresponds to the height of {}
3721
the displayed character in pixels. The maximum value of {}
3722
'{\f2\b fontsize}' {}
3723
is 48 pixels, and the default value is 8 pixels high. {}
3724
Fixed or proportional spacing may be selected by appending the {}
3725
"FS" or "PS" modifiers, respectively. The default is "FS". {}
3726
To display atom labels on the screen use the RasMol {}
3727
'{\uldb label}{\v label}' {}
3728
command and to change the colour of displayed labels, use {}
3729
the {}
3730
'{\uldb colour labels}{\v colour}' {}
3731
command. {}
3732
\par\page\par
3733
+{\footnote doc}
3734
#{\footnote setfontstroke}
3735
${\footnote Set FontStroke}
3736
K{\footnote set fontstroke}
3737
{\b Set FontStroke}\par\par
3738
K{\footnote fontstroke}
3739
\tx1200
3740
{\f2\b Syntax:\tab
3741
set fontstroke \{<value>\}\par
3742
}\pard\par
3743
The RasMol {}
3744
'{\f2\b set fontstroke}' {}
3745
command is used to control the size of the stroke width of the {}
3746
characters that form atom labels. This value is the radius in {}
3747
pixels of cylinders used to form the strokes. The special value {}
3748
of "0" is the default used for the normal single pixel stroke width, {}
3749
which allows for rapid drawing and rotation of the image. {}
3750
Non-zero values are provided to allow for more artistic atom {}
3751
labels for publication at the expense of extra time in rendering {}
3752
the image. {}
3753
\par\par
3754
When wider strokes are used, a larger font size is recommend, e.g. {}
3755
by using the RasMol {}
3756
'{\uldb set fontsize 24 PS}{\v setfontsize}' {}
3757
command, followed by {}
3758
'{\f2\b set fontstroke 2}' {}
3759
\par\par
3760
To display atom labels on the screen use the RasMol {}
3761
'{\uldb label}{\v label}' {}
3762
command, and to change the colour of displayed labels use {}
3763
the {}
3764
'{\uldb colour labels}{\v colour}' {}
3765
command. {}
3766
\par\page\par
3767
+{\footnote doc}
3768
#{\footnote sethbonds}
3769
${\footnote Set HBonds}
3770
K{\footnote set hbonds}
3771
{\b Set HBonds}\par\par
3772
K{\footnote hbonds}
3773
K{\footnote sidechain}
3774
K{\footnote backbone}
3775
\tx1200
3776
{\f2\b Syntax:\tab
3777
set hbonds backbone\line\tab
3778
set hbonds sidechain\par
3779
}\pard\par
3780
The RasMol {}
3781
'{\f2\b hbonds}' {}
3782
parameter determines whether hydrogen bonds are drawn between {}
3783
the donor and acceptor atoms of the hydrogen bond, {}
3784
'{\f2\b set hbonds sidechain}' {}
3785
or between the alpha carbon atoms of the protein backbone and between {}
3786
the phosphorous atoms of the nucleic acid backbone, {}
3787
'{\f2\b set hbonds backbone}'. {}
3788
The actual display of hydrogen bonds is controlled by the {}
3789
'{\uldb hbonds}{\v hbonds}' {}
3790
command. Drawing hydrogen bonds between protein alpha carbons or {}
3791
nucleic acid phosphorous atoms is useful when the rest of the molecule {}
3792
is shown in only a schematic representation such as {}
3793
'{\uldb backbone}{\v backbone}', {}
3794
'{\uldb ribbons}{\v ribbons}' {}
3795
or {}
3796
'{\uldb strands}{\v strands}'. {}
3797
This parameter is similar to the RasMol {}
3798
'{\uldb ssbonds}{\v setssbonds}' {}
3799
parameter. {}
3800
\par\page\par
3801
+{\footnote doc}
3802
#{\footnote sethetero}
3803
${\footnote Set Hetero}
3804
K{\footnote set hetero}
3805
{\b Set Hetero}\par\par
3806
K{\footnote hetero}
3807
\tx1200
3808
{\f2\b Syntax:\tab
3809
set hetero <boolean>\par
3810
}\pard\par
3811
The RasMol {}
3812
'{\f2\b hetero}' {}
3813
parameter is used to modify the 'default' behaviour of the RasMol {}
3814
'{\uldb select}{\v select}' {}
3815
command, i.e. the behaviour of {}
3816
'{\f2\b select}' {}
3817
without any parameters. When this value is {}
3818
'{\f2\b false}', {}
3819
the default {}
3820
'{\uldb select}{\v select}' {}
3821
region does not include any heterogeneous atoms (refer to the {}
3822
predefined set {}
3823
'{\uldb hetero}{\v heteroset}' {}
3824
). When this value is {}
3825
'{\f2\b true}', {}
3826
the default {}
3827
'{\uldb select}{\v select}' {}
3828
region may contain hetero atoms. This parameter is similar to {}
3829
the RasMol {}
3830
'{\uldb hydrogen}{\v sethydrogen}' {}
3831
parameter which determines whether hydrogen atoms should be {}
3832
included in the default set. If both {}
3833
'{\f2\b hetero}' {}
3834
and {}
3835
'{\uldb hydrogen}{\v sethydrogen}' {}
3836
are {}
3837
'{\f2\b true}', {}
3838
'{\uldb select}{\v select}' {}
3839
without any parameters is equivalent to {}
3840
'{\uldb select all}{\v select}'. {}
3841
\par\page\par
3842
+{\footnote doc}
3843
#{\footnote sethourglass}
3844
${\footnote Set HourGlass}
3845
K{\footnote set hourglass}
3846
{\b Set HourGlass}\par\par
3847
K{\footnote hourglass}
3848
\tx1200
3849
{\f2\b Syntax:\tab
3850
set hourglass \{<boolean>\}\par
3851
}\pard\par
3852
The RasMol {}
3853
'{\f2\b hourglass}' {}
3854
parameter allows the user to enable and disable the use of the 'hour {}
3855
glass' cursor used by RasMol to indicate that the program is currently {}
3856
busy drawing the next frame. The command {}
3857
'{\f2\b set hourglass on}' {}
3858
enables the indicator, whilst {}
3859
'{\f2\b set hourglass off}' {}
3860
prevents RasMol from changing the cursor. This is useful when spinning {}
3861
the molecule, running a sequence of commands from a script file or {}
3862
using interprocess communication to execute complex sequences of {}
3863
commands. In these cases a 'flashing' cursor may be distracting. {}
3864
\par\page\par
3865
+{\footnote doc}
3866
#{\footnote sethydrogen}
3867
${\footnote Set Hydrogen}
3868
K{\footnote set hydrogen}
3869
{\b Set Hydrogen}\par\par
3870
K{\footnote hydrogen}
3871
\tx1200
3872
{\f2\b Syntax:\tab
3873
set hydrogen <boolean>\par
3874
}\pard\par
3875
The RasMol {}
3876
'{\f2\b hydrogen}' {}
3877
parameter is used to modify the "default" behaviour of the RasMol {}
3878
'{\uldb select}{\v select}' {}
3879
command, i.e. the behaviour of {}
3880
'{\f2\b select}' {}
3881
without any parameters. When this value is {}
3882
'{\f2\b false}', {}
3883
the default {}
3884
'{\uldb select}{\v select}' {}
3885
region does not include any hydrogen, deuterium or tritium atoms (refer {}
3886
to the predefined set {}
3887
'{\uldb hydrogen}{\v hydrogenset}' {}
3888
). When this value is {}
3889
'{\f2\b true}', {}
3890
the default {}
3891
'{\uldb select}{\v select}' {}
3892
region may contain hydrogen atoms. This parameter is similar to {}
3893
the RasMol {}
3894
'{\uldb hetero}{\v sethetero}' {}
3895
parameter which determines whether heterogeneous atoms should be {}
3896
included in the default set. If both {}
3897
'{\f2\b hydrogen}' {}
3898
and {}
3899
'{\uldb hetero}{\v sethetero}' {}
3900
are {}
3901
'{\f2\b true}', {}
3902
'{\uldb select}{\v select}' {}
3903
without any parameters is equivalent to {}
3904
'{\uldb select all}{\v select}'. {}
3905
\par\page\par
3906
+{\footnote doc}
3907
#{\footnote setkinemage}
3908
${\footnote Set Kinemage}
3909
K{\footnote set kinemage}
3910
{\b Set Kinemage}\par\par
3911
K{\footnote mage}
3912
K{\footnote kinemage}
3913
\tx1200
3914
{\f2\b Syntax:\tab
3915
set kinemage <boolean>\par
3916
}\pard\par
3917
The RasMol {}
3918
'{\f2\b set kinemage}' {}
3919
command controls the amount of detail stored in a Kinemage output {}
3920
file generated by the RasMol {}
3921
'{\uldb write kinemage}{\v write}' {}
3922
command. The output kinemage files are intended to be displayed by {}
3923
David Richardson's Mage program. {}
3924
'{\f2\b set kinemage false}', {}
3925
the default, only stores the currently displayed representation in {}
3926
the generated output file. The command {}
3927
'{\f2\b set kinemage true}', {}
3928
generates a more complex Kinemage that contains both the wireframe {}
3929
and backbone representations as well as the coordinate axes, {}
3930
bounding box and crystal unit cell. {}
3931
\par\page\par
3932
+{\footnote doc}
3933
#{\footnote setmenus}
3934
${\footnote Set Menus}
3935
K{\footnote set menus}
3936
{\b Set Menus}\par\par
3937
K{\footnote menus}
3938
\tx1200
3939
{\f2\b Syntax:\tab
3940
set menus <boolean>\par
3941
}\pard\par
3942
The RasMol {}
3943
'{\f2\b set menus}' {}
3944
command enables the canvas window's menu buttons or menu bar. This {}
3945
command is typically only used by graphical user interfaces or to {}
3946
create as large an image as possible when using Microsoft Windows. {}
3947
\par\page\par
3948
+{\footnote doc}
3949
#{\footnote setmonitor}
3950
${\footnote Set Monitor}
3951
K{\footnote set monitor}
3952
{\b Set Monitor}\par\par
3953
K{\footnote menus}
3954
\tx1200
3955
{\f2\b Syntax:\tab
3956
set monitor <boolean>\par
3957
}\pard\par
3958
The RasMol {}
3959
'{\f2\b set monitor}' {}
3960
command enables {}
3961
'{\uldb monitors}{\v monitor}'. {}
3962
The distance monitor labels may be turned off with the command {}
3963
'{\f2\b set monitor off}', {}
3964
and re-enabled with the command {}
3965
'{\f2\b set monitor on}'. {}
3966
{}
3967
\par\page\par
3968
+{\footnote doc}
3969
#{\footnote setmouse}
3970
${\footnote Set Mouse}
3971
K{\footnote set mouse}
3972
{\b Set Mouse}\par\par
3973
K{\footnote mouse}
3974
K{\footnote rasmol}
3975
K{\footnote insight}
3976
K{\footnote quanta}
3977
\tx1200
3978
{\f2\b Syntax:\tab
3979
set mouse rasmol\line\tab
3980
set mouse insight\line\tab
3981
set mouse quanta\par
3982
}\pard\par
3983
The RasMol {}
3984
'{\f2\b set mouse}' {}
3985
command sets the rotation, translation, scaling and zooming mouse {}
3986
bindings. The default value is {}
3987
'{\f2\b rasmol}' {}
3988
which is suitable for two button mice (for three button mice the {}
3989
second and third buttons are synonymous); X-Y rotation is controlled {}
3990
by the first button, and X-Y translation by the second. Additional {}
3991
functions are controlled by holding a modifier key on the keyboard. {}
3992
[Shift] and the first button performs scaling, [shift] and the second {}
3993
button performs Z-rotation, and [control] and the first mouse button {}
3994
controls the clipping plane. The {}
3995
'{\f2\b insight}' {}
3996
and {}
3997
'{\f2\b quanta}' {}
3998
options provide the same mouse bindings as other packages for experienced {}
3999
users. {}
4000
\par\page\par
4001
+{\footnote doc}
4002
#{\footnote setpicking}
4003
${\footnote Set Picking}
4004
K{\footnote set picking}
4005
{\b Set Picking}\par\par
4006
K{\footnote picking}
4007
\tx1200
4008
{\f2\b Syntax:\tab
4009
set picking <boolean>\line\tab
4010
set picking off\line\tab
4011
set picking none\line\tab
4012
set picking ident\line\tab
4013
set picking distance\line\tab
4014
set picking monitor\line\tab
4015
set picking angle\line\tab
4016
set picking torsion\line\tab
4017
set picking label\line\tab
4018
set picking centre\line\tab
4019
set picking center\line\tab
4020
set picking coord\line\tab
4021
set picking bond\line\tab
4022
set picking atom\line\tab
4023
set picking group\line\tab
4024
set picking chain\par
4025
}\pard\par
4026
The RasMol {}
4027
'{\f2\b set picking}' {}
4028
series of commands affects how a user may interact with a {}
4029
molecule displayed on the screen in RasMol. {}
4030
\par\par
4031
{\f2\b Enabling/Disabling Atom Identification Picking}: {}
4032
Clicking on an atom with the mouse results in identification and {}
4033
the display of its residue name, residue number, atom name, atom serial {}
4034
number and chain in the command window. This behavior may be disabled {}
4035
with the command {}
4036
'{\f2\b set picking none}' {}
4037
and restored with the command {}
4038
'{\f2\b set picking ident}'. {}
4039
The command {}
4040
'{\f2\b set picking coord}' {}
4041
adds the atomic coordinates of the atom to the display. {}
4042
\par\par
4043
Disabling picking, by using {}
4044
'{\f2\b set picking off}' {}
4045
is useful when executing the {}
4046
'{\uldb pause}{\v pause}' {}
4047
command in RasMol scripts as it prevents the display of {}
4048
spurious message on the command line while the script is suspended. {}
4049
\par\par
4050
{\f2\b Measuring Distances, Angles and Torsions}: {}
4051
Interactive measurement of distances, angles and torsions {}
4052
is achieved using the commands: {}
4053
'{\f2\b set picking distance}', {}
4054
'{\f2\b set picking monitor}', {}
4055
'{\f2\b set picking angle}' {}
4056
and {}
4057
'{\f2\b set picking torsion}', {}
4058
respectively. In these modes, clicking on an atom results in it {}
4059
being identified on the rasmol command line. In addition every {}
4060
atom picked increments a modulo counter such that in distance {}
4061
mode, every second atom displays the distance (or distance monitor) {}
4062
between this atom and the previous one. In angle mode, every {}
4063
third atom displays the angle between the previous three atoms {}
4064
and in torsion mode every fourth atom displays the torsion between {}
4065
the last four atoms. By holding down the shift key while picking an {}
4066
atom, this modulo counter is not incremented and allows, for {}
4067
example, the distances of consecutive atoms from a fixed atom to {}
4068
be displayed. See the {}
4069
'{\uldb monitor}{\v monitor}' {}
4070
command for how to control the display of distance monitor lines and labels. {}
4071
\par\par
4072
{\f2\b Labelling Atoms with the Mouse}: {}
4073
The mouse may also be used to toggle the display of an atom label {}
4074
on a given atom. The RasMol command {}
4075
'{\f2\b set picking label}' {}
4076
removes a label from a picked atom if it already has one or {}
4077
displays a concise label at that atom position otherwise. {}
4078
\par\par
4079
{\f2\b Centring Rotation with the Mouse}: {}
4080
A molecule may be centred on a specified atom position using the {}
4081
RasMol commands {}
4082
'{\f2\b set picking centre}' {}
4083
or {}
4084
'{\f2\b set picking center}'. {}
4085
In this mode, picking an atom causes all futher rotations to be {}
4086
about that point. {}
4087
\par\par
4088
{\f2\b Picking a Bond as a Rotation Axis}: {}
4089
Any bond may be picked as an axis of rotation for the portion of {}
4090
the molecule beyond the second atom selected. This feature should {}
4091
be used with caution, since, naturally, it changes the conformation {}
4092
of the molecule. After executing {}
4093
'{\f2\b set picking bond}' {}
4094
or using the equivalent "Pick Bond" in the "Settings" menu, {}
4095
a bond to be rotated is picked with the same sort of mouse clicks {}
4096
as are used for picking atoms for a distance measurement. Normally {}
4097
this should be done where a bond exists, but if no bond exists, it {}
4098
will be added. The bond cannot be used for rotation if it is part {}
4099
of a ring of any size. All bonds selected for rotation are remembered {}
4100
so that they can be properly reported when writing a script, but {}
4101
only the most recently selected bond may be actively rotated. {}
4102
\par\par
4103
{\f2\b Enabling Atom/Group/Chain Selection Picking}: {}
4104
Atoms, groups and chains may be selected (as if with the {}
4105
'{\f2\b select}' {}
4106
command), with the {}
4107
'{\f2\b set picking atom}', {}
4108
'{\f2\b set picking group}', {}
4109
'{\f2\b set picking chain}' {}
4110
commands. For each of these commands, the shift key may be used to {}
4111
have a new selection added to the old, and the control key may be {}
4112
used to have a new selection deleted from the old. When the {}
4113
'{\f2\b set picking atom}' {}
4114
command is given, the mouse can be used to pick or to drag a box around {}
4115
the atoms for which selection is desired. When the {}
4116
'{\f2\b set picking group}' {}
4117
command is given, picking any an atom will cause selection {}
4118
of all atoms which agree in residue number with the picked atom, {}
4119
even if in different chains. {}
4120
When the {}
4121
'{\f2\b set picking chain}' {}
4122
command is given, picking any atom will cause selection {}
4123
of all atoms which agree in chain identifier with the picked atom. {}
4124
\par\page\par
4125
+{\footnote doc}
4126
#{\footnote setplay}
4127
${\footnote Set Play}
4128
K{\footnote set play}
4129
{\b Set Play}\par\par
4130
K{\footnote play}
4131
\tx1200
4132
{\f2\b Syntax:\tab
4133
set play.fps \{<value>\}\par
4134
}\pard\par
4135
The RasMol {}
4136
'{\f2\b set play.fps}' {}
4137
command gives the number of frames per second for playback by the {}
4138
'{\uldb play}{\v play}' {}
4139
command (default 24 frames per second). {}
4140
\par\par
4141
In the current release of RasMol, the play timing is not controlled {}
4142
by this parameter. {}
4143
\par\page\par
4144
+{\footnote doc}
4145
#{\footnote setradius}
4146
${\footnote Set Radius}
4147
K{\footnote set radius}
4148
{\b Set Radius}\par\par
4149
K{\footnote radius}
4150
\tx1200
4151
{\f2\b Syntax:\tab
4152
set radius \{<value>\}\par
4153
}\pard\par
4154
The RasMol {}
4155
'{\f2\b set radius}' {}
4156
command is used to alter the behaviour of the RasMol {}
4157
'{\uldb dots}{\v dots}' {}
4158
command depending upon the value of the {}
4159
'{\uldb solvent}{\v setsolvent}' {}
4160
parameter. {}
4161
When {}
4162
'{\uldb solvent}{\v setsolvent}' {}
4163
is {}
4164
'{\f2\b true}', {}
4165
the {}
4166
'{\f2\b radius}' {}
4167
parameter controls whether a true van der Waals' surface {}
4168
is generated by the {}
4169
'{\uldb dots}{\v dots}' {}
4170
command. If the value of {}
4171
'{\f2\b radius}' {}
4172
is anything other than zero, that value is used as the {}
4173
radius of each atom instead of its true vdW value. When {}
4174
the value of {}
4175
'{\uldb solvent}{\v setsolvent}' {}
4176
is {}
4177
'{\f2\b true}', {}
4178
this parameter determines the 'probe sphere' (solvent) radius. {}
4179
The parameter may be given as an integer in rasmol units or {}
4180
containing a decimal point in Angstroms. The default value of {}
4181
this parameter is determined by the value of {}
4182
'{\uldb solvent}{\v setsolvent}' {}
4183
and changing {}
4184
'{\uldb solvent}{\v setsolvent}' {}
4185
resets {}
4186
'{\f2\b radius}' {}
4187
to its new default value. {}
4188
\par\page\par
4189
+{\footnote doc}
4190
#{\footnote setrecord}
4191
${\footnote Set Record}
4192
K{\footnote set record}
4193
{\b Set Record}\par\par
4194
K{\footnote play}
4195
\tx1200
4196
{\f2\b Syntax:\tab
4197
set record.aps \{<value>\}\par
4198
\tab set record.fps \{<value>\}
4199
\tab set record.dwell \{<value>\}
4200
}\pard\par
4201
The RasMol {}
4202
'{\f2\b set record.aps}' {}
4203
gives the maximum on-screen velocity in Angstroms per second in animating {}
4204
translations, rotations and zooms (default 10 A/second).
