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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/rasmol.doc
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%% RasMol V2.7.4.2 Manual
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%% RasMol 2.7.4.2
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%% RasMol V2.7.5 Manual
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%% RasMol 2.7.5
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%% RasMol
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%% Molecular Graphics Visualisation Tool
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%% 19 November 2007 (rev. 17 March 2008)
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%% 13 June 2009 (rev. 17 July 2009)
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%%
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%% Based on RasMol 2.6 by Roger Sayle
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%% Biomolecular Structures Group, Glaxo Wellcome Research & Development,
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%% RasMol 2.7.4 Nov 07
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%% RasMol 2.7.4.1 Jan 08
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%% RasMol 2.7.4.2 Mar 08
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%% RasMol 2.7.5 Jun 09
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%% RasMol 2.7.5.1 Jul 09
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%%
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%% RasMol 2.7.3 incorporates changes by Clarice Chigbo, Ricky Chachra,
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%% and Mamoru Yamanishi. Work on RasMol 2.7.3 supported in part by
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%% grants DBI-0203064, DBI-0315281 and EF-0312612 from the U.S. National
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%% Science Foundation and grant DE-FG02-03ER63601 from the U.S. Department
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%% of Energy. RasMol 2.7.4 incorporates changes by G. Todorov, Nan Jia,
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%% N. Darakev, P. Kamburov, G. McQuillan, J. Jemilawon. Work on RasMol
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%% 2.7.4 supported in part by grant 1R15GM078077-01 from the National
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%% Institute of General Medical Sciences (NIGMS). The content is solely
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%% the responsibility of the authors and does not necessarily represent
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%% the official views of the funding organizations.
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%% RasMol 2.7.5 incorporates changes by T. Ikonen, G. McQuillan, N. Darakev
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%% and L. Andrews (via the neartree package). Work on RasMol 2.7.5
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%% supported in part by grant 1R15GM078077-01 from the National Institute
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%% of General Medical Sciences (NIGMS), U.S. National Institutes of Health
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%% and by grant ER63601-1021466-0009501 from the Office of Biological &
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%% Environmental Research (BER), Office of Science, U. S. Department of
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%% Energy. RasMol 2.7.4 incorporated changes by G. Todorov, Nan Jia,
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%% N. Darakev, P. Kamburov, G. McQuillan, and J. Jemilawon. Work on RasMol
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%% 2.7.4 supported in part by grant 1R15GM078077-01 from the NIGMS/NIH and
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%% grant ER63601-1021466-0009501 from BER/DOE. RasMol 2.7.3 incorporates
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%% changes by Clarice Chigbo, Ricky Chachra, and Mamoru Yamanishi. Work
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%% on RasMol 2.7.3 supported in part by grants DBI-0203064, DBI-0315281
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%% and EF-0312612 from the U.S. National Science Foundation and grant
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%% DE-FG02-03ER63601 from BER/DOE. The content is solely the responsibility
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%% of the authors and does not necessarily represent the official views of
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%% the funding organizations.
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%%
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%% The code for use of RasMol under GTK in RasMol 2.7.4.2 was written by
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%% Teemu Ikonen.
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%% The code for use of RasMol under GTK in RasMol 2.7.4.2 was written by
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%% Teemu Ikonen.
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%%
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%% and Incorporating Translations by
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%% Author Item Language
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%% This Release by
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%% Herbert J. Bernstein, Bernstein + Sons, P.O. Box 177, Bellport, NY, USA
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%% yaya@bernstein-plus-sons.com
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%% Copyright (C) Herbert J. Bernstein 1998-2008
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%% Copyright (C) Herbert J. Bernstein 1998-2009
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%%
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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
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%% and November 2007, January 2008 and March 2008 for RasMol version 2.7.4.