4205
\par\par
4206
The RasMol {}
4207
'{\f2\b set record.aps}' {}
4208
command gives number of frames per second for recording by the {}
4209
'{\uldb record}{\v record}' {}
4210
command (default 24 frames per second). {}
4211
\par\par
4212
The RasMol {}
4213
'{\f2\b set record.dwell}' {}
4214
command sets the time in seconds to dwell on a change in appearance {}
4215
(default .5 sec). {}
4216
\par\page\par
4217
+{\footnote doc}
4218
#{\footnote setshadepower}
4219
${\footnote Set ShadePower}
4220
K{\footnote set shadepower}
4221
{\b Set ShadePower}\par\par
4222
K{\footnote shadepower}
4223
\tx1200
4224
{\f2\b Syntax:\tab
4225
set shadepower \{<value>\}\par
4226
}\pard\par
4227
The {}
4228
'{\f2\b shadepower}' {}
4229
parameter (adopted from RasTop) determines the shade repartition (the contrast) {}
4230
used in rendering solid objects. This value between 0 and 100 adjusts {}
4231
shading on an object surface oriented along the direction to the {}
4232
light source. Changing the shadepower parameter does not change the {}
4233
maximum or the minimum values of this shading, as does changing the {}
4234
'{\uldb ambient}{\v setambient}' {}
4235
parameter. A value of 100 concentrates the light on the top of spheres, {}
4236
giving a highly specular, glassy rendering (see the {}
4237
'{\uldb specpower}{\v setspecpower}' {}
4238
parameter). {}
4239
A value of 0 distributes the light on the entire object. {}
4240
\par\par
4241
This implementation of shadepower differs from the one in RasTop {}
4242
only in the choice of range (0 to 100 versus -20 to 20 in RasTop). {}
4243
\par\page\par
4244
+{\footnote doc}
4245
#{\footnote setshadow}
4246
${\footnote Set Shadow}
4247
K{\footnote set shadow}
4248
{\b Set Shadow}\par\par
4249
K{\footnote shadow}
4250
\tx1200
4251
{\f2\b Syntax:\tab
4252
set shadow <boolean>\par
4253
}\pard\par
4254
The RasMol {}
4255
'{\f2\b set shadow}' {}
4256
command enables and disables ray-tracing of the currently rendered image. {}
4257
Currently only the spacefilling representation is shadowed or can cast {}
4258
shadows. Enabling shadowing will automatically disable the Z-clipping {}
4259
(slabbing) plane using the command {}
4260
'{\uldb slab off}{\v slab}'. {}
4261
Ray-tracing typically takes about several seconds for a moderately sized protein. {}
4262
It is recommended that shadowing be normally disabled whilst the {}
4263
molecule is being transformed or manipulated, and only enabled once {}
4264
an appropiate viewpoint is selected, to provide a greater impression {}
4265
of depth. {}
4266
\par\page\par
4267
+{\footnote doc}
4268
#{\footnote setslabmode}
4269
${\footnote Set SlabMode}
4270
K{\footnote set slabmode}
4271
{\b Set SlabMode}\par\par
4272
K{\footnote slabmode}
4273
K{\footnote reject}
4274
K{\footnote half}
4275
K{\footnote hollow}
4276
K{\footnote solid}
4277
K{\footnote section}
4278
\tx1200
4279
{\f2\b Syntax:\tab
4280
set slabmode <slabmode>\par
4281
}\pard\par
4282
The RasMol {}
4283
'{\f2\b slabmode}' {}
4284
parameter controls the rendering method of objects cut by the {}
4285
slabbing (z-clipping) plane. Valid slabmode parameters are {}
4286
{\f2\b "reject"}, {\f2\b "half"}, {\f2\b "hollow"}, {}
4287
{\f2\b "solid"} and {\f2\b "section"}. {}
4288
\par\page\par
4289
+{\footnote doc}
4290
#{\footnote setsolvent}
4291
${\footnote Set Solvent}
4292
K{\footnote set solvent}
4293
{\b Set Solvent}\par\par
4294
K{\footnote solvent}
4295
\tx1200
4296
{\f2\b Syntax:\tab
4297
set solvent <boolean>\par
4298
}\pard\par
4299
The RasMol {}
4300
'{\f2\b set solvent}' {}
4301
command is used to control the behaviour of the RasMol {}
4302
'{\uldb dots}{\v dots}' {}
4303
command. Depending upon the value of the {}
4304
'{\f2\b solvent}' {}
4305
parameter, the {}
4306
'{\uldb dots}{\v dots}' {}
4307
command either generates a van der Waals' or a solvent {}
4308
accessible surface around the currently selected set of {}
4309
atoms. Changing this parameter automatically resets the {}
4310
value of the RasMol {}
4311
'{\uldb radius}{\v setradius}' {}
4312
parameter. {}
4313
The command {}
4314
'{\f2\b set solvent false}', {}
4315
the default value, indicates that a van der Waals' surface {}
4316
should be generated and resets the value of {}
4317
'{\uldb radius}{\v setradius}' {}
4318
to zero. The command {}
4319
'{\f2\b set solvent true}' {}
4320
indicates that a 'Connolly' or 'Richards' solvent {}
4321
accessible surface should be drawn and sets the {}
4322
'{\uldb radius}{\v setradius}' {}
4323
parameter, the solvent radius, to 1.2 Angstroms (or 300 {}
4324
RasMol units). {}
4325
\par\page\par
4326
+{\footnote doc}
4327
#{\footnote setspecular}
4328
${\footnote Set Specular}
4329
K{\footnote set specular}
4330
{\b Set Specular}\par\par
4331
K{\footnote specular}
4332
\tx1200
4333
{\f2\b Syntax:\tab
4334
set specular <boolean>\par
4335
}\pard\par
4336
The RasMol {}
4337
'{\f2\b set specular}' {}
4338
command enables and disables the display of specular highlights on {}
4339
solid objects drawn by RasMol. Specular highlights appear as white {}
4340
reflections of the light source on the surface of the object. The {}
4341
current RasMol implementation uses an approximation function to {}
4342
generate this highlight. {}
4343
\par\par
4344
The specular highlights on the surfaces of solid objects may be {}
4345
altered by using the specular reflection coefficient, which is {}
4346
altered using the RasMol {}
4347
'{\uldb set specpower}{\v setspecpower}' {}
4348
command. {}
4349
\par\page\par
4350
+{\footnote doc}
4351
#{\footnote setspecpower}
4352
${\footnote Set SpecPower}
4353
K{\footnote set specpower}
4354
{\b Set SpecPower}\par\par
4355
K{\footnote specpower}
4356
\tx1200
4357
{\f2\b Syntax:\tab
4358
set specpower \{<value>\}\par
4359
}\pard\par
4360
The {}
4361
'{\f2\b specpower}' {}
4362
parameter determines the shininess of solid objects rendered by {}
4363
RasMol. This value between 0 and 100 adjusts the reflection {}
4364
coefficient used in specular highlight calculations. The specular {}
4365
highlights are enabled and disabled by the RasMol {}
4366
'{\uldb set specular}{\v setspecular}' {}
4367
command. Values around 20 or 30 produce plastic looking surfaces. {}
4368
High values represent more shiny surfaces such as metals, while {}
4369
lower values produce more diffuse/dull surfaces. {}
4370
\par\page\par
4371
+{\footnote doc}
4372
#{\footnote setssbonds}
4373
${\footnote Set SSBonds}
4374
K{\footnote set ssbonds}
4375
{\b Set SSBonds}\par\par
4376
K{\footnote ssbonds}
4377
K{\footnote backbone}
4378
K{\footnote sidechain}
4379
\tx1200
4380
{\f2\b Syntax:\tab
4381
set ssbonds backbone\line\tab
4382
set ssbonds sidechain\par
4383
}\pard\par
4384
The RasMol {}
4385
'{\f2\b ssbonds}' {}
4386
parameter determines whether disulphide bridges are drawn between {}
4387
the sulphur atoms in the sidechain (the default) or between the alpha {}
4388
carbon atoms in the backbone of the cysteines residues. The actual {}
4389
display of disulphide bridges is controlled by the {}
4390
'{\uldb ssbonds}{\v ssbonds}' {}
4391
command. Drawing disulphide bridges between alpha carbons is useful {}
4392
when the rest of the protein is shown in only a schematic {}
4393
representation such as {}
4394
'{\uldb backbone}{\v backbone}', {}
4395
'{\uldb ribbons}{\v ribbons}' {}
4396
or {}
4397
'{\uldb strands}{\v strands}'. {}
4398
This parameter is similar to the RasMol {}
4399
'{\uldb hbonds}{\v sethbonds}' {}
4400
parameter. {}
4401
\par\page\par
4402
+{\footnote doc}
4403
#{\footnote setstereo}
4404
${\footnote Set Stereo}
4405
K{\footnote set stereo}
4406
{\b Set Stereo}\par\par
4407
K{\footnote stereo}
4408
\tx1200
4409
{\f2\b Syntax:\tab
4410
set stereo <boolean>\line\tab
4411
set stereo [-] <number>\par
4412
}\pard\par
4413
The RasMol {}
4414
'{\f2\b set stereo}' {}
4415
parameter controls the separation between the left and {}
4416
right images. Turning stereo on and off doesn't reposition {}
4417
the centre of the molecule. {}
4418
\par\par
4419
Stereo viewing of a molecule may be turned on (and off) either {}
4420
by selecting {}
4421
'{\f2\b Stereo}' {}
4422
from the {}
4423
'{\f2\b Options}' {}
4424
menu, or by typing the commands {}
4425
'{\f2\b stereo on}' {}
4426
or {}
4427
'{\f2\b stereo off}'. {}
4428
\par\par
4429
The separation angle between the two views may be adjusted with the {}
4430
'{\f2\b set stereo [-] <number>}' {}
4431
command, where positive values result in crossed eye viewing and {}
4432
negative values in relaxed (wall-eyed) viewing. Currently, stereo viewing {}
4433
is not supported in {}
4434
'{\uldb vector PostScript}{\v setvectps}' {}
4435
output files. {}
4436
\par\page\par
4437
+{\footnote doc}
4438
#{\footnote setstrands}
4439
${\footnote Set Strands}
4440
K{\footnote set strands}
4441
{\b Set Strands}\par\par
4442
K{\footnote strands}
4443
\tx1200
4444
{\f2\b Syntax:\tab
4445
set strands \{<value>\}\par
4446
}\pard\par
4447
The RasMol {}
4448
'{\f2\b strands}' {}
4449
parameter controls the number of parallel strands that are displayed {}
4450
in the ribbon representations of proteins. The permissible values for {}
4451
this parameter are 1, 2, 3, 4, 5 and 9. The default value is 5. The {}
4452
number of strands is constant for all ribbons being displayed. {}
4453
However, the ribbon width (the separation between strands) may be {}
4454
controlled on a residue by residue basis using the RasMol {}
4455
'{\uldb ribbons}{\v ribbons}' {}
4456
command. {}
4457
\par\page\par
4458
+{\footnote doc}
4459
#{\footnote settransparent}
4460
${\footnote Set Transparent}
4461
K{\footnote set transparent}
4462
{\b Set Transparent}\par\par
4463
K{\footnote transparent}
4464
\tx1200
4465
{\f2\b Syntax:\tab
4466
set transparent <boolean>\par
4467
}\pard\par
4468
The RasMol {}
4469
'{\f2\b transparent}' {}
4470
parameter controls the writing of transparent GIFs by the {}
4471
'{\uldb write gif <filename>}{\v write}' {}
4472
command. This may be controlled by the {}
4473
'{\f2\b set transparent on}' {}
4474
and {}
4475
'{\f2\b set transparent off}' {}
4476
commands. {}
4477
\par\page\par
4478
+{\footnote doc}
4479
#{\footnote setunitcell}
4480
${\footnote Set UnitCell}
4481
K{\footnote set unitcell}
4482
{\b Set UnitCell}\par\par
4483
K{\footnote unitcell}
4484
\tx1200
4485
{\f2\b Syntax:\tab
4486
set unitcell <boolean>\par
4487
}\pard\par
4488
The RasMol {}
4489
'{\f2\b unitcell}' {}
4490
parameter controls the display of the crystallographic unit cell on {}
4491
the current display. The crystal cell is only enabled if the appropriate {}
4492
crystal symmetry information is contained in the PDB, CIF or mmCIF data {}
4493
file. The {}
4494
RasMol command {}
4495
'{\uldb show symmetry}{\v show}' {}
4496
display details of the crystal's space group and unit cell axes. The {}
4497
'{\f2\b set unitcell}' {}
4498
command is similar to the commands {}
4499
'{\uldb set axes}{\v setaxes}' {}
4500
and {}
4501
'{\uldb set boundbox}{\v setboundbox}' {}
4502
that display orthogonal coordinate axes and the bounding box, {}
4503
respectively. {}
4504
\par\page\par
4505
+{\footnote doc}
4506
#{\footnote setvectps}
4507
${\footnote Set VectPS}
4508
K{\footnote set vectps}
4509
{\b Set VectPS}\par\par
4510
K{\footnote vectps}
4511
\tx1200
4512
{\f2\b Syntax:\tab
4513
set vectps <boolean>\par
4514
}\pard\par
4515
The RasMol {}
4516
'{\f2\b vectps}' {}
4517
parameter is use to control the way in which the RasMol {}
4518
'{\uldb write}{\v write}' {}
4519
command generates vector PostScript output files. The command {}
4520
'{\f2\b set vectps on}' {}
4521
enables the use of black outlines around spheres and cylinder bonds {}
4522
producing "cartoon-like" high resolution output. However, the current {}
4523
implementation of RasMol incorrectly cartoons spheres that are intersected {}
4524
by more than one other sphere. Hence "ball and stick" models are rendered {}
4525
correctly but not large spacefilling spheres models. Cartoon outlines {}
4526
can be disabled, the default, by the command {}
4527
'{\f2\b set vectps off}'. {}
4528
\par\page\par
4529
+{\footnote doc}
4530
#{\footnote setwrite}
4531
${\footnote Set Write}
4532
K{\footnote set write}
4533
{\b Set Write}\par\par
4534
K{\footnote write}
4535
\tx1200
4536
{\f2\b Syntax:\tab
4537
set write <boolean>\par
4538
}\pard\par
4539
The RasMol {}
4540
'{\f2\b write}' {}
4541
parameter controls the use of the {}
4542
'{\uldb save}{\v save}' {}
4543
and {}
4544
'{\uldb write}{\v write}' {}
4545
commands within scripts, but it may only be executed from the {}
4546
command line. By default, this value is {}
4547
'{\f2\b false}', {}
4548
prohibiting the generation of files in any scripts executed at {}
4549
start-up (such as those launched from a WWW browser). However, {}
4550
animators may start up RasMol interactively: type {}
4551
'{\f2\b set write on}' {}
4552
and then execute a script to generate each frame using the {}
4553
source command. {}
4554
\par\page\par
4555
+{\footnote doc}
4556
#{\footnote chexprs}
4557
${\footnote Atom Expressions}
4558
{\fs24\b Atom Expressions}\par\par
4559
RasMol atom expressions uniquely identify an arbitrary group of atoms {}
4560
within a molecule. Atom expressions are composed of either primitive {}
4561
expressions, {}
4562
predefined sets, {}
4563
comparison operators, {}
4564
'{\f2\b within}' {}
4565
expressions, {}
4566
or logical (boolean) combinations of the above expression types. {}
4567
\par\par
4568
The logical operators allow complex queries to be constructed out of {}
4569
simpler ones using the standard boolean connectives {}
4570
'{\f2\b and}', {}
4571
'{\f2\b or}' {}
4572
and {}
4573
'{\f2\b not}'. {}
4574
These may be abbreviated by the symbols {}
4575
"{\f2\b &}", "{\f2\b |}" and "{\f2\b !}", {}
4576
respectively. Parentheses (brackets) may be used to alter the {}
4577
precedence of the operators. For convenience, a comma may also {}
4578
be used for boolean disjunction. {}
4579
\par\par
4580
The atom expression is evaluated for each atom, hence {}
4581
'{\f2\b protein and backbone}' {}
4582
selects protein backbone atoms, not the protein and [nucleic] acid {}
4583
backbone atoms! {}
4584
\par\par
4585
\cellx1200\cellx4500
4586
\intbl
4587
Examples:\cell {\f2\b backbone and not helix}\cell\row\intbl
4588
\cell {\f2\b within( 8.0, ser70 )}\cell\row\intbl
4589
\cell {\f2\b not (hydrogen or hetero)}\cell\row\intbl
4590
\cell {\f2\b not *.FE and hetero}\cell\row\intbl
4591
\cell {\f2\b 8, 12, 16, 20-28}\cell\row\intbl
4592
\cell {\f2\b arg, his, lys}\cell\row
4593
\pard\par\trowd
4594
\par\par
4595
\tx250\li250\fi-250
4596
{\f1\'b7}\tab
4597
{\uldb Primitive Expressions}{\v primitiveexpressions}\par
4598
{\f1\'b7}\tab
4599
{\uldb Predefined Sets}{\v predefinedsets}\par
4600
{\f1\'b7}\tab
4601
{\uldb Comparison Operators}{\v comparisonoperators}\par
4602
{\f1\'b7}\tab
4603
{\uldb Within Expressions}{\v withinexpressions}\par
4604
{\f1\'b7}\tab
4605
{\uldb Example Expressions}{\v exampleexpressions}\par
4606
\pard
4607
\par\page\par
4608
+{\footnote doc}
4609
#{\footnote exampleexpressions}
4610
${\footnote Example Expressions}
4611
K{\footnote example expressions}
4612
{\b Example Expressions}\par\par
4613
The following table gives some useful examples of RasMol {}
4614
atom expressions. {}
4615
\par\par
4616
\tx1500\li1500\fi-1250
4617
{\b Expression}
4618
\tab{\b Interpretation}\line\par
4619
{\f2\b *}
4620
\tab All atoms\par
4621
{\f2\b cys}
4622
\tab Atoms in cysteines\par
4623
{\f2\b hoh}
4624
\tab Atoms in heterogeneous water molecules\par
4625
{\f2\b as?}
4626
\tab Atoms in either asparagine or aspartic acid\par
4627
{\f2\b *120}
4628
\tab Atoms at residue 120 of all chains\par
4629
{\f2\b *p}
4630
\tab Atoms in chain P\par
4631
{\f2\b *.n?}
4632
\tab Nitrogen atoms\par
4633
{\f2\b cys.sg}
4634
\tab Sulphur atoms in cysteine residues\par
4635
{\f2\b ser70.c?}
4636
\tab Carbon atoms in serine-70\par
4637
{\f2\b hem*p.fe}
4638
\tab Iron atoms in the Heme groups of chain P\par
4639
{\f2\b *.*;A}
4640
\tab All atoms in alternate conformation A\par
4641
{\f2\b */4}
4642
\tab All atoms in model 4\par
4643
\par\pard
4644
\par\page\par
4645
+{\footnote doc}
4646
#{\footnote primitiveexpressions}
4647
${\footnote Primitive Expressions}
4648
K{\footnote primitive expressions}
4649
{\b Primitive Expressions}\par\par
4650
RasMol primitive expressions are the fundamental building blocks {}
4651
of atom expressions. There are two types of primitive expression. {}
4652
The first type is used to identify a given residue number or range {}
4653
of residue numbers. A single residue is identified by its number {}
4654
(position in the sequence), and a range is specified by lower and {}
4655
upper bounds separated by a hyphen character. For example {}
4656
'{\f2\b select 5,6,7,8}' {}
4657
is also {}
4658
'{\f2\b select 5-8}'. {}
4659
Note that this selects the given residue numbers in all macromolecule {}
4660
chains. {}
4661
\par\par
4662
The second type of primitive expression specifies a sequence of fields {}
4663
that must match for a given atom. The first part specifies a residue {}
4664
(or group of residues) and an optional second part specifies the atoms {}
4665
within those residues. The first part consists of a residue name, {}
4666
optionally followed by a residue number and/or chain identifier. {}
4667
\par\par
4668
A residue name typically consists of up to three alphabetic characters, {}
4669
which are case insensitive. Hence the primitive expressions {}
4670
'{\f2\b SER}' {}
4671
and {}
4672
'{\f2\b ser}' {}
4673
are equivalent, identifying all serine residues. {}
4674
Residue names that contain non-alphabetic characters, such as {}
4675
sulphate groups, may be delimited using square brackets, i.e. {}
4676
'{\f2\b [SO4]}'. {}
4677
\par\par
4678
The residue number is intended to be the residue's position in {}
4679
the macromolecule sequence, but negative sequence numbers, gaps {}
4680
in numbering, or even reverse numbering are permitted in the PDB format. {}
4681
Care must be taken when specifying both residue name and number. {}
4682
If the group at the specified position isn't the specified residue {}
4683
then no atoms are selected. {}
4684
\par\par
4685
The chain identifier is typically a single case-insensitive {}
4686
alphabetic or numeric character. Numeric chain identifiers must {}
4687
be distinguished or separated from residue numbers by a colon {}
4688
character. For example, {}
4689
'{\f2\b SER70A}' {}
4690
for the alphabetic chain identifier, "A", or {}
4691
'{\f2\b SER70:1}' {}
4692
for the numeric chain identifier, "1". {}
4693
\par\par
4694
The second part consists of a period character followed by an atom {}
4695
name. An atom name may be up to four alphabetic or numeric characters. {}
4696
An optional semicolon followed by an alternate conformation {}
4697
identifier may be appended. An optional slash followed by a {}
4698
model number may also be appended. {}
4699
\par\par
4700
An atom name may be up to four alphabetic or numeric characters. {}
4701
\par\par
4702
An asterisk may be used as a wild card for a whole field and a {}
4703
question mark as a single character wildcard. {}
4704
\par\page\par
4705
+{\footnote doc}
4706
#{\footnote comparisonoperators}
4707
${\footnote Comparison Operators}
4708
K{\footnote comparison operators}
4709
{\b Comparison Operators}\par\par
4710
Parts of a molecule may also be distinguished using equality, {}
4711
inequality and ordering operators on their properties. The format {}
4712
of such comparison expression is a property name, followed by a {}
4713
comparison operator and then an integer value. {}
4714
\par\par
4715
The atom properties that may be used in RasMol are {}
4716
'{\f2\b atomno}' {}
4717
for the atom serial number, {}
4718
'{\f2\b elemno}' {}
4719
for the atom's atomic number (element), {}
4720
'{\f2\b resno}' {}
4721
for the residue number, {}
4722
'{\f2\b radius}' {}
4723
for the spacefill radius in RasMol units (or zero if not represented {}
4724
as a sphere) and {}
4725
'{\f2\b temperature}' {}
4726
for the PDB isotropic temperature value. {}
4727
\par\par
4728
The equality operator is denoted either {}
4729
"{\f2\b =}" or "{\f2\b ==}". {}
4730
The inequality operator as either {}
4731
"{\f2\b <>}", "{\f2\b !=}" or "{\f2\b /=}". {}
4732
The ordering operators are {}
4733
"{\f2\b <}" {}
4734
for less than, {}
4735
"{\f2\b <=}" {}
4736
for less than or equal to, {}
4737
"{\f2\b >}" {}
4738
for greater than, and {}
4739
"{\f2\b >=}" {}
4740
for greater than or equal to. {}
4741
\par\par
4742
\tx1500
4743
{\f2\b Examples:
4744
\tab resno < 23\par
4745
\tab temperature >= 900\par
4746
\tab atomno == 487\par
4747
}\pard\par
4748
\par\page\par
4749
+{\footnote doc}
4750
#{\footnote withinexpressions}
4751
${\footnote Within Expressions}
4752
K{\footnote within expressions}
4753
{\b Within Expressions}\par\par
4754
K{\footnote within}
4755
A RasMol {}
4756
'{\f2\b within}' {}
4757
expression allows atoms to be selected on their proximity to {}
4758
another set of atoms. A {}
4759
'{\f2\b within}' {}
4760
expression takes two parameters separated by a comma and surrounded {}
4761
by parentheses. The first argument is an integer value called the {}
4762
"cut-off" distance of the within expression and the second argument {}
4763
is any valid atom expression. The cut-off distance is expressed in {}
4764
either integer RasMol units or Angstroms containing a decimal point. {}
4765
An atom is selected if it is within the cut-off distance of any of {}
4766
the atoms defined by the second argument. This allows complex {}
4767
expressions to be constructed containing nested {}
4768
'{\f2\b within}' {}
4769
expressions. {}
4770
\par\par
4771
For example, the command {}
4772
'{\f2\b select within(3.2,backbone)}' {}
4773
selects any atom within a 3.2 Angstrom radius of any atom in a {}
4774
protein or nucleic acid backbone. {}
4775
'{\f2\b Within}' {}
4776
expressions are particularly useful for selecting the atoms {}
4777
around an active site. {}
4778
\par\page\par
4779
+{\footnote doc}
4780
#{\footnote predefinedsets}
4781
${\footnote Predefined Sets}
4782
K{\footnote predefined sets}
4783
{\b Predefined Sets}\par\par
4784
K{\footnote sets}
4785
RasMol atom expressions may contain predefined sets. These sets {}
4786
are single keywords that represent portions of a molecule of interest. {}
4787
Predefined sets are often abbreviations of primitive atom expressions. {}
4788
In some cases the use of predefined sets allows selection of areas of {}
4789
a molecule that could not otherwise be distinguished. {}
4790
A list of the currently predefined sets {}
4791
is given below. {}
4792
In addition to the sets listed here, RasMol also treats element names {}
4793
(and their plurals) as predefined sets containing all atoms of that {}
4794
element type, i.e. the command {}
4795
'{\uldb select oxygen}{\v select}' {}
4796
is equivalent to the command {}
4797
'{\uldb select elemno=8}{\v select}'. {}
4798
\par\par
4799
\cellx1200\cellx2400\cellx3600\cellx4800
4800
\intbl
4801
{\uldb at}{\v atset}\cell
4802
{\uldb acidic}{\v acidicset}\cell
4803
{\uldb acyclic}{\v acyclicset}\cell
4804
{\uldb aliphatic}{\v aliphaticset}\cell
4805
\row\intbl
4806
{\uldb alpha}{\v alphaset}\cell
4807
{\uldb amino}{\v aminoset}\cell
4808
{\uldb aromatic}{\v aromaticset}\cell
4809
{\uldb backbone}{\v backboneset}\cell
4810
\row\intbl
4811
{\uldb basic}{\v basicset}\cell
4812
{\uldb bonded}{\v bondedset}\cell
4813
{\uldb buried}{\v buriedset}\cell
4814
{\uldb cg}{\v cgset}\cell
4815
\row\intbl
4816
{\uldb charged}{\v chargedset}\cell
4817
{\uldb cyclic}{\v cyclicset}\cell
4818
{\uldb cystine}{\v cystineset}\cell
4819
{\uldb helix}{\v helixset}\cell
4820
\row\intbl
4821
{\uldb hetero}{\v heteroset}\cell
4822
{\uldb hydrogen}{\v hydrogenset}\cell
4823
{\uldb hydrophobic}{\v hydrophobicset}\cell
4824
{\uldb ions}{\v ionsset}\cell
4825
\row\intbl
4826
{\uldb large}{\v largeset}\cell
4827
{\uldb ligand}{\v ligandset}\cell
4828
{\uldb medium}{\v mediumset}\cell
4829
{\uldb neutral}{\v neutralset}\cell
4830
\row\intbl
4831
{\uldb nucleic}{\v nucleicset}\cell
4832
{\uldb polar}{\v polarset}\cell
4833
{\uldb protein}{\v proteinset}\cell
4834
{\uldb purine}{\v purineset}\cell
4835
\row\intbl
4836
{\uldb pyrimidine}{\v pyrimidineset}\cell
4837
{\uldb selected}{\v selectedset}\cell
4838
{\uldb sheet}{\v sheetset}\cell
4839
{\uldb sidechain}{\v sidechainset}\cell
4840
\row\intbl
4841
{\uldb small}{\v smallset}\cell
4842
{\uldb solvent}{\v solventset}\cell
4843
{\uldb surface}{\v surfaceset}\cell
4844
{\uldb turn}{\v turnset}\cell
4845
\row\intbl
4846
{\uldb water}{\v waterset}\cell \cell \cell \cell
4847
\row\pard\par\trowd
4848
\par\page\par
4849
+{\footnote doc}
4850
#{\footnote atset}
4851
${\footnote AT Set}
4852
K{\footnote at set}
4853
{\b AT Set}\par\par
4854
K{\footnote at}
4855
This set contains the atoms in the complementary nucleotides {}
4856
adenosine and thymidine (A and T, respectively). All nucleotides {}
4857
are classified as either the set {}
4858
'{\f2\b at}' {}
4859
or the set {}
4860
'{\uldb cg}{\v cgset}' {}
4861
This set is equivalent to the RasMol atom expressions {}
4862
"{\f2\b a,t}", {}
4863
and {}
4864
"{\f2\b nucleic and not cg}". {}
4865
\par\page\par
4866
+{\footnote doc}
4867
#{\footnote acidicset}
4868
${\footnote Acidic Set}
4869
K{\footnote acidic set}
4870
{\b Acidic Set}\par\par
4871
K{\footnote acidic}
4872
The set of acidic amino acids. {}
4873
These are the residue types Asp and Glu. {}
4874
All amino acids are classified as either {}
4875
'{\f2\b acidic}', {}
4876
'{\uldb basic}{\v basicset}' {}
4877
'{\f2\b or}' {}
4878
'{\uldb neutral}{\v neutralset}'. {}
4879
This set is equivalent to the RasMol atom expressions {}
4880
"{\f2\b asp, glu}" {}
4881
and {}
4882
"{\f2\b amino and not (basic or neutral)}". {}
4883
\par\page\par
4884
+{\footnote doc}
4885
#{\footnote acyclicset}
4886
${\footnote Acyclic Set}
4887
K{\footnote acyclic set}
4888
{\b Acyclic Set}\par\par
4889
K{\footnote acyclic}
4890
The set of atoms in amino acids not containing a cycle or {}
4891
ring. All amino acids are classified as either {}
4892
'{\uldb cyclic}{\v cyclicset}' {}
4893
or {}
4894
'{\f2\b acyclic}'. {}
4895
This set is equivalent to the RasMol atom expression {}
4896
"{\f2\b amino and not cyclic}". {}
4897
\par\page\par
4898
+{\footnote doc}
4899
#{\footnote aliphaticset}
4900
${\footnote Aliphatic Set}
4901
K{\footnote aliphatic set}
4902
{\b Aliphatic Set}\par\par
4903
K{\footnote aliphatic}
4904
This set contains the aliphatic amino acids. {}
4905
These are the amino acids Ala, Gly, Ile, Leu and Val. {}
4906
This set is equivalent to the RasMol atom expression {}
4907
"{\f2\b ala, gly, ile, leu, val}". {}
4908
\par\page\par
4909
+{\footnote doc}
4910
#{\footnote alphaset}
4911
${\footnote Alpha Set}
4912
K{\footnote alpha set}
4913
{\b Alpha Set}\par\par
4914
K{\footnote alpha}
4915
The set of alpha carbons in the protein molecule. This set is {}
4916
approximately equivalent to the RasMol atom expression {}
4917
"{\f2\b *.CA}". {}
4918
This command should not be confused with the predefined set {}
4919
'{\uldb helix}{\v helixset}' {}
4920
which contains the atoms in the amino acids of the protein's {}
4921
alpha helices. {}
4922
\par\page\par
4923
+{\footnote doc}
4924
#{\footnote aminoset}
4925
${\footnote Amino Set}
4926
K{\footnote amino set}
4927
{\b Amino Set}\par\par
4928
K{\footnote amino}
4929
This set contains all the atoms contained in amino acid residues. {}
4930
This is useful for distinguishing the protein from the nucleic {}
4931
acid and heterogeneous atoms in the current molecule database. {}
4932
\par\page\par
4933
+{\footnote doc}
4934
#{\footnote aromaticset}
4935
${\footnote Aromatic Set}
4936
K{\footnote aromatic set}
4937
{\b Aromatic Set}\par\par
4938
K{\footnote aromatic}
4939
The set of atoms in amino acids containing aromatic rings. {}
4940
These are the amino acids His, Phe, Trp and Tyr. {}
4941
Because they contain aromatic rings all members of this {}
4942
set are member of the predefined set {}
4943
'{\uldb cyclic}{\v cyclicset}'. {}
4944
This set is equivalent to the RasMol atom expressions {}
4945
"{\f2\b his, phe, trp, tyr}" {}
4946
and {}
4947
"{\f2\b cyclic and not pro}". {}
4948
\par\page\par
4949
+{\footnote doc}
4950
#{\footnote backboneset}
4951
${\footnote Backbone Set}
4952
K{\footnote backbone set}
4953
{\b Backbone Set}\par\par
4954
K{\footnote backbone}
4955
K{\footnote mainchain}
4956
This set contains the four atoms of each amino acid that form the {}
4957
polypeptide N-C-C-O backbone of proteins, and the atoms of the sugar {}
4958
phosphate backbone of nucleic acids. {}
4959
Use the RasMol predefined sets {}
4960
'{\f2\b protein}' {}
4961
and {}
4962
'{\f2\b nucleic}' {}
4963
to distinguish between the two forms of backbone. {}
4964
Atoms in nucleic acids and proteins are either {}
4965
'{\f2\b backbone}' {}
4966
or {}
4967
'{\uldb sidechain}{\v sidechainset}'. {}
4968
This set is equivalent to the RasMol expression {}
4969
"{\f2\b (protein or nucleic) and not sidechain}". {}
4970
\par\par
4971
The predefined set {}
4972
'{\f2\b mainchain}' {}
4973
is synonymous with the set {}
4974
'{\f2\b backbone}'. {}
4975
\par\page\par
4976
+{\footnote doc}
4977
#{\footnote basicset}
4978
${\footnote Basic Set}
4979
K{\footnote basic set}
4980
{\b Basic Set}\par\par
4981
K{\footnote basic}
4982
The set of basic amino acids. {}
4983
These are the residue types Arg, His and Lys. {}
4984
All amino acids are classified as either {}
4985
'{\uldb acidic}{\v acidicset}', {}
4986
'{\f2\b basic}' {}
4987
or {}
4988
'{\uldb neutral}{\v neutralset}'. {}
4989
This set is equivalent to the RasMol atom expressions {}
4990
"{\f2\b arg, his, lys}" {}
4991
and {}
4992
"{\f2\b amino and not (acidic or neutral)}". {}
4993
\par\page\par
4994
+{\footnote doc}
4995
#{\footnote bondedset}
4996
${\footnote Bonded Set}
4997
K{\footnote bonded set}
4998
{\b Bonded Set}\par\par
4999
K{\footnote bonded}
5000
This set contain all the atoms in the current molecule database that {}
5001
are bonded to at least one other atom. {}
5002
\par\page\par
5003
+{\footnote doc}
5004
#{\footnote buriedset}
5005
${\footnote Buried Set}
5006
K{\footnote buried set}
5007
{\b Buried Set}\par\par
5008
K{\footnote buried}
5009
This set contains the atoms in those amino acids that tend {}
5010
(prefer) to be buried inside protein, away from contact with {}
5011
solvent molecules. This set refers to the amino acids {}
5012
preference and not the actual solvent accessibility for {}
5013
the current protein. {}
5014
All amino acids are classified as either {}
5015
'{\uldb surface}{\v surfaceset}' {}
5016
or {}
5017
'{\f2\b buried}'. {}
5018
This set is equivalent to the RasMol atom expression {}
5019
"{\f2\b amino and not surface}". {}
5020
\par\page\par
5021
+{\footnote doc}
5022
#{\footnote cgset}
5023
${\footnote CG Set}
5024
K{\footnote cg set}
5025
{\b CG Set}\par\par
5026
K{\footnote cg}
5027
This set contains the atoms in the complementary nucleotides {}
5028
cytidine and guanosine (C and G, respectively). All nucleotides {}
5029
are classified as either the set {}
5030
'{\uldb at}{\v atset}' {}
5031
or the set {}
5032
'{\f2\b cg}' {}
5033
This set is equivalent to the RasMol atom expressions {}
5034
"{\f2\b c,g}" {}
5035
and {}
5036
"{\f2\b nucleic and not at}". {}
5037
\par\page\par
5038
+{\footnote doc}
5039
#{\footnote chargedset}
5040
${\footnote Charged Set}
5041
K{\footnote charged set}
5042
{\b Charged Set}\par\par
5043
K{\footnote charged}
5044
This set contains the charged amino acids. These are the amino {}
5045
acids that are either {}
5046
'{\uldb acidic}{\v acidicset}' {}
5047
or {}
5048
'{\uldb basic}{\v basicset}'. {}
5049
Amino acids are classified as being either {}
5050
'{\f2\b charged}' {}
5051
or {}
5052
'{\uldb neutral}{\v neutralset}'. {}
5053
This set is equivalent to the RasMol atom expressions {}
5054
"{\f2\b acidic or basic}" {}
5055
and {}
5056
"{\f2\b amino and not neutral}". {}
5057
\par\page\par
5058
+{\footnote doc}
5059
#{\footnote cyclicset}
5060
${\footnote Cyclic Set}
5061
K{\footnote cyclic set}
5062
{\b Cyclic Set}\par\par
5063