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%%
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%%
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%% Documentation Last Updated 22 March 2008
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%% Documentation Last Updated 17 July 2009
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%% Edited by Herbert J. Bernstein and Frances C. Bernstein
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%%
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%% Please read the file NOTICE for important notices which apply to this
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%% Initial screen for help file
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%%
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PTRasMol 2.7.4 is a molecular graphics program intended for the visualisation
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PTRasMol 2.7.5 is a molecular graphics program intended for the visualisation
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PTof proteins, nucleic acids and small molecules, based on Roger Sayles'
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PTRasMol_2.6. The program is aimed at display, teaching and generation of
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PTpublication quality images. RasMol runs on Microsoft Windows, Apple
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%% ASCII Text Headers
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%%
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TR R a s M o l v 2 . 7 . 4 . 1
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TR R a s M o l v 2 . 7 . 5
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TR =============================
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TR Molecular Graphics Visualisation Tool
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TR 19 November 2007 (rev. 17 March 2008)
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TR 13 June 2009 (rev. 17 July 2009)
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TR
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TR Based on RasMol 2.6 by Roger Sayle
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TR Biomolecular Structures Group, Glaxo Wellcome Research & Development,
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TR RasMol 2.7.4 Nov 07
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TR RasMol 2.7.4.1 Jan 08
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TR RasMol 2.7.4.2 Mar 08
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TR
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TR RasMol 2.7.3 incorporates changes by Clarice Chigbo, Ricky Chachra,
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TR and Mamoru Yamanishi. Work on RasMol 2.7.3 supported in part by
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TR grants DBI-0203064, DBI-0315281 and EF-0312612 from the U.S. National
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TR Science Foundation and grant DE-FG02-03ER63601 from the U.S. Department
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TR of Energy. RasMol 2.7.4 incorporates changes by G. Todorov, Nan Jia,
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TR N. Darakev, P. Kamburov, G. McQuillan, J. Jemilawon. Work on RasMol
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TR 2.7.4 supported in part by grant 1R15GM078077-01 from the National
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TR Institute of General Medical Sciences (NIGMS). The content is solely
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TR the responsibility of the authors and does not necessarily represent
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TR the official views of the funding organizations.
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TR
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TR The code for use of RasMol under GTK in RasMol 2.7.4.2 was written by
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TR Teemu Ikonen.
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TR RasMol 2.7.5 Jun 09
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TR RasMol 2.7.5.1 Jul 09
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TR
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TR RasMol 2.7.5 incorporates changes by T. Ikonen, G. McQuillan, N. Darakev
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TR and L. Andrews (via the neartree package). Work on RasMol 2.7.5
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TR supported in part by grant 1R15GM078077-01 from the National Institute
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TR of General Medical Sciences (NIGMS), U.S. National Institutes of Health
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TR and by grant ER63601-1021466-0009501 from the Office of Biological &
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TR Environmental Research (BER), Office of Science, U. S. Department of
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TR Energy. RasMol 2.7.4 incorporated changes by G. Todorov, Nan Jia,
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TR N. Darakev, P. Kamburov, G. McQuillan, and J. Jemilawon. Work on RasMol
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TR 2.7.4 supported in part by grant 1R15GM078077-01 from the NIGMS/NIH and
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TR grant ER63601-1021466-0009501 from BER/DOE. RasMol 2.7.3 incorporates
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TR changes by Clarice Chigbo, Ricky Chachra, and Mamoru Yamanishi. Work
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TR on RasMol 2.7.3 supported in part by grants DBI-0203064, DBI-0315281
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TR and EF-0312612 from the U.S. National Science Foundation and grant
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TR DE-FG02-03ER63601 from BER/DOE. The content is solely the responsibility
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TR of the authors and does not necessarily represent the official views of
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TR the funding organizations.
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TR
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TR The code for use of RasMol under GTK in RasMol 2.7.4.2 was written by
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TR Teemu Ikonen.
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TR
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TR and Incorporating Translations by
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TR Author Item Language
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TR This Release by
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TR Herbert J. Bernstein, Bernstein + Sons, P.O. Box 177, Bellport, NY, USA
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TR yaya@bernstein-plus-sons.com
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TR Copyright (C) Herbert J. Bernstein 1998-2008
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TR Copyright (C) Herbert J. Bernstein 1998-2009
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TR
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TR The original RasMol manual was created by Roger Sayle. In July 1996,
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TR Dr. Margaret Wong of the Chemistry Department, Swinburne University
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TR and November 2007, January 2008 and March 2008 for RasMol version 2.7.4.