K{\footnote cyclic}
5064
The set of atoms in amino acids containing a cycle or rings. {}
5065
All amino acids are classified as either {}
5066
'{\f2\b cyclic}' {}
5067
or {}
5068
'{\uldb acyclic}{\v acyclicset}'. {}
5069
This set consists of the amino acids His, Phe, Pro, Trp and Tyr. {}
5070
The members of the predefined set {}
5071
'{\uldb aromatic}{\v aromaticset}' {}
5072
are members of this set. {}
5073
The only cyclic but non-aromatic amino acid is proline. {}
5074
This set is equivalent to the RasMol atom expressions {}
5075
"{\f2\b his, phe, pro, trp, tyr}" {}
5076
and {}
5077
"{\f2\b aromatic or pro}" {}
5078
and {}
5079
"{\f2\b amino and not acyclic}". {}
5080
\par\page\par
5081
+{\footnote doc}
5082
#{\footnote cystineset}
5083
${\footnote Cystine Set}
5084
K{\footnote cystine set}
5085
{\b Cystine Set}\par\par
5086
K{\footnote cystine}
5087
This set contains the atoms of cysteine residues that form part {}
5088
of a disulphide bridge, i.e. half cystines. RasMol automatically {}
5089
determines disulphide bridges, if neither the predefined set {}
5090
'{\f2\b cystine}' {}
5091
nor the RasMol {}
5092
'{\uldb ssbonds}{\v ssbonds}' {}
5093
command have been used since the molecule was loaded. The set of {}
5094
free cysteines may be determined using the RasMol atom expression {}
5095
"{\f2\b cys and not cystine}". {}
5096
\par\page\par
5097
+{\footnote doc}
5098
#{\footnote helixset}
5099
${\footnote Helix Set}
5100
K{\footnote helix set}
5101
{\b Helix Set}\par\par
5102
K{\footnote helix}
5103
This set contains all atoms that form part of a protein alpha {}
5104
helix as determined by either the PDB file author or Kabsch and {}
5105
Sander's DSSP algorithm. By default, RasMol uses the secondary {}
5106
structure determination given in the PDB file if it exists. {}
5107
Otherwise, it uses the DSSP algorithm as used by the RasMol {}
5108
'{\uldb structure}{\v structure}' {}
5109
command. {}
5110
\par\par
5111
This predefined set should not be confused with the predefined set {}
5112
'{\uldb alpha}{\v alphaset}' {}
5113
which contains the alpha carbon atoms of a protein. {}
5114
\par\page\par
5115
+{\footnote doc}
5116
#{\footnote heteroset}
5117
${\footnote Hetero Set}
5118
K{\footnote hetero set}
5119
{\b Hetero Set}\par\par
5120
K{\footnote hetero}
5121
This set contains all the heterogeneous atoms in the molecule. These {}
5122
are the atoms described by HETATM entries in the PDB file. These {}
5123
typically contain water, cofactors and other solvents and ligands. All {}
5124
'{\f2\b hetero}' {}
5125
atoms are classified as either {}
5126
'{\uldb ligand}{\v ligandset}' {}
5127
or {}
5128
'{\uldb solvent}{\v solventset}' {}
5129
atoms. These heterogeneous {}
5130
'{\uldb solvent}{\v solventset}' {}
5131
atoms are further classified as either {}
5132
'{\uldb water}{\v waterset}' {}
5133
or {}
5134
'{\uldb ions}{\v ionsset}'. {}
5135
\par\page\par
5136
+{\footnote doc}
5137
#{\footnote hydrogenset}
5138
${\footnote Hydrogen Set}
5139
K{\footnote hydrogen set}
5140
{\b Hydrogen Set}\par\par
5141
K{\footnote hydrogen}
5142
This predefined set contains all the hydrogen, deuterium and tritium atoms {}
5143
of the current molecule. This predefined set is equivalent to the {}
5144
RasMol atom expression {}
5145
"{\f2\b elemno=1}". {}
5146
\par\page\par
5147
+{\footnote doc}
5148
#{\footnote hydrophobicset}
5149
${\footnote Hydrophobic Set}
5150
K{\footnote hydrophobic set}
5151
{\b Hydrophobic Set}\par\par
5152
K{\footnote hydrophobic}
5153
This set contains all the hydrophobic amino acids. {}
5154
These are the amino acids Ala, Leu, Val, Ile, Pro, Phe, Met and Trp. {}
5155
All amino acids are classified as either {}
5156
'{\f2\b hydrophobic}' {}
5157
or {}
5158
'{\uldb polar}{\v polarset}'. {}
5159
This set is equivalent to the RasMol atom expressions {}
5160
"{\f2\b ala, leu, val, ile, pro, phe, met, trp}" {}
5161
and {}
5162
"{\f2\b amino and not polar}". {}
5163
\par\page\par
5164
+{\footnote doc}
5165
#{\footnote ionsset}
5166
${\footnote Ions Set}
5167
K{\footnote ions set}
5168
{\b Ions Set}\par\par
5169
K{\footnote ions}
5170
This set contains all the heterogeneous phosphate and sulphate ions in {}
5171
the current molecule data file. A large number of these ions are {}
5172
sometimes associated with protein and nucleic acid structures determined {}
5173
by X-ray crystallography. These atoms tend to clutter an image. All {}
5174
'{\uldb hetero}{\v heteroset}' {}
5175
atoms are classified as either {}
5176
'{\uldb ligand}{\v ligandset}' {}
5177
or {}
5178
'{\uldb solvent}{\v solventset}' {}
5179
atoms. All {}
5180
'{\uldb solvent}{\v solventset}' {}
5181
atoms are classified as either {}
5182
'{\uldb water}{\v waterset}' {}
5183
or {}
5184
'{\f2\b ions}'. {}
5185
\par\page\par
5186
+{\footnote doc}
5187
#{\footnote largeset}
5188
${\footnote Large Set}
5189
K{\footnote large set}
5190
{\b Large Set}\par\par
5191
K{\footnote large}
5192
All amino acids are classified as either {}
5193
'{\uldb small}{\v smallset}', {}
5194
'{\uldb medium}{\v mediumset}' {}
5195
or {}
5196
'{\f2\b large}'. {}
5197
This set is equivalent to the RasMol atom expression {}
5198
"{\f2\b amino and not (small or medium)}". {}
5199
\par\page\par
5200
+{\footnote doc}
5201
#{\footnote ligandset}
5202
${\footnote Ligand Set}
5203
K{\footnote ligand set}
5204
{\b Ligand Set}\par\par
5205
K{\footnote ligand}
5206
This set contains all the heterogeneous cofactor and ligand moieties that {}
5207
are contained in the current molecule data file. This set is defined {}
5208
to be all {}
5209
'{\uldb hetero}{\v heteroset}' {}
5210
atoms that are not {}
5211
'{\uldb solvent}{\v solventset}' {}
5212
atoms. Hence this set is equivalent to the RasMol atom expression {}
5213
"{\f2\b hetero and not solvent}". {}
5214
\par\page\par
5215
+{\footnote doc}
5216
#{\footnote mediumset}
5217
${\footnote Medium Set}
5218
K{\footnote medium set}
5219
{\b Medium Set}\par\par
5220
K{\footnote medium}
5221
All amino acids are classified as either {}
5222
'{\uldb small}{\v smallset}', {}
5223
'{\f2\b medium}' {}
5224
or {}
5225
'{\uldb large}{\v largeset}'. {}
5226
This set is equivalent to the RasMol atom expression {}
5227
"{\f2\b amino and not (large or small)}". {}
5228
\par\page\par
5229
+{\footnote doc}
5230
#{\footnote neutralset}
5231
${\footnote Neutral Set}
5232
K{\footnote neutral set}
5233
{\b Neutral Set}\par\par
5234
K{\footnote neutral}
5235
The set of neutral amino acids. {}
5236
All amino acids are classified as either {}
5237
'{\uldb acidic}{\v acidicset}', {}
5238
'{\uldb basic}{\v basicset}' {}
5239
or {}
5240
'{\f2\b neutral}'. {}
5241
This set is equivalent to the RasMol atom expression {}
5242
"{\f2\b amino and not (acidic or basic)}". {}
5243
\par\page\par
5244
+{\footnote doc}
5245
#{\footnote nucleicset}
5246
${\footnote Nucleic Set}
5247
K{\footnote nucleic set}
5248
{\b Nucleic Set}\par\par
5249
K{\footnote nucleic}
5250
The set of all atoms in nucleic acids, which consists of the four {}
5251
nucleotide bases adenosine, cytidine, guanosine and thymidine (A, {}
5252
C, G and T, respectively). All neucleotides are classified as either {}
5253
'{\uldb purine}{\v purineset}' {}
5254
or {}
5255
'{\uldb pyrimidine}{\v pyrimidineset}'. {}
5256
This set is equivalent to the RasMol atom expressions {}
5257
"{\f2\b a,c,g,t}" {}
5258
and {}
5259
"{\f2\b purine or pyrimidine}". {}
5260
The symbols for RNA nucleotides (U, +U, I, 1MA, 5MC, OMC, {}
5261
1MG, 2MG, M2G, 7MG, OMG, YG, H2U, 5MU, and PSU) are also {}
5262
recognized as members of this set. {}
5263
\par\page\par
5264
+{\footnote doc}
5265
#{\footnote polarset}
5266
${\footnote Polar Set}
5267
K{\footnote polar set}
5268
{\b Polar Set}\par\par
5269
K{\footnote polar}
5270
This set contains the polar amino acids. {}
5271
All amino acids are classified as either {}
5272
'{\uldb hydrophobic}{\v hydrophobicset}' {}
5273
or {}
5274
'{\f2\b polar}'. {}
5275
This set is equivalent to the RasMol atom expression {}
5276
"{\f2\b amino and not hydrophobic}". {}
5277
\par\page\par
5278
+{\footnote doc}
5279
#{\footnote proteinset}
5280
${\footnote Protein Set}
5281
K{\footnote protein set}
5282
{\b Protein Set}\par\par
5283
K{\footnote protein}
5284
The set of all atoms in proteins. This consists of the RasMol {}
5285
predefined set {}
5286
'{\uldb amino}{\v aminoset}' {}
5287
and common post-translation modifications. {}
5288
\par\page\par
5289
+{\footnote doc}
5290
#{\footnote purineset}
5291
${\footnote Purine Set}
5292
K{\footnote purine set}
5293
{\b Purine Set}\par\par
5294
K{\footnote purine}
5295
The set of purine nucleotides. {}
5296
These are the bases adenosine and guanosine (A and G, respectively). {}
5297
All nucleotides are either {}
5298
'{\f2\b purines}' {}
5299
or {}
5300
'{\uldb pyrimidines}{\v pyrimidineset}'. {}
5301
This set is equivalent to the RasMol atom expressions {}
5302
"{\f2\b a,g}" {}
5303
and {}
5304
"{\f2\b nucleic and not pyrimidine}". {}
5305
\par\page\par
5306
+{\footnote doc}
5307
#{\footnote pyrimidineset}
5308
${\footnote Pyrimidine Set}
5309
K{\footnote pyrimidine set}
5310
{\b Pyrimidine Set}\par\par
5311
K{\footnote pyrimidine}
5312
The set of pyrimidine nucleotides. {}
5313
These are the bases cytidine and thymidine (C and T, respectively). {}
5314
All nucleotides are either {}
5315
'{\uldb purines}{\v purineset}' {}
5316
or {}
5317
'{\f2\b pyrimidines}'. {}
5318
This set is equivalent to the RasMol atom expressions {}
5319
"{\f2\b c,t}" {}
5320
and {}
5321
"{\f2\b nucleic and not purine}". {}
5322
\par\page\par
5323
+{\footnote doc}
5324
#{\footnote selectedset}
5325
${\footnote Selected Set}
5326
K{\footnote selected set}
5327
{\b Selected Set}\par\par
5328
K{\footnote selected}
5329
This set contains the set of atoms in the currently selected {}
5330
region. The currently selected region is defined by the preceding {}
5331
'{\uldb select}{\v select}' {}
5332
or {}
5333
'{\uldb restrict}{\v restrict}' {}
5334
command and not the atom expression containing the {}
5335
'{\f2\b selected}' {}
5336
keyword. {}
5337
\par\page\par
5338
+{\footnote doc}
5339
#{\footnote sheetset}
5340
${\footnote Sheet Set}
5341
K{\footnote sheet set}
5342
{\b Sheet Set}\par\par
5343
K{\footnote sheet}
5344
This set contains all atoms that form part of a protein beta {}
5345
sheet as determined by either the PDB file author or Kabsch and {}
5346
Sander's DSSP algorithm. By default, RasMol uses the secondary {}
5347
structure determination given in the PDB file if it exists. {}
5348
Otherwise, it uses the DSSP algorithm as used by the RasMol {}
5349
'{\uldb structure}{\v structure}' {}
5350
command. {}
5351
\par\page\par
5352
+{\footnote doc}
5353
#{\footnote sidechainset}
5354
${\footnote Sidechain Set}
5355
K{\footnote sidechain set}
5356
{\b Sidechain Set}\par\par
5357
K{\footnote sidechain}
5358
This set contains the functional sidechains of any amino acids {}
5359
and the base of each nucleotide. These are the atoms not part of {}
5360
the polypeptide N-C-C-O backbone of proteins or the sugar {}
5361
phosphate backbone of nucleic acids. {}
5362
Use the RasMol predefined sets {}
5363
'{\f2\b protein}' {}
5364
and {}
5365
'{\f2\b nucleic}' {}
5366
to distinguish between the two forms of sidechain. {}
5367
Atoms in nucleic acids and proteins are either {}
5368
'{\uldb backbone}{\v backboneset}' {}
5369
or {}
5370
'{\f2\b sidechain}'. {}
5371
This set is equivalent to the RasMol expression {}
5372
"{\f2\b (protein or nucleic) and not backbone}". {}
5373
\par\page\par
5374
+{\footnote doc}
5375
#{\footnote smallset}
5376
${\footnote Small Set}
5377
K{\footnote small set}
5378
{\b Small Set}\par\par
5379
K{\footnote small}
5380
All amino acids are classified as either {}
5381
'{\f2\b small}', {}
5382
'{\uldb medium}{\v mediumset}' {}
5383
or {}
5384
'{\uldb large}{\v largeset}'. {}
5385
This set is equivalent to the RasMol atom expression {}
5386
"{\f2\b amino and not (medium or large)}". {}
5387
\par\page\par
5388
+{\footnote doc}
5389
#{\footnote solventset}
5390
${\footnote Solvent Set}
5391
K{\footnote solvent set}
5392
{\b Solvent Set}\par\par
5393
K{\footnote solvent}
5394
This set contains the solvent atoms in the molecule coordinate file. {}
5395
These are the heterogeneous water molecules, phosphate and sulphate {}
5396
ions. All {}
5397
'{\uldb hetero}{\v heteroset}' {}
5398
atoms are classified as either {}
5399
'{\uldb ligand}{\v ligandset}' {}
5400
or {}
5401
'{\f2\b solvent}' {}
5402
atoms. All {}
5403
'{\f2\b solvent}' {}
5404
atoms are classified as either {}
5405
'{\uldb water}{\v waterset}' {}
5406
or {}
5407
'{\uldb ions}{\v ionsset}'. {}
5408
This set is equivalent to the RasMol atom expressions {}
5409
"{\f2\b hetero and not ligand}" {}
5410
and {}
5411
"{\f2\b water or ions}". {}
5412
\par\page\par
5413
+{\footnote doc}
5414
#{\footnote surfaceset}
5415
${\footnote Surface Set}
5416
K{\footnote surface set}
5417
{\b Surface Set}\par\par
5418
K{\footnote surface}
5419
This set contains the atoms in those amino acids that tend {}
5420
(prefer) to be on the surface of proteins, in contact with {}
5421
solvent molecules. This set refers to the amino acids {}
5422
preference and not the actual solvent accessibility for {}
5423
the current protein. {}
5424
All amino acids are classified as either {}
5425
'{\f2\b surface}' {}
5426
or {}
5427
'{\uldb buried}{\v buriedset}'. {}
5428
This set is equivalent to the RasMol atom expression {}
5429
"{\f2\b amino and not buried}". {}
5430
\par\page\par
5431
+{\footnote doc}
5432
#{\footnote turnset}
5433
${\footnote Turn Set}
5434
K{\footnote turn set}
5435
{\b Turn Set}\par\par
5436
K{\footnote turn}
5437
This set contains all atoms that form part of a protein turns {}
5438
as determined by either the PDB file author or Kabsch and {}
5439
Sander's DSSP algorithm. By default, RasMol uses the secondary {}
5440
structure determination given in the PDB file if it exists. {}
5441
Otherwise, it uses the DSSP algorithm as used by the RasMol {}
5442
'{\uldb structure}{\v structure}' {}
5443
command. {}
5444
\par\page\par
5445
+{\footnote doc}
5446
#{\footnote waterset}
5447
${\footnote Water Set}
5448
K{\footnote water set}
5449
{\b Water Set}\par\par
5450
K{\footnote water}
5451
This set contains all the heterogeneous water molecules in the current {}
5452
database. A large number of water molecules are sometimes associated {}
5453
with protein and nucleic acid structures determined by X-ray {}
5454
crystallography. These atoms tend to clutter an image. {}
5455
All {}
5456
'{\uldb hetero}{\v heteroset}' {}
5457
atoms are classified as either {}
5458
'{\uldb ligand}{\v ligandset}' {}
5459
or {}
5460
'{\uldb solvent}{\v solventset}' {}
5461
atoms. The {}
5462
'{\uldb solvent}{\v solventset}' {}
5463
atoms are further classified as either {}
5464
'{\f2\b water}' {}
5465
or {}
5466
'{\uldb ions}{\v ionsset}'. {}
5467
\par\page\par
5468
+{\footnote doc}
5469
#{\footnote setsummary}
5470
${\footnote Set Summary}
5471
K{\footnote set summary}
5472
{\b Set Summary}\par\par
5473
K{\footnote summary}
5474
The table below summarises RasMol's classification of the common amino acids. {}
5475
\par\par
5476
{\trowd \trgaph36\trleft-36 \cellx1116\cellx1490
5477
\cellx1864\cellx2238\cellx2612\cellx2986\cellx3360\cellx3734\cellx4108\cellx4482\cellx4856\cellx5230\cellx5604\cellx5978\cellx6352\cellx6726\cellx7100\cellx7474\cellx7848\cellx8222\cellx8596\pard\plain
5478
\qc\keep\keepn\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl
5479
{\f0\fs20 Predefined\cell }\pard \qc\keep\keepn\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl
5480
{\f0\fs12 ALA\cell ARG\cell ASN\cell ASP\cell CYS\cell GLU\cell GLN\cell GLY\cell HIS\cell }\pard \qc\keep\keepn\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl
5481
{\f0\fs12 ILE\cell }\pard \qc\keep\keepn\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl
5482
{\f0\fs12 LEU\cell LYS\cell MET\cell PHE\cell PRO\cell SER\cell THR\cell TRP\cell TYR\cell }\pard
5483
\qc\keep\keepn\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl
5484
{\f0\fs12 VAL\cell }\pard \intbl {\f20\fs12 \row }\trowd
5485
\trgaph36\trleft-36 \cellx1116\cellx1490\cellx1864\cellx2238\cellx2612\cellx2986\cellx3360\cellx3734\cellx4108\cellx4482\cellx4856\cellx5230\cellx5604\cellx5978\cellx6352\cellx6726\cellx7100\cellx7474\cellx7848\cellx8222
5486
\cellx8596\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\f0\fs20 set\cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f0 A\cell R\cell N\cell D\cell C\cell E\cell Q\cell G\cell H\cell }\pard
5487
\qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f0 I\cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f0 L\cell K\cell M\cell F\cell P\cell S\cell T\cell W\cell Y\cell }\pard
5488
\qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f0 V\cell }\pard \intbl {\b\f0 \row }\trowd \trgaph36\trleft-36 \cellx1116\cellx1490
5489
\cellx1864\cellx2238\cellx2612\cellx2986
5490
\cellx3360\cellx3734\cellx4108\cellx4482
5491
\cellx4856\cellx5230\cellx5604
5492
\cellx5978\cellx6352\cellx6726\cellx7100
5493
\cellx7474\cellx7848\cellx8222\cellx8596\pard
5494
\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\f0\fs20 acidic\cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 \cell \cell \cell {\f1\'b7} \cell \cell {\f1\'b7} \cell \cell \cell \cell }\pard
5495
\qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 \cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 \cell \cell \cell \cell \cell \cell \cell \cell \cell }\pard
5496
\qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 \cell }\pard \intbl {\b\f22\fs20 \row }\trowd \trgaph36\trleft-36 \cellx1116
5497
\cellx1490\cellx1864\cellx2238\cellx2612\cellx2986\cellx3360\cellx3734\cellx4108\cellx4482\cellx4856\cellx5230\cellx5604\cellx5978\cellx6352\cellx6726\cellx7100\cellx7474\cellx7848\cellx8222\cellx8596\pard \tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl
5498
{\f0\fs20 acyclic\cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 {\f1\'b7} \cell {\f1\'b7} \cell {\f1\'b7} \cell {\f1\'b7} \cell {\f1\'b7} \cell {\f1\'b7} \cell
5499
{\f1\'b7} \cell {\f1\'b7} \cell \cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 {\f1\'b7} \cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 {\f1\'b7} \cell {\f1\'b7} \cell {\f1\'b7} \cell \cell \cell
5500
{\f1\'b7} \cell {\f1\'b7} \cell \cell \cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 {\f1\'b7} \cell }\pard \intbl {\b\f22\fs20 \row }\pard \tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\f0\fs20 aliphatic\cell }\pard
5501
\qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 {\f1\'b7} \cell \cell \cell \cell \cell \cell \cell {\f1\'b7} \cell \cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 {\f1\'b7} \cell }\pard
5502
\qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 {\f1\'b7} \cell \cell \cell \cell \cell \cell \cell \cell \cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 {\f1\'b7} \cell }\pard \intbl {\b\f22\fs20 \row
5503
}\pard \tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\f0\fs20 aromatic\cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 \cell \cell \cell \cell \cell \cell \cell \cell {\f1\'b7} \cell }\pard
5504
\qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 \cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 \cell \cell \cell {\f1\'b7} \cell \cell \cell \cell {\f1\'b7} \cell {\f1\'b7} \cell }\pard
5505
\qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 \cell }\pard \intbl {\b\f22\fs20 \row }\pard \tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\f0\fs20 basic\cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {
5506
\b\f2\fs20 \cell {\f1\'b7} \cell \cell \cell \cell \cell \cell \cell {\f1\'b7} \cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 \cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 \cell {\f1\'b7}
5507
\cell \cell \cell \cell \cell \cell \cell \cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 \cell }\pard \intbl {\b\f22\fs20 \row }\pard \tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\f0\fs20 buried\cell }\pard
5508
\qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 {\f1\'b7} \cell \cell \cell \cell {\f1\'b7} \cell \cell \cell \cell \cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 {\f1\'b7} \cell }\pard
5509
\qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 {\f1\'b7} \cell \cell {\f1\'b7} \cell {\f1\'b7} \cell \cell \cell \cell {\f1\'b7} \cell \cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 {\f1\'b7} \cell }\pard \intbl
5510
{\b\f22\fs20 \row }\pard \tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\f0\fs20 charged\cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 \cell {\f1\'b7} \cell \cell {\f1\'b7} \cell \cell {\f1\'b7} \cell \cell \cell {\f1\'b7}
5511
\cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 \cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 \cell {\f1\'b7} \cell \cell \cell \cell \cell \cell \cell \cell }\pard
5512
\qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 \cell }\pard \intbl {\b\f22\fs20 \row }\pard \tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\f0\fs20 cyclic\cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {
5513
\b\f2\fs20 \cell \cell \cell \cell \cell \cell \cell \cell {\f1\'b7} \cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 \cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 \cell \cell \cell
5514
{\f1\'b7} \cell {\f1\'b7} \cell \cell \cell {\f1\'b7} \cell {\f1\'b7} \cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 \cell }\pard \intbl {\b\f22\fs20 \row }\pard \tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\f0\fs20
5515
hydrophobic\cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 {\f1\'b7} \cell \cell \cell \cell \cell \cell \cell {\f1\'b7} \cell \cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 {\f1\'b7} \cell
5516
}\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 {\f1\'b7} \cell \cell {\f1\'b7} \cell {\f1\'b7} \cell {\f1\'b7} \cell \cell \cell {\f1\'b7} \cell {\f1\'b7} \cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20
5517
{\f1\'b7} \cell }\pard \intbl {\b\f22\fs20 \row }\pard \tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\f0\fs20 large\cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 \cell {\f1\'b7} \cell \cell \cell \cell {\f1\'b7} \cell
5518
{\f1\'b7} \cell \cell {\f1\'b7} \cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 {\f1\'b7} \cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 {\f1\'b7} \cell {\f1\'b7} \cell {\f1\'b7} \cell {\f1\'b7} \cell
5519
\cell \cell \cell {\f1\'b7} \cell {\f1\'b7} \cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 \cell }\pard \intbl {\b\f22\fs20 \row }\pard \tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\f0\fs20 medium\cell }\pard
5520
\qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 \cell \cell {\f1\'b7} \cell {\f1\'b7} \cell {\f1\'b7} \cell \cell \cell \cell \cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 \cell }\pard
5521
\qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 \cell \cell \cell \cell {\f1\'b7} \cell \cell {\f1\'b7} \cell \cell \cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 {\f1\'b7} \cell }\pard \intbl {\b\f22\fs20
5522
\row }\pard \tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\f0\fs20 negative\cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 \cell \cell \cell {\f1\'b7} \cell \cell {\f1\'b7} \cell \cell \cell \cell }\pard
5523
\qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 \cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 \cell \cell \cell \cell \cell \cell \cell \cell \cell }\pard
5524
\qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 \cell }\pard \intbl {\b\f22\fs20 \row }\pard \tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\f0\fs20 neutral\cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {
5525
\b\f2\fs20 {\f1\'b7} \cell \cell {\f1\'b7} \cell \cell {\f1\'b7} \cell \cell {\f1\'b7} \cell {\f1\'b7} \cell {\f1\'b7} \cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 {\f1\'b7} \cell }\pard
5526
\qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 {\f1\'b7} \cell \cell {\f1\'b7} \cell {\f1\'b7} \cell {\f1\'b7} \cell {\f1\'b7} \cell {\f1\'b7} \cell {\f1\'b7} \cell {\f1\'b7} \cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {
5527
\b\f2\fs20 {\f1\'b7} \cell }\pard \intbl {\b\f22\fs20 \row }\pard \tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\f0\fs20 polar\cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 \cell {\f1\'b7} \cell {\f1\'b7} \cell
5528
{\f1\'b7} \cell {\f1\'b7} \cell {\f1\'b7} \cell {\f1\'b7} \cell \cell {\f1\'b7} \cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 \cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 \cell {\f1\'b7} \cell
5529
\cell \cell \cell {\f1\'b7} \cell {\f1\'b7} \cell \cell \cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 \cell }\pard \intbl {\b\f22\fs20 \row }\pard \tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\f0\fs20 positive\cell
5530
}\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 \cell {\f1\'b7} \cell \cell \cell \cell \cell \cell \cell {\f1\'b7} \cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 \cell }\pard
5531
\qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl
5532
{\b\f2\fs20 \cell {\f1\'b7} \cell \cell \cell \cell \cell \cell \cell \cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl
5533
{\b\f2\fs20 \cell }\pard \intbl {\b\f22\fs20 \row }\pard
5534
\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl
5535
{\f0\fs20 small\cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl {\b\f2\fs20 {\f1\'b7} \cell \cell \cell \cell \cell \cell \cell {\f1\'b7} \cell \cell }\pard
5536
\qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl
5537
{\b\f2\fs20 \cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl
5538
{\b\f2\fs20 \cell \cell \cell \cell \cell {\f1\'b7} \cell \cell \cell \cell }\pard
5539
\qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl
5540
{\b\f2\fs20 \cell }\pard \intbl
5541
{\b\f22\fs20 \row }\trowd \trgaph36\trleft-36 \cellx1116
5542
\cellx1490\cellx1864\cellx2238\cellx2612\cellx2986\cellx3360\cellx3734\cellx4108\cellx4482\cellx4856\cellx5230\cellx5604\cellx5978\cellx6352\cellx6726\cellx7100\cellx7474\cellx7848\cellx8222\cellx8596\pard \tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl
5543
{\f0\fs20 surface\cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl
5544
{\b\f2\fs20 \cell {\f1\'b7} \cell {\f1\'b7} \cell {\f1\'b7} \cell \cell {\f1\'b7} \cell {\f1\'b7} \cell {\f1\'b7} \cell {\f1\'b7} \cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl
5545
{\b\f2\fs20 \cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl
5546
{\b\f2\fs20 \cell {\f1\'b7} \cell \cell \cell {\f1\'b7} \cell {\f1\'b7} \cell {\f1\'b7} \cell \cell {\f1\'b7} \cell }\pard \qc\tx1080\tx2700\tx4320\tx5940\tx7560\tx8640\intbl
5547
{\b\f2\fs20 \cell }\pard \intbl
5548
{\b\f22\fs20 \row\pard\par\trowd }
5549
\par\page\par}
5550
\par\page\par
5551
+{\footnote doc}
5552
#{\footnote chcolours}
5553
${\footnote Colour Schemes}
5554
{\fs24\b Colour Schemes}\par\par
5555
The RasMol {}
5556
'{\uldb colour}{\v colour}' {}
5557
command allows different objects (such as atoms, bonds and ribbon segments) {}
5558
to be given a specified colour. Typically this colour is either a RasMol {}
5559
predefined colour name or an RGB triple. Additionally RasMol also supports {}
5560
'{\uldb alt}{\v altcolours}', {}
5561
'{\uldb amino}{\v aminocolours}', {}
5562
'{\uldb chain}{\v chaincolours}', {}
5563
'{\uldb charge}{\v chargecolours}', {}
5564
'{\uldb cpk}{\v cpkcolours}', {}
5565
'{\uldb group}{\v groupcolours}', {}
5566
'{\uldb model}{\v nmrmodelcolours}', {}
5567
'{\uldb shapely}{\v shapelycolours}', {}
5568
'{\uldb structure}{\v structurecolours}', {}
5569
'{\uldb temperature}{\v temperaturecolours}' {}
5570
or {}
5571
'{\uldb user}{\v usercolours}' {}
5572
colour schemes for atoms, and {}
5573
'{\uldb hbond type}{\v hbondtypecolours}' {}
5574
colour scheme for hydrogen bonds and {}
5575
'{\uldb electrostatic potential}{\v potentialcolours}' {}
5576
colour scheme for dot surfaces. {}
5577
The 24 currently predefined colour {}
5578
names are {}
5579
listed below with their corresponding RGB triplet. {}
5580
\par\par
5581
{\cellx1200\cellx3200
5582
\intbl
5583
Black\cell [0,0,0]\cell\row\intbl
5584
Orange\cell [255,165,0]\cell\row\intbl
5585
Blue\cell [0,0,255]\cell\row\intbl
5586
Pink\cell [255,101,117]\cell\row\intbl
5587
BlueTint\cell [175,214,255]\cell \row\intbl
5588
PinkTint\cell [255,171,187]\cell\row\intbl
5589
Brown\cell [175,117,89]\cell\row\intbl
5590
Purple\cell [160,32,240]\cell\row\intbl
5591
Cyan\cell [0,255,255]\cell\row\intbl
5592
Red\cell [255,0,0]\cell\row\intbl
5593
Gold\cell [255,156,0]\cell\row\intbl
5594
RedOrange\cell [255,69,0]\cell\row\intbl
5595
Grey\cell [125,125,125]\cell\row\intbl
5596
SeaGreen\cell [0,250,109]\cell\row\intbl
5597
Green\cell [0,255,0]\cell\row\intbl
5598
SkyBlue\cell [58,144,255]\cell\row\intbl
5599
GreenBlue\cell [46,139,87]\cell\row\intbl
5600
Violet\cell [238,130,238]\cell\row\intbl
5601
GreenTint\cell [152,255,179]\cell\row\intbl
5602
White\cell [255,255,255]\cell\row\intbl
5603
HotPink\cell [255,0,101]\cell\row\intbl
5604
Yellow\cell [255,255,0]\cell\row\intbl
5605
Magenta\cell [255,0,255]\cell\row\intbl
5606
YellowTint\cell [246,246,117]\cell\row\pard\par\trowd}
5607
\par\par
5608
If you frequently wish to use a colour not predefined, you can write {}
5609
a one-line script. For example, if you make the file {}
5610
'{\f2\b grey.col}' {}
5611
containing the line, {}
5612
'{\uldb colour [180,180,180] #grey}{\v colour}', {}
5613
then the command {}
5614
'{\uldb script grey.col}{\v script}' {}
5615
colours the currently selected atom set grey. {}
5616
\par\page\par
5617
+{\footnote doc}
5618
#{\footnote altcolours}
5619
${\footnote Alt Colours}
5620
K{\footnote alt colours}
5621
{\b Alt Colours}\par\par
5622
The RasMol {}
5623
'{\f2\b alt}' {}
5624
(Alternate Conformer) {}
5625
colour scheme codes the base {}
5626
structure with one colour and applies a limited number of colours to each {}
5627
alternate conformer. In a RasMol built for 8-bit colour systems, 4 colours {}
5628
are allowed for alternate conformers. Otherwise, 8 colours are available. {}
5629
\par\page\par
5630
+{\footnote doc}
5631
#{\footnote aminocolours}
5632
${\footnote Amino Colours}
5633
K{\footnote amino colours}
5634
{\b Amino Colours}\par\par
5635
The RasMol {}
5636
'{\f2\b amino}' {}
5637
colour scheme colours amino acids according to traditional amino acid {}
5638
properties. The purpose of colouring is to identify amino acids in an {}
5639
unusual or surprising environment. The outer parts of a protein that are {}
5640
polar are visible (bright) colours and non-polar residues darker. Most {}
5641
colours are hallowed by tradition. This colour scheme is similar to the {}
5642
'{\uldb shapely}{\v shapelycolours}' {}
5643
scheme. {}
5644
\par\par
5645
{\cellx1800\cellx3500\cellx5500
5646
\intbl
5647
ASP, GLU\cell Bright Red\cell [230,10,10]\cell\row\intbl
5648
LYS, ARG\cell Blue\cell [20,90,255]\cell\row\intbl
5649
CYS, MET\cell Yellow\cell [230,230,0]\cell\row\intbl
5650
SER, THR\cell Orange\cell [250,150,0]\cell\row\intbl
5651
PHE, TYR\cell Mid Blue\cell [50,50,170]\cell\row\intbl
5652
ASN, GLN\cell Cyan\cell [230,230,0]\cell\row\intbl
5653
GLY\cell Light Grey\cell [235,235,235]\cell\row\intbl
5654
LEU, VAL, ILE\cell Green\cell [15,130,15]\cell\row\intbl
5655
ALA\cell Dark Grey\cell [200,200,200]\cell\row\intbl
5656
TRP\cell Purple\cell [180,90,180]\cell\row\intbl
5657
HIS\cell Pale Blue\cell [130,130,210]\cell\row\intbl
5658
PRO\cell Flesh\cell [220,150,130]\cell\row\intbl
5659
Others\cell Tan\cell [190,160,110]\cell
5660
\row\pard\par\trowd}
5661
\par\page\par
5662
+{\footnote doc}
5663
#{\footnote chaincolours}
5664
${\footnote Chain Colours}
5665
K{\footnote chain colours}
5666
{\b Chain Colours}\par\par
5667
The RasMol {}
5668
'{\f2\b chain}' {}
5669
colour scheme assigns each macromolecular chain a unique colour. This {}
5670
colour scheme is particularly useful for distinguishing the parts of {}
5671
multimeric structure or the individual 'strands' of a DNA chain. {}
5672
'{\f2\b Chain}' {}
5673
can be selected from the RasMol {}
5674
'{\f2\b Colours}' {}
5675
menu. {}
5676
\par\page\par
5677
+{\footnote doc}
5678
#{\footnote chargecolours}
5679
${\footnote Charge Colours}
5680
K{\footnote charge colours}
5681
{\b Charge Colours}\par\par
5682
The RasMol {}
5683
'{\f2\b charge}' {}
5684
colour scheme colour codes each atom according to the charge value {}
5685
stored in the input file (or beta factor field of PDB files). High {}
5686
values are coloured in blue (positive) and lower values coloured in {}
5687
red (negative). Rather than use a fixed scale this scheme determines {}
5688
the maximum and minimum values of the charge/temperature field and {}
5689
interpolates from red to blue appropriately. Hence, green cannot be {}
5690
assumed to be 'no net charge' charge. {}
5691
\par\par
5692
The difference between the {}
5693
'{\uldb charge}{\v chargecolours}' {}
5694
and {}
5695
'{\f2\b temperature}' {}
5696
colour schemes is that increasing temperature values proceed from blue {}
5697
to red, whereas increasing charge values go from red to blue. {}
5698
\par\par
5699
If the charge/temperature field stores reasonable values it is possible {}
5700
to use the RasMol {}
5701
'{\uldb colour dots potential}{\v potentialcolours}' {}
5702
command to colour code a dot surface (generated by the {}
5703
'{\uldb dots}{\v dots}' {}
5704
command) by electrostatic potential. {}
5705
\par\page\par
5706
+{\footnote doc}
5707
#{\footnote cpkcolours}
5708
${\footnote CPK Colours}
5709
K{\footnote cpk colours}
5710
{\b CPK Colours}\par\par
5711
The RasMol {}
5712
'{\f2\b cpk}' {}
5713
colour scheme is based upon the colours of the popular plastic {}
5714
spacefilling models which were developed by Corey, Pauling and later {}
5715
improved by Kultun. This colour scheme colours 'atom' objects by the {}
5716
atom (element) type. This is the scheme conventionally used by chemists. {}
5717
The assignment of the most commonly used element types to colours is {}
5718
given below. {}
5719
\par\par
5720
The assignment of element type to colours is given below. {}
5721
\par\par
5722
\cellx2000\cellx4000\cellx6500
5723
\intbl
5724
Carbon\cell light grey\cell [200,200,200]\cell\row\intbl
5725
Oxygen\cell red\cell [240,0,0]\cell\row\intbl
5726
Hydrogen\cell white\cell [255,255,255]\cell\row\intbl
5727
Nitrogen\cell sky blue\cell [143,143,255]\cell\row\intbl
5728
Sulphur\cell yellow\cell [255,200,50]\cell\row\intbl
5729
Phosphorous\cell orange\cell [255,165,0]\cell\row\intbl
5730
Chlorine\cell green\cell [0,255,0]\cell\row\intbl
5731
Bromine, Zinc\cell brown\cell [165,42,42]\cell\row\intbl
5732
Sodium\cell blue\cell [0,0,255]\cell\row\intbl
5733
Iron\cell orange\cell [255,165,0]\cell\row\intbl
5734
Magnesium\cell forest green\cell [34,139,34]\cell\row\intbl
5735
Calcium \cell dark grey\cell [128,128,144]\cell\row\intbl
5736
unknown\cell deep pink\cell [255,20,147]\cell\row\pard\par
5737
\trowd
5738
\par\par
5739
The assignment of element type to colours for the cpknew colour scheme is given below. {}
5740
\par\par
5741
\cellx2000\cellx4000\cellx6500
5742
\intbl
5743
Carbon\cell light grey\cell [211,211,211]\cell\row\intbl
5744
Oxygen\cell red\cell [255,0,0]\cell\row\intbl
5745
Hydrogen\cell white\cell [255,255,255]\cell\row\intbl
5746
Nitrogen\cell sky blue\cell [135,206,235]\cell\row\intbl
5747
Sulphur\cell yellow\cell [255,255,0]\cell\row\intbl
5748
Phosphorous\cell orange\cell [255,170,0]\cell\row\intbl
5749
Chlorine\cell green\cell [0,255,0]\cell\row\intbl
5750
Bromine, Zinc\cell brown\cell [128,40,40]\cell\row\intbl
5751
Sodium\cell blue\cell [0,0,255]\cell\row\intbl
5752
Iron\cell orange\cell [255,170,0]\cell\row\intbl
5753
Magnesium\cell forest green\cell [34,139,34]\cell\row\intbl
5754
Calcium \cell dark grey\cell [105,105,105]\cell\row\intbl
5755
unknown\cell deep pink\cell [255,22,145]\cell\row\pard\par
5756
\trowd
5757
\par\page\par
5758
+{\footnote doc}
5759
#{\footnote groupcolours}
5760
${\footnote Group Colours}
5761
K{\footnote group colours}
5762
{\b Group Colours}\par\par
5763
The RasMol {}
5764
'{\f2\b group}' {}
5765
colour scheme colour codes residues by their position in a macromolecular {}
5766
chain. Each chain is drawn as a smooth spectrum from blue through green, {}
5767
yellow and orange to red. Hence the N terminus of proteins and 5' terminus {}
5768
of nucleic acids are coloured red and the C terminus of proteins and 3' {}
5769
terminus of nucleic acids are drawn in blue. If a chain has a large number {}
5770
of heterogeneous molecules associated with it, the macromolecule may not be {}
5771
drawn in the full 'range' of the spectrum. {}
5772
'{\f2\b Group}' {}
5773
can be selected from the RasMol {}
5774
'{\f2\b Colours}' {}
5775
menu. {}
5776
\par\par
5777
If a chain has a large number of heterogeneous molecules associated with it, {}
5778
the macromolecule may not be drawn in the full range of the spectrum. When {}
5779
RasMol performs group colouring it decides the range of colours it uses from {}
5780
the residue numbering given in the PDB file. Hence the lowest residue {}
5781
number is displayed in blue and the highest residue number is displayed as {}
5782
red. Unfortunately, if a PDB file contains a large number of heteroatoms, {}
5783
such as water molecules, that occupy the high residue numbers, the protein {}
5784
is displayed in the blue-green end of the spectrum and the waters in the {}
5785
yellow-red end of the spectrum. This is aggravated by there typically being {}
5786
many more water molecules than amino acid residues. The solution to this {}
5787
problem is to use the command {}
5788
'{\uldb set hetero off}{\v sethetero}' {}
5789
before applying the group {}
5790
colour scheme. This can also be achieved by toggling {}
5791
'{\f2\b Hetero Atoms}' {}
5792
on the {}
5793
'{\f2\b Options}' {}
5794
menu before selecting {}
5795
'{\f2\b Group}' {}
5796
on the {}
5797
'{\f2\b Colour}' {}
5798
menu. This command {}
5799
instructs RasMol to only use non-hetero residues in the group colour scaling. {}
5800
\par\page\par
5801
+{\footnote doc}
5802
#{\footnote nmrmodelcolours}
5803
${\footnote NMR Model Colours}
5804
K{\footnote nmr model colours}
5805
{\b NMR Model Colours}\par\par
5806
The RasMol {}
5807
'{\f2\b model}' {}
5808
colour scheme codes each NMR model with a distinct {}
5809
colour. The NMR model number is taken as a numeric value. High values {}
5810
are coloured in blue and lower values coloured in red. Rather than use a {}
5811
fixed scale this scheme determines the maximum value of the {}
5812
NMR model number and interpolates from red to blue appropriately. {}
5813
\par\page\par
5814
+{\footnote doc}
5815
#{\footnote shapelycolours}
5816
${\footnote Shapely Colours}
5817
K{\footnote shapely colours}
5818
{\b Shapely Colours}\par\par
5819
The RasMol {}
5820
'{\f2\b shapely}' {}
5821
colour scheme colour codes residues by amino acid property. This scheme {}
5822
is based upon Bob Fletterick's "Shapely Models". Each amino acid and {}
5823
nucleic acid residue is given a unique colour. The {}
5824
'{\f2\b shapely}' {}
5825
colour scheme is used by David Bacon's Raster3D program. This colour {}
5826
scheme is similar to the {}
5827
'{\uldb amino}{\v aminocolours}' {}
5828
colour scheme. {}
5829
\par\par
5830
\cellx2000\cellx3700\cellx5500
5831
\intbl
5832
ALA\cell Medium Green\cell [140,255,140]\cell\row\intbl
5833
GLY\cell White\cell [255,255,255]\cell\row\intbl
5834
LEU\cell Olive Green\cell [ 69, 94, 69]\cell\row\intbl
5835
SER\cell Medium Orange\cell [255,112, 66]\cell\row\intbl
5836
VAL\cell Light Purple\cell [255,140,255]\cell\row\intbl
5837
THR\cell Dark Orange\cell [184, 76, 0]\cell\row\intbl
5838
LYS\cell Royal Blue\cell [ 71, 71,184]\cell\row\intbl
5839
ASP\cell Dark Rose\cell [160, 0, 66]\cell\row\intbl
5840
ILE\cell Dark Green\cell [ 0, 76, 0]\cell\row\intbl
5841
ASN\cell Light Salmon\cell [255,124,112]\cell\row\intbl
5842
GLU\cell Dark Brown\cell [102, 0, 0]\cell\row\intbl
5843
PRO\cell Dark Grey\cell [ 82, 82, 82]\cell\row\intbl
5844
ARG\cell Dark Blue\cell [ 0, 0,124]\cell\row\intbl
5845
PHE\cell Olive Grey\cell [ 83, 76, 66]\cell\row\intbl
5846
GLN\cell Dark Salmon\cell [255, 76, 76]\cell\row\intbl
5847
TYR\cell Medium Brown\cell [140,112, 76]\cell\row\intbl
5848
HIS\cell Medium Blue\cell [112,112,255]\cell\row\intbl
5849
CYS\cell Medium Yellow\cell [255,255,112]\cell\row\intbl
5850
MET\cell Light Brown\cell [184,160, 66]\cell\row\intbl
5851
TRP\cell Olive Brown\cell [ 79, 70, 0]\cell\row\intbl
5852
ASX,GLX,PCA,HYP\cell Medium Purple\cell [255, 0,255]\cell\row\intbl
5853
A\cell Light Blue\cell [160,160,255]\cell\row\intbl
5854
C\cell Light Orange\cell [255,140, 75] \cell\row\intbl
5855
G\cell Medium Salmon\cell [255,112,112]\cell\row\intbl
5856
T\cell Light Green\cell [160,255,160]\cell\row\intbl
5857
Backbone\cell Light Grey\cell [184,184,184]\cell\row\intbl
5858
Special\cell Dark Purple\cell [ 94, 0, 94]\cell\row\intbl
5859
Default\cell Medium Purple\cell [255, 0,255]\cell\row\pard\par
5860
\trowd
5861
\par\page\par
5862
+{\footnote doc}
5863
#{\footnote structurecolours}
5864
${\footnote Structure Colours}
5865
K{\footnote structure colours}
5866
{\b Structure Colours}\par\par
5867
The RasMol {}
5868
'{\f2\b structure}' {}
5869
colour scheme colours the molecule by protein secondary structure. {}
5870
Alpha helices are coloured magenta, [240,0,128], beta sheets are {}
5871
coloured yellow, [255,255,0], turns are coloured pale blue, [96,128,255] {}
5872
and all other residues are coloured white. The secondary structure {}
5873
is either read from the PDB file (HELIX, SHEET and TURN records), if available, {}
5874
or determined using Kabsch and Sander's DSSP algorithm. The RasMol {}
5875
'{\uldb structure}{\v structure}' {}
5876
command may be used to force DSSP's structure assignment to be used. {}
5877
\par\page\par
5878
+{\footnote doc}
5879
#{\footnote temperaturecolours}
5880
${\footnote Temperature Colours}
5881
K{\footnote temperature colours}
5882
{\b Temperature Colours}\par\par
5883
The RasMol {}
5884
'{\f2\b temperature}' {}
5885
colour scheme colour codes each atom according to the anisotropic {}
5886
temperature (beta) value stored in the PDB file. Typically this gives {}
5887
a measure of the mobility/uncertainty of a given atom's position. High {}
5888
values are coloured in warmer (red) colours and lower values in colder {}
5889
(blue) colours. This feature is often used to associate a "scale" value {}
5890
[such as amino acid variability in viral mutants] with each atom in a {}
5891
PDB file, and colour the molecule appropriately. {}
5892
\par\par
5893
The difference between the {}
5894
'{\f2\b temperature}' {}
5895
and {}
5896
'{\uldb charge}{\v chargecolours}' {}
5897
colour schemes is that increasing temperature values proceed from blue {}
5898
to red, whereas increasing charge values go from red to blue. {}
5899
\par\page\par
5900
+{\footnote doc}
5901
#{\footnote usercolours}
5902
${\footnote User Colours}
5903
K{\footnote user colours}
5904
{\b User Colours}\par\par
5905
The RasMol {}
5906
'{\f2\b user}' {}
5907
colour scheme allows RasMol to use the colour scheme stored in the {}
5908
PDB file. The colours for each atom are stored in COLO records placed {}
5909
in the PDB data file. This convention was introduced by David Bacon's {}
5910
Raster3D program. {}
5911
\par\page\par
5912
+{\footnote doc}
5913
#{\footnote hbondtypecolours}
5914
${\footnote HBond Type Colours}
5915
K{\footnote hbond type colours}
5916
{\b HBond Type Colours}\par\par
5917
The RasMol {}
5918
'{\f2\b type}' {}
5919
colour scheme applies only to hydrogen bonds, hence is used in the command {}
5920
'{\f2\b colour hbonds type}'. {}
5921
This scheme colour codes each hydrogen bond according to the {}
5922
distance along a protein chain between hydrogen bond donor and acceptor. {}
5923
This schematic representation was introduced by Belhadj-Mostefa and {}
5924
Milner-White. This representation gives a good insight into protein {}
5925
secondary structure (hbonds forming alpha helices appear red, those {}
5926
forming sheets appear yellow and those forming turns appear magenta). {}
5927
\par\par
5928
{\cellx2000\cellx3000\cellx4700
5929
\intbl
5930
Offset\cell Colour\cell Triple\cell\row\intbl
5931
+2\cell white \cell [255,255,255]\cell\row\intbl
5932
+3\cell magenta\cell [255,0,255]\cell\row\intbl
5933
+4\cell red \cell [255,0,0]\cell\row\intbl
5934
+5\cell orange \cell [255,165,0]\cell\row\intbl
5935
-3\cell cyan \cell [0,255,255]\cell\row\intbl
5936
-4\cell green \cell [0,255,0]\cell\row\intbl
5937
default\cell yellow\cell [255,255,0]\cell\row
5938
\pard\par\trowd}
5939
\par\page\par
5940
+{\footnote doc}
5941
#{\footnote potentialcolours}
5942
${\footnote Potential Colours}
5943
K{\footnote potential colours}
5944
{\b Potential Colours}\par\par
5945
The RasMol {}
5946
'{\f2\b potential}' {}
5947
colour scheme applies only to dot surfaces, hence is used in the command {}
5948
'{\f2\b colour dots potential}'. {}
5949
This scheme colours each currently displayed dot by the electrostatic {}
5950
potential at that point in space. This potential is calculated using {}
5951
Coulomb's law taking the temperature/charge field of the input file to {}
5952
be the charge assocated with that atom. This is the same interpretation {}
5953
used by the {}
5954
'{\uldb colour charge}{\v chargecolours}' {}
5955
command. Like the {}
5956
'{\uldb charge}{\v chargecolours}' {}
5957
colour scheme low values are blue/white and high values are red. {}
5958
The table below shows the static assignment of colours using a {}
5959
dielectric constant value of 10. {}
5960
\par\par
5961
\cellx2000\cellx3000\cellx5500
5962
\intbl
5963
{ 25 < V }\cell red \cell [255,0,0]\cell\row\intbl
5964
{ 10 < V < 25}\cell orange\cell [255,165,0]\cell\row\intbl
5965
{ 3 < V < 10}\cell yellow\cell [255,255,0]\cell\row\intbl
5966
{ 0 < V < 3}\cell green \cell [0,255,0]\cell\row\intbl
5967
{ -3 < V < 0}\cell cyan \cell [0,255,255]\cell\row\intbl
5968
{-10 < V < -3}\cell blue \cell [0.0.255]\cell\row\intbl
5969
{-25 < V < -10}\cell purple\cell [160,32,240]\cell\row\intbl
5970
{ V < -25}\cell white \cell [255,255,255]\cell\row
5971
\pard\par\trowd
5972
\par\page\par
5973
+{\footnote doc}
5974
#{\footnote codes}
5975
#{\footnote aminoacidcodes}
5976
${\footnote Amino Acid Codes}
5977
K{\footnote amino acid codes}
5978
{\b Amino Acid Codes}\par\par
5979
The following table lists the names, single letter and three letter {}
5980
codes of each of the amino acids. {}
5981
\par\par
5982
{\cellx1650\cellx2050\cellx2650\cellx4300\cellx4700\cellx5400
5983
\intbl
5984
Alanine\cell A\cell ALA\cell Arginine\cell R\cell ARG\cell\row\intbl
5985
Asparagine\cell N\cell ASN\cell Aspartic acid\cell D\cell ASP\cell\row\intbl
5986
Cysteine\cell C\cell CYS\cell Glutamic acid\cell E\cell GLU\cell\row\intbl
5987
Glutamine\cell Q\cell GLN\cell Glycine\cell G\cell GLY\cell\row\intbl
5988
Histidine\cell H\cell HIS\cell Isoleucine\cell I\cell ILE\cell\row\intbl
5989
Leucine\cell L\cell LEU\cell Lysine\cell K\cell LYS\cell\row\intbl
5990
Methionine\cell M\cell MET\cell Phenylalanine\cell F\cell PHE\cell\row\intbl
5991
Proline\cell P\cell PRO\cell Serine\cell S\cell SER\cell\row\intbl
5992
Threonine\cell T\cell THR\cell Tryptophan\cell W\cell TRP\cell\row\intbl
5993
Tyrosine\cell Y\cell TYR\cell Valine\cell V\cell VAL\cell\row
5994
\pard\par\trowd}
5995
\par\page\par
5996
+{\footnote doc}
5997
#{\footnote booleanexpression}
5998
#{\footnote booleans}
5999
${\footnote Booleans}
6000
K{\footnote booleans}
6001
{\b Booleans}\par\par
6002
A boolean parameter is a truth value. Valid boolean values are 'true' and {}
6003
'false', and their synonyms 'on' and 'off'. Boolean parameters are commonly {}
6004
used by RasMol to either enable or disable a representation or option. {}
6005
\par\page\par
6006
+{\footnote doc}
6007
#{\footnote chfile}
6008
${\footnote File}
6009
{\fs24\b File Formats}\par\par
6010
\par\par
6011
{\f2\b Protein Data Bank Files} {}
6012
\par\par
6013
If you do not have the PDB documentation, you may find the {}
6014
following summary of the PDB file format useful. The Protein Data Bank {}
6015
is a computer-based archival database for macromolecular structures. {}
6016
The database was established in 1971 by Brookhaven National {}
6017
Laboratory, Upton, New York, as a public domain repository for resolved {}
6018
crystallographic structures. The Bank uses a uniform format to store {}
6019
atomic coordinates and partial bond connectivities as derived from {}
6020
crystallographic studies. In 1999 the Protein Data Bank moved {}
6021
to the Research Collaboratory for Structural Biology. {}
6022
\par\par
6023
PDB file entries consist of records of 80 characters each. Using the {}
6024
punched card analogy, columns 1 to 6 contain a record-type identifier, {}
6025
the columns 7 to 70 contain data. In older entries, columns 71 to 80 {}
6026
are normally blank, {}
6027
but may contain sequence information added by library management {}
6028
programs. In new entries conforming to the 1996 PDB format, there {}
6029
is other information in those columns. The first four characters of {}
6030
the record identifier are {}
6031
sufficient to identify the type of record uniquely, and the syntax of {}
6032
each record is independent of the order of records within any entry for {}
6033
a particular macromolecule. {}
6034
\par\par
6035
The only record types that are of major interest to the RasMol program {}
6036
are the ATOM and HETATM records which describe the position of each {}
6037
atom. ATOM/HETATM records contain standard atom names and residue {}
6038
abbreviations, along with sequence identifiers, coordinates in {}
6039
Angstrom units, occupancies and thermal motion factors. The exact {}
6040
details are given below as a FORTRAN format statement. The "fmt" {}
6041
column indicates use of the field in all PDB formats, {}
6042
in the 1992 and earlier formats or in the 1996 and later formats. {}
6043
\par\par
6044
FORMAT(6A1,I5,1X,A4,A1,A3,1X,A1,I4,A1,3X,3F8.3,2F6.2,1X,I3,2X,A4,2A2)
6045
\par\par
6046
{\cellx1250\cellx6000\cellx6500
6047
\intbl
6048
Column \cell Content \cell fmt\cell\row\intbl
6049
1-6 \cell 'ATOM' or 'HETATM' \cell all\cell\row\intbl
6050
7-11 \cell Atom serial number (may have gaps) \cell all\cell\row\intbl
6051
13-16 \cell Atom name, in IUPAC standard format \cell all\cell\row\intbl
6052
17 \cell Alternate location indicator indicated by A, B or C \cell all\cell\row\intbl
6053
18-20 \cell Residue name, in IUPAC standard format \cell all\cell\row\intbl
6054
23-26 \cell Residue sequence number \cell all\cell\row\intbl
6055
27 \cell Code for insertions of residues (i.e. 66A & 66B) \cell all\cell\row\intbl
6056
31-38 \cell X coordinate \cell all\cell\row\intbl
6057
39-46 \cell Y coordinate \cell all\cell\row\intbl
6058
47-54 \cell Z coordinate \cell all\cell\row\intbl
6059
55-60 \cell Occupancy \cell all\cell\row\intbl
6060
61-66 \cell Temperature factor \cell all\cell\row\intbl
6061
68-70 \cell Footnote number \cell 92\cell\row\intbl
6062
73-76 \cell Segment Identifier (left-justified) \cell 96\cell\row\intbl
6063
77-78 \cell Element Symbol (right-justified) \cell 96\cell\row\intbl
6064
79-80 \cell Charge on the Atom \cell 96\cell\row}
6065
\pard\par\trowd
6066
\par\par
6067
Residues occur in order starting from the N-terminal residue {}
6068
for proteins and {}
6069
5'-terminus for nucleic acids. If the residue sequence is known, {}
6070
certain atom serial numbers may be omitted to allow for future insertion {}
6071
of any missing atoms. Within each residue, atoms are ordered in a {}
6072
standard manner, starting with the backbone (N-C-C-O for proteins) and {}
6073
proceeding in increasing remoteness from the alpha carbon, along the {}
6074
side chain. {}
6075
\par\par
6076
HETATM records are used to define post-translational modifications and {}
6077
cofactors associated with the main molecule. TER records are {}
6078
interpreted as breaks in the main molecule's backbone. {}
6079
\par\par
6080
If present, RasMol also inspects HEADER, COMPND, HELIX, SHEET, TURN, {}
6081
CONECT, CRYST1, SCALE, MODEL, ENDMDL, EXPDTA and END records. Information such as the {}
6082
name, database code, revision date and classification of the molecule {}
6083
are extracted from HEADER and COMPND records, initial secondary {}
6084
structure assignments are taken from HELIX, SHEET and TURN records, and {}
6085
the end of the file may be indicated by an END record. {}
6086
\par\page\par
6087
+{\footnote doc}
6088
#{\footnote rasmolinterpretationofpdbfields}
6089
${\footnote RasMol Interpretation of PDB fields}
6090
K{\footnote rasmol interpretation of pdb fields}
6091
{\b RasMol Interpretation of PDB fields}\par\par
6092
Atoms located at 9999.000, 9999.000, 9999.000 are assumed to be Insight {}
6093
pseudo atoms and are ignored by RasMol. Atom names beginning ' Q' are {}
6094
also assumed to be pseudo atoms or position markers. {}
6095
\par\par
6096
When a data file contains an NMR structure, multiple conformations may {}
6097
be placed in a single PDB file delimited by pairs of MODEL and ENDMDL {}
6098
records. RasMol displays all the NMR models contained in the file. {}
6099
\par\par
6100
Residue names "CSH", "CYH" and "CSM" are considered pseudonyms for {}
6101
cysteine "CYS". Residue names "WAT", "H20", "SOL" and "TIP" are {}
6102
considered pseudonyms for water "HOH". The residue name "D20" is {}
6103
consider heavy water "DOD". The residue name "SUL" is considered a {}
6104
sulphate ion "SO4". The residue name "CPR" is considered to be {}
6105
cis-proline and is translated as "PRO". The residue name "TRY" is {}
6106
considered a pseudonym for tryptophan "TRP". {}
6107
\par\par
6108
RasMol uses the HETATM fields to define the sets hetero, water, solvent {}
6109
and ligand. Any group with the name "HOH", "DOD", "SO4" or "PO4" (or {}
6110
aliased to one of these names by the preceding rules) is considered a {}
6111
solvent and is considered to be defined by a HETATM field. {}
6112
\par\par
6113
RasMol only respects CONECT connectivity records in PDB files containing {}
6114
fewer than 256 atoms. This is explained in more detail in the section on {}
6115
determining molecule connectivity. CONECT records that define a bond {}
6116
more than once are interpreted as specifying the bond order of that {}
6117
bond, i.e. a bond specified twice is a double bond and a bond specified {}
6118
three (or more) times is a triple bond. This is not a standard PDB feature. {}
6119
\par\page\par
6120
+{\footnote doc}
6121
#{\footnote pdbcolourschemespecification}
6122
${\footnote PDB Colour Scheme Specification}
6123
K{\footnote pdb colour scheme specification}
6124
{\b PDB Colour Scheme Specification}\par\par
6125
RasMol also accepts the supplementary COLO record type in the PDB {}
6126
files. This record format was introduced by David Bacon's Raster3D {}
6127
program for specifying the colour scheme to be used when rendering the {}
6128
molecule. This extension is not currently supported by the PDB. The {}
6129
COLO record has the same basic record type as the ATOM and HETATM {}
6130
records described above. {}
6131
\par\par
6132
Colours are assigned to atoms using a matching process. The Mask field {}
6133
is used in the matching process as follows. First RasMol reads in and {}
6134
remembers all the ATOM, HETATM and COLO records in input order. When the {}
6135
user-defined ('User') colour scheme is selected, RasMol goes through {}
6136
each remembered ATOM/HETATM record in turn, and searches for a COLO {}
6137
record that matches in all of columns 7 through 30. The first such COLO {}
6138
record to be found determines the colour and radius of the atom. {}
6139
\par\par
6140
\pard\par
6141
{\cellx1250\cellx4500
6142
\intbl
6143
Column \cell Content \cell\row\intbl
6144
1-6 \cell 'COLOR' or 'COLOUR' \cell\row\intbl
6145
7-30 \cell Mask (described below) \cell\row\intbl
6146
31-38 \cell Red component \cell\row\intbl
6147
39-46 \cell Green component \cell\row\intbl
6148
47-54 \cell Blue component \cell\row\intbl
6149
55-60 \cell Sphere radius in Angstroms \cell\row\intbl
6150
61-70 \cell Comments \cell\row}
6151
\pard\par\trowd
6152
\par\par
6153
Note that the Red, Green and Blue components are in the same positions {}
6154
as the X, Y, and Z components of an ATOM or HETA record, and the van {}
6155
der Waals radius goes in the place of the Occupancy. The Red, Green and {}
6156
Blue components must all be in the range 0 to 1. {}
6157
\par\par
6158
In order that one COLO record can provide colour and radius {}
6159
specifications for more than one atom (e.g. based on residue, atom {}
6160
type, or any other criterion for which labels can be given somewhere in {}
6161
columns 7 through 30), a 'don't-care' character, the hash mark "#" {}
6162
(number or sharp sign) is used. This character, when found in a COLO {}
6163
record, matches any character in the corresponding column in a {}
6164
ATOM/HETATM record. All other characters must match identically to count {}
6165
as a match. As an extension to the specification, any atom that fails {}
6166
to match a COLO record is displayed in white. {}
6167
\par\page\par
6168
+{\footnote doc}
6169
#{\footnote multiplenmrmodels}
6170
${\footnote Multiple NMR Models}
6171
K{\footnote multiple nmr models}
6172
{\b Multiple NMR Models}\par\par
6173
RasMol loads all of the NMR models from a PDB file no matter which {}
6174
command is used: {}
6175
'{\uldb load pdb <filename>}{\v load}' {}
6176
or {}
6177
'{\uldb load nmrpdb <filename>}{\v load}' {}
6178
\par\par
6179
Once multiple NMR conformations have been loaded they may be {}
6180
manipulated with the atom expression extensions described in {}
6181
'{\uldb Primitive Expressions}{\v primitiveexpressions}'. {}
6182
In particular, the command {}
6183
'{\uldb restrict */1}{\v restrict}' {}
6184
will restrict the display to the first model only. {}
6185
\par\page\par
6186
+{\footnote doc}
6187
#{\footnote cifandmmcifformatfiles}
6188
${\footnote CIF and mmCIF Format Files}
6189
K{\footnote cif and mmcif format files}
6190
{\b CIF and mmCIF Format Files}\par\par
6191
CIF is the IUCr standard for presentation of small molecules and mmCIF {}
6192
is intended as the replacement for the fixed-field PDB format for {}
6193
presentation of macromolecular structures. RasMol can accept data sets {}
6194
in either format. {}
6195
\par\par
6196
There are many useful sites on the World Wide Web where information {}
6197
tools and software related to CIF, mmCIF and the PDB can be found. The {}
6198
following are good starting points for exploration: {}
6199
\par\par
6200
The International Union of Crystallography (IUCr) provides access to {}
6201
software, dictionaries, policy statements and documentation relating to {}
6202
CIF and mmCIF at: IUCr, Chester, England (www.iucr.org/iucr-top/cif/) {}
6203
with many mirror sites. {}
6204
\par\par
6205
The Nucleic Acid Database Project provides access to its entries, {}
6206
software and documentation, with an mmCIF page giving access to the {}
6207
dictionary and mmCIF software tools at Rutgers University, New Jersey, {}
6208
USA (http://ndbserver.rutgers.edu/NDB/mmcif) with many mirror sites. {}
6209
\par\par
6210
This version of RasMol restricts CIF or mmCIF tag values to essentially {}
6211
the same conventions as are used for the fixed-field PDB format. Thus {}
6212
chain identifiers and alternate conformation identifiers are limited to {}
6213
a single character, atom names are limited to 4 characters, etc. RasMol {}
6214
interprets the following CIF and mmCIF tags: {}
6215
\pard \qj
6216
{\f2 \par }\trowd \trgaph80\trleft-80
6217
\cellx3232\cellx6544\cellx8848\pard \qj\intbl
6218
{\b\f2 mmCIF tag}{\f2 \cell }\pard \qj\intbl
6219
{\b\f2 CIF tag\cell }\pard \qj\intbl
6220
{\b\f2 Used for\cell }\pard \intbl {\f2 \row }\trowd
6221
\trgaph80\trleft-80 \cellx3232\cellx6544\cellx8848\pard
6222
\qj\intbl {\f2 _struct_biol.details\cell }\pard \qj\intbl
6223
{\f2 \cell }\pard \qj\intbl {\f2 Info.classification\cell }\pard \intbl
6224
{\f2 \row }\pard \qj\intbl {\f2
6225
_database_2.database_code\cell }\pard \qj\intbl {\f2 \cell }\pard \qj\intbl
6226
{\f2 Info.identcode\cell }\pard \intbl {\f2 \row }\pard \qj\intbl
6227
{\f2 _entry.id\cell }\pard \qj\intbl {\f2 \cell }\pard \qj\intbl
6228
{\f2 \cell }\pard \intbl {\f2 \row
6229
}\pard \qj\intbl {\f2 _struct_biol.id\cell }\pard \qj\intbl
6230
{\f2 \cell }\pard \qj\intbl {\f2 \cell }\pard \intbl
6231
{\f2 \row }\pard \qj\intbl {\f2 _struct.title\cell }\pard \qj\intbl
6232
{\f2 \cell }\pard \qj\intbl {\f2 Info.moleculename\cell }\pard
6233
\intbl {\f2 \row }\pard \qj\intbl {\f2 _chemical_name_common\cell }\pard \qj\intbl
6234
{\f2 \cell }\pard \qj\intbl {\f2 \cell }\pard \intbl {\f2 \row }\pard \qj\intbl
6235
{\f2 _chemical_name_systematic\cell }\pard \qj\intbl {\f2 \cell }\pard \qj\intbl
6236
{\f2 \cell }\pard \intbl {\f2 \row }\pard \qj\intbl
6237
{\f2 _chemical_name_mineral\cell }\pard \qj\intbl
6238
{\f2 \cell }\pard \qj\intbl {\f2 \cell }\pard \intbl
6239
{\f2 \row }\pard \qj\intbl {\f2 \cell }\pard \qj\intbl
6240
{\f2 \cell }\pard \qj\intbl {\f2 \cell }\pard \intbl
6241
{\f2 \row }\pard \qj\intbl {\f2 _symmetry.\par
6242
space_group_name_H-M\cell }\pard \qj\intbl
6243
{\f2 _symmetry\par
6244
_space_group_name_H-M\cell }\pard \qj\intbl
6245
{\f2 Info.spacegroup\cell }\pard \intbl
6246
{\f2 \row }\pard \qj\intbl {\f2 _cell.length_a\cell }\pard \qj\intbl
6247
{\f2 _cell_length_a\cell }\pard \qj\intbl {\f2 Info.cell\cell }\pard \intbl
6248
{\f2 \row }\pard
6249
\qj\intbl {\f2 _cell.length_b\cell }\pard \qj\intbl
6250
{\f2 _cell_length_b\cell }\pard \qj\intbl
6251
{\f2 \cell }\pard \intbl {\f2 \row }\pard \qj\intbl
6252
{\f2 _cell.length_c\cell }\pard \qj\intbl
6253
{\f2 _cell_length_c\cell }\pard \qj\intbl {\f2 \cell }\pard
6254
\intbl {\f2 \row }\pard \qj\intbl {\f2 _cell.angle_alpha\cell }\pard \qj\intbl
6255
{\f2 _cell_angle_alpha\cell }\pard \qj\intbl {\f2 \cell }\pard \intbl
6256
{\f2 \row }\pard \qj\intbl {\f2 _cell.angle_beta\cell }\pard \qj\intbl
6257
{\f2 _cell_angle_beta\cell
6258
}\pard \qj\intbl {\f2 \cell }\pard \intbl {\f2 \row }\pard \qj\intbl
6259
{\f2 _cell.angle_gamma\cell }\pard \qj\intbl
6260
{\f2 _cell_angle_beta\cell }\pard \qj\intbl
6261
{\f2 \cell }\pard \intbl {\f2 \row }\pard \qj\intbl
6262
{\f2 \cell }\pard \qj\intbl {\f2
6263
\cell }\pard \qj\intbl {\f2 \cell }\pard \intbl
6264
{\f2 \row }\pard \qj\intbl {\f2 _atom_sites.\par
6265
fract_transf_matrix[1][1]\cell }\pard \qj\intbl {\f2 _atom_sites\par
6266
_fract_tran_matrix_11\cell }\pard \qj\intbl {\f2 Used to compute\par
6267
orthogonal coords\cell }\pard \intbl {\f2 \row }\pard \qj\intbl
6268
{\f2 ...\cell }\pard \qj\intbl {\f2 ...\cell }\pard \qj\intbl
6269
{\f2 \cell }\pard \intbl {\f2 \row }\pard \qj\intbl
6270
{\f2 _atom_sites.\par
6271
fract_transf_vector[1]\cell }\pard \qj\intbl
6272
{\f2 _atom_sites\par
6273
_fract_tran_vector_1\cell }\pard \qj\intbl
6274
{\f2 \cell }\pard \intbl {\f2 \row }\pard \qj\intbl
6275
{\f2 ...\cell }\pard \qj\intbl {\f2 ...\cell }\pard \qj\intbl
6276
{\f2 \cell }\pard \intbl {\f2 \row }\pard \qj\intbl {\f2 _atom_sites.\par
6277
cartn_transf_matrix[1][1]\cell }\pard \qj\intbl
6278
{\f2 _atom_sites\par
6279
_cartn_tran_matrix_11\cell }\pard \qj\intbl
6280
{\f2 Alternative to\par
6281
compute orth. coords\cell }\pard \intbl
6282
{\f2 \row }\pard \qj\intbl {\f2 ...\cell }\pard \qj\intbl
6283
{\f2 ...\cell }\pard \qj\intbl {\f2 \cell }\pard \intbl
6284
{\f2 \row }\pard \qj\intbl {\f2 _atom_sites.\par
6285
cartn_transf_vector[1]\cell }\pard \qj\intbl {\f2 _atom_sites\par
6286
_cartn_tran_vector_1\cell }\pard \qj\intbl {\f2 \cell }\pard \intbl
6287
{\f2 \row }\pard \qj\intbl {\f2 ...\cell }\pard \qj\intbl
6288
{\f2 ...\cell }\pard \qj\intbl {\f2 \cell }\pard \intbl
6289
{\f2 \row }\pard \qj\intbl {\f2 \cell }\pard \qj\intbl {\f2
6290
\cell }\pard \qj\intbl {\f2 \cell }\pard \intbl
6291
{\f2 \row }\pard \qj\intbl {\f2 _atom_site.cartn_x\cell }\pard \qj\intbl
6292
{\f2 _atom_site_cartn_x\cell }\pard \qj\intbl
6293
{\f2 atomic coordinates\cell }\pard \intbl
6294
{\f2 \row }\pard \qj\intbl {\f2 ...
6295
\cell }\pard \qj\intbl {\f2 ...\cell }\pard \qj\intbl
6296
{\f2 \cell }\pard \intbl {\f2 \row }\pard \qj\intbl
6297
{\f2 or\cell }\pard \qj\intbl {\f2 \cell }\pard \qj\intbl
6298
{\f2 \cell }\pard \intbl {\f2 \row }\pard \qj\intbl
6299
{\f2 _atom_site.fract_x\cell
6300
}\pard \qj\intbl {\f2 _atom_site_fract_x\cell }\pard \qj\intbl
6301
{\f2 \cell }\pard \intbl {\f2 \row }\pard \qj\intbl
6302
{\f2 ...\cell }\pard \qj\intbl {\f2 ...\cell }\pard \qj\intbl
6303
{\f2 \cell }\pard \intbl {\f2 \row }\pard \qj\intbl
6304
{\f2 \cell }\pard
6305
\qj\intbl {\f2 \cell }\pard \qj\intbl {\f2 \cell }\pard \intbl
6306
{\f2 \row }\pard \qj\intbl {\f2 _struct_conn.id\cell }\pard \qj\intbl
6307
{\f2 \cell }\pard \qj\intbl {\f2 bonds\cell }\pard \intbl
6308
{\f2 \row }\pard \qj\intbl {\f2 ...\cell }\pard
6309
\qj\intbl {\f2 \cell }\pard \qj\intbl {\f2 \cell }\pard \intbl
6310
{\f2 \row }\pard \qj\intbl {\f2 _geom_bond.atom_site_id_1\cell }\pard \qj\intbl
6311
{\f2 _geom_bond_atom_site_label_1\cell }\pard \qj\intbl {\f2 \cell }\pard \intbl
6312
{\f2 \row }\pard
6313
\qj\intbl {\f2 ...\cell }\pard \qj\intbl {\f2 ...\cell }\pard \qj\intbl
6314
{\f2 \cell }\pard \intbl {\f2 \row }\pard \qj\intbl {\f2 \cell }\pard \qj\intbl
6315
{\f2 \cell }\pard \qj\intbl {\f2 \cell }\pard \intbl {\f2 \row }\pard \qj\intbl
6316
{\f2
6317
_struct_conf.id\cell }\pard \qj\intbl {\f2 \cell }\pard \qj\intbl
6318
{\f2 helices, sheets, turns\cell }\pard \intbl {\f2 \row }\pard \qj\intbl
6319
{\f2 _struct_sheet_range.id\cell }\pard \qj\intbl {\f2 \cell }\pard \qj\intbl
6320
{\f2 \cell }\pard \intbl {\f2
6321
\row }\trowd \trgaph80\trleft-80
6322
\cellx3232\cellx6544\cellx8848\pard \qj\intbl
6323
{\f2 ...\cell }\pard \qj\intbl {\f2 \cell }\pard \qj\intbl
6324
{\f2 \cell }\pard \intbl {\f2 \row }\pard \qj {\f2 \par
6325
\par }
6326
A search is made through multiple data blocks for the desired tags, so {}
6327
a single dataset may be composed from multiple data blocks, but {}
6328
multiple data sets may not be stacked in the same file. {}
6329
\par\page\par
6330
+{\footnote doc}
6331
#{\footnote chmacspec}
6332
${\footnote Machine-Specific Support}
6333
{\fs24\b Machine-Specific Support}\par\par
6334
\par\par
6335
In the following sections, support for {}
6336
'{\uldb Monochrome X-Windows}{\v monochromexwindowssupport}', {}
6337
'{\uldb Tcl/Tk IPC}{\v tcltkipcsupport}', {}
6338
'{\uldb UNIX sockets based IPC}{\v unixsocketsbasedipc}', {}
6339
'{\uldb Compiling RasWin with Borland and MetroWerks}{\v compilingraswinwithborlandandmetrowerks}' {}
6340
are described. {}
6341
\par\page\par
6342
+{\footnote doc}
6343
#{\footnote monochromexwindowssupport}
6344
${\footnote Monochrome X-Windows Support}
6345
K{\footnote monochrome x-windows support}
6346
{\b Monochrome X-Windows Support}\par\par
6347
RasMol supports the many {}
6348
monochrome UNIX workstations typically found in academia, such as low-end {}
6349
SUN workstations and NCD X-terminals. The X11 version of RasMol (when {}
6350
compiled in 8 bit mode) now detects black and white X-Windows displays and {}
6351
enables dithering automatically. The use of run-time error diffusion dithering {}
6352
means that all display modes of RasMol are available when in monochrome {}
6353
mode. For best results, users should experiment with the set ambient {}
6354
command to ensure the maximum contrast in resulting images. {}
6355
\par\page\par
6356
+{\footnote doc}
6357
#{\footnote tcltkipcsupport}
6358
${\footnote Tcl/Tk IPC support}
6359
K{\footnote tcl/tk ipc support}
6360
{\b Tcl/Tk IPC support}\par\par
6361
Version 4 of Tk {}
6362
graphics library changed the protocol used to communicate between Tk {}
6363
applications. RasMol version 2.6 was modified such that it could {}
6364
communicate with both this new protocol and the previous version 3 protocol {}
6365
supported by RasMol v2.5. Although Tcl/Tk 3.x applications may only {}
6366
communicate with other 3.x applications and Tcl/Tk 4.x applications with other {}
6367
4.x applications, these changes allow RasMol to communicate between {}
6368
processes with both protocols (potentially concurrently). {}
6369
\par\page\par
6370
+{\footnote doc}
6371
#{\footnote unixsocketsbasedipc}
6372
${\footnote UNIX sockets based IPC}
6373
K{\footnote unix sockets based ipc}
6374
{\b UNIX sockets based IPC}\par\par
6375
The UNIX implementation of RasMol {}
6376
supports BSD-style socket communication. An identical socket mechanism is {}
6377
also being developed for VMS, Apple Macintosh and Microsoft Windows {}
6378
systems. This should allow RasMol to interactively display results of a {}
6379
computation on a remote host. The current protocol acts as a TCP/IP server on {}
6380
port 21069 that executes command lines until either the command {}
6381
'{\f2\b exit}' {}
6382
or the {}
6383
command {}
6384
'{\f2\b quit}' {}
6385
is typed. The command {}
6386
exit {}
6387
from the RasMol server, the command {}
6388
'{\f2\b quit}' {}
6389
both disconnects the current {}
6390
session and terminates RasMol. This functionality may be tested using the {}
6391
UNIX command {}
6392
'{\f2\b telnet <hostname> 21069}'. {}
6393
\par\page\par
6394
+{\footnote doc}
6395
#{\footnote compilingraswinwithborlandandmetrowerks}
6396
${\footnote Compiling RasWin with Borland and MetroWerks}
6397
K{\footnote compiling raswin with borland and metrowerks}
6398
{\b Compiling RasWin with Borland and MetroWerks}\par\par
6399
A number of changes were made to the {}
6400
source code in the transition from version 2.5 to 2.6 to allow {}
6401
the Microsoft Windows version of RasMol to compile {}
6402
using the Borland C/C++ compiler. These fixes include name changes for the {}
6403
standard library and special code to avoid a bug in _fmemset. {}
6404
Additional changes were made in the transition from 2.6 to 2.7 to {}
6405
allow compilation with the MetroWerks compilers. {}
6406
\par\page\par
6407
+{\footnote doc}
6408
#{\footnote chbib}
6409
${\footnote Bibliography}
6410
{\fs24\b Bibliography}\par\par
6411
\par\par
6412
{\f2\b Molecular Graphics} {}
6413
\par\par
6414
[1] Nelson Max, "Computer Representation of Molecular Surfaces", IEEE {}
6415
Computer Graphics and Applications, pp.21-29, August 1983. {}
6416
\par\par
6417
[2] Arthur M. Lesk, "Protein Architecture: A Practical Approach", IRL {}
6418
Press Publishers, 1991. {}
6419
\par\par
6420
{\f2\b Molecular Graphics Programs} {}
6421
\par\par
6422
[3] Per J. Kraulis, "MOLSCRIPT: A Program to Produce both Detailed and {}
6423
Schematic Plots of Protein Structures", Journal of Applied {}
6424
Crystallography, Vol.24, pp.946-950, 1991. {}
6425
\par\par
6426
[4] David Bacon and Wayne F. Anderson, "A Fast Algorithm for Rendering {}
6427
Space-Filling Molecule Pictures", Journal of Molecular Graphics, Vol.6, {}
6428
No.4, pp.219-220, December 1988. {}
6429
\par\par
6430
[5] David C. Richardson and Jane S. Richardson, "The Kinemage: A tool {}
6431
for Scientific Communication", Protein Science, Vol.1, No.1,pp.3-9, {}
6432
January 1992. {}
6433
\par\par
6434
[6] Mike Carson, "RIBBONS 2.0", Journal of Applied Crystallography, {}
6435
Vol.24, pp.958-961, 1991. {}
6436
\par\par
6437
[7] Conrad C. Huang, Eric F. Pettersen, Teri E. Klein, Thomas E. {}
6438
Ferrin and Robert Langridge, "Conic: A Fast Renderer for {}
6439
Space-Filling Molecules with Shadows", Journal of Molecular Graphics, {}
6440
Vol.9, No.4, pp.230-236, December 1991. {}
6441
\par\par
6442
{\f2\b Molecular Biology Algorithms} {}
6443
\par\par
6444
[8] Wolfgang Kabsch and Christian Sander, "Dictionary of Protein {}
6445
Secondary Structure: Pattern Recognition of Hydrogen-Bonded and {}
6446
Geometrical Features", Biopolymers, Vol.22, pp.2577-2637, 1983. {}
6447
\par\par
6448
[9] Michael L. Connolly, "Solvent-Accessible Surfaces of Proteins and Nucleic {}
6449
Acids", Science, Vol.221, No.4612, pp.709-713, August 1983. {}
6450
\par\par
6451
[10] Khaled Belhadj-Mostefa, Ron Poet and E. James Milner-White, {}
6452
"Displaying Inter-Main Chain Hydrogen Bond Patterns in Proteins", {}
6453
Journal of Molecular Graphics, Vol.9, No.3, pp.194-197, September 1991. {}
6454
\par\par
6455
[11] Mike Carson, "Ribbon Models of Macromolecules", Journal of {}
6456
Molecular Graphics, Vol.5, No.2, pp.103-106, June 1987. {}
6457
\par\par
6458
[12] Mike Carson and Charles E. Bugg, "Algorithm for Ribbon Models of {}
6459
Proteins", Journal of Molecular Graphics, Vol.4, No.2, pp.121-122, June {}
6460
1986. {}
6461
\par\par
6462
[13] H. Iijima, J. B. Dunbar Jr. and G. Marshall, "Calibration of {}
6463
Effective van der Waals Atomic Contact Radii for Proteins and {}
6464
Peptides", Proteins: Structure, Functions and Genetics, Vol.2, {}
6465
pp.330-339,1987. {}
6466
\par\par
6467
{\f2\b Graphics Algorithms} {}
6468
\par\par
6469
[14] J. Foley, A. van Dam, S. Feiner and J. Hughes, "Computer Graphics: {}
6470
Principles and Practice", 2nd Edition, Addison Wesley Publishers, 1990. {}
6471
\par\par
6472
[15] J. Cleary and G. Wyvill, "Analysis of an Algorithm for Fast Ray {}
6473
Tracing using Uniform Space Subdivision", The Visual Computer, Vol.4, {}
6474
pp.65-83, 1988. {}
6475
\par\par
6476
[16] Thomas Porter,"Spherical Shading", Computer Graphics Vol.12, ACM {}
6477
SIGGRAPH, pp.282-285, 1978. {}
6478
\par\par
6479
[17] Jean-Michel Cense, "Exact Visibility Calculation for Space-Filling {}
6480
Molecular Models", Journal of Molecular Graphics, Vol.9, No.3, {}
6481
pp.191-193, September 1991. {}
6482
\par\par
6483
[18] Chris Schafmeister, "Fast Algorithm for Generating CPK Images on {}
6484
Graphics Workstations", Journal of Molecular Graphics, Vol.8, No.4, {}
6485
pp.201-206, December 1990. {}
6486
\par\par
6487
[19] Bruce A. Johnson, "MSURF: A Rapid and General Program for the {}
6488
Representation of Molecular Surfaces", Journal of Molecular Graphics, {}
6489
Vol.5, No.3, pp.167-169, September 1987. {}
6490
\par\par
6491
{\f2\b File Formats} {}
6492
\par\par
6493
[20] Frances C. Bernstein et al., "The Protein Data Bank: A {}
6494
Computer-Based Archival File for Macromolecular Structures", Journal of {}
6495
Molecular Biology, Vol.112, pp.535-542, 1977. {}
6496
\par\par
6497
[21] Arthur Dalby, James G. Nourse, W. Douglas Hounshell, Ann K. I. {}
6498
Gushurst, David L. Grier, Burton A. Leland and John Laufer, "Description {}
6499
of Several Chemical File Formats Used by Computer Programs Developed at {}
6500
Molecular Design Limited", Journal of Chemical Information and Computer {}
6501
Sciences, Vol.32, No.3, pp.244-255, 1992. {}
6502
\par\par
6503
[22] Adobe Systems Inc., "PostScript Language Reference Manual", {}
6504
Addison-Wesley Publishers, Reading, Mass., 1985. {}
6505
\par\par
6506
[23] Philip E. Bourne et al., "The Macromolecular Crystallographic {}
6507
Information File (mmCIF)", Meth. Enzymol. (1997) 277, 571-590. {}
6508
\par\par
6509
[24] Sydney R. Hall, "The STAR File: a New Format for Electronic Data {}
6510
Transfer and Archiving", Journal of Chemical Information and Computer {}
6511
Sciences, Vol. 31, 326-333, 1991. {}
6512
\par\page\par
6513
+{\footnote doc}
6514
}
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