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TR
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TR
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TR Documentation Last Updated 22 March 2008
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TR Documentation Last Updated 17 July 2009
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TR Edited by Herbert J. Bernstein and Frances C. Bernstein
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TR
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TR Please read the file NOTICE for important notices which apply to this
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%% UNIX man(1) Headers
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%%
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MR.PU
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MR.TH RASMOL 1 "March 2008"
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MR.TH RASMOL 1 "July 2009"
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MR.SH NAME
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MRrasmol \- Molecular Graphics Visualisation Tool v2.7.4.2
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MRrasmol \- Molecular Graphics Visualisation Tool v2.7.5
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%%
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%% VMS Help Headers
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RR}\deff0\fs20
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RR#{\footnote rasmol}
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RR${\footnote RasMol V2.7.4.2}
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RR${\footnote RasMol V2.7.5}
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RR+{\footnote doc}
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RR{\fs8 \par }{\fs28\b RasMol V2.7.4.2}{\fs8 \line }
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RR{\fs8 \par }{\fs28\b RasMol V2.7.5}{\fs8 \line }
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RR{\fs24\b Molecular Graphics Visualisation Tool}\line\pard
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RP
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%%
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RR{\fs16 \tab RasMol 2.7.3.1 \tab Apr 06 }\line
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RR{\fs16 \tab RasMol 2.7.4 \tab Nov 07 }\line
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RR{\fs16 \tab RasMol 2.7.4.1 \tab Jan 08 }\line
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RR{\fs16 \tab RasMol 2.7.4.2 \tab Mar 08 }
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RR{\fs16 \tab RasMol 2.7.4.2 \tab Mar 08 }\line
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RR{\fs16 \tab RasMol 2.7.5 \tab Jun 09 }\line
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RR{\fs16 \tab RasMol 2.7.5.1 \tab Jul 09 }
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RR{\fs8 \par\par }
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RR{\fs16 RasMol 2.7.3 incorporates changes by Clarice Chigbo, Ricky Chachra,}\line
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RR{\fs16 and Mamoru Yamanishi. Work on RasMol 2.7.3 supported in part by}\line
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RR{\fs16 grants DBI-0203064, DBI-0315281 and EF-0312612 from the U.S. National}\line
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RR{\fs16 Science Foundation and grant DE-FG02-03ER63601 from the U.S. Department}\line
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RR{\fs16 of Energy. RasMol 2.7.4 incorporates changes by G. Todorov, Nan Jia,}\line
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RR{\fs16 N. Darakev, P. Kamburov, G. McQuillan, J. Jemilawon. Work on RasMol}\line
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RR{\fs16 2.7.4 supported in part by grant 1R15GM078077-01 from the National}\line
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RR{\fs16 Institute of General Medical Sciences (NIGMS). The content is solely}\line
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RR{\fs16 the responsibility of the authors and does not necessarily represent}\line
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RR{\fs16 the official views of the funding organizations.}\line
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RR{\fs16 RasMol 2.7.5 incorporates changes by T. Ikonen, G. McQuillan, N. Darakev}\line
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RR{\fs16 and L. Andrews (via the neartree package). Work on RasMol 2.7.5}\line
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RR{\fs16 supported in part by grant 1R15GM078077-01 from the National Institute}\line
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RR{\fs16 of General Medical Sciences (NIGMS), U.S. National Institutes of Health}\line
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RR{\fs16 and by grant ER63601-1021466-0009501 from the Office of Biological &}\line
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RR{\fs16 Environmental Research (BER), Office of Science, U. S. Department of}\line
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RR{\fs16 Energy. RasMol 2.7.4 incorporated changes by G. Todorov, Nan Jia,}\line
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RR{\fs16 N. Darakev, P. Kamburov, G. McQuillan, and J. Jemilawon. Work on RasMol}\line
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RR{\fs16 2.7.4 supported in part by grant 1R15GM078077-01 from the NIGMS/NIH and}\line
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RR{\fs16 grant ER63601-1021466-0009501 from BER/DOE. RasMol 2.7.3 incorporates}\line
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RR{\fs16 changes by Clarice Chigbo, Ricky Chachra, and Mamoru Yamanishi. Work}\line
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RR{\fs16 on RasMol 2.7.3 supported in part by grants DBI-0203064, DBI-0315281}\line
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RR{\fs16 and EF-0312612 from the U.S. National Science Foundation and grant}\line
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RR{\fs16 DE-FG02-03ER63601 from BER/DOE. The content is solely the responsibility}\line
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RR{\fs16 of the authors and does not necessarily represent the official views of}\line
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RR{\fs16 the funding organizations.}\line
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RR{\fs8 \par\par }
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RR{\fs16 The code for use of RasMol under GTK in RasMol 2.7.4.2 was written by}\line
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RR{\fs16 Teemu Ikonen.}\line
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RTJanuary 2008 and March 2008 for RasMol version 2.7.4.
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RR}
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RR{\fs16 Documentation Last Updated 18 March 2008}\line
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RR{\fs16 Documentation Last Updated 17 July 2009}\line
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RR{\fs16 Edited by Herbert J. Bernstein and Frances C. Bernstein}
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RP
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RR{\fs16 Please read the file NOTICE for important notices which apply to this}\line
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HR<!doctype html public "-//IETF//DTD HTML 2.0//EN">
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HR<HTML>
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HR<HEAD>
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HR<title>RasMol V2.7.4 Manual</title>
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HR<title>RasMol V2.7.5 Manual</title>
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HR</HEAD>
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HR<BODY BACKGROUND="http://www.rasmol.org/software/rasmol/html_graphics/rasmolwallpaper.jpg">
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HR<font face="Helvetica,Arial,Times" size=3>
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HR<font color="#0808A0">
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HR<H1 ALIGN=CENTER>Manual<BR>
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HRRasMol 2.7.4.2</H1>
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HRRasMol 2.7.5</H1>
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HR<center>
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HR<table celpadding=0>
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HR<td valign=top bgcolor="#FFFFA0"><font face="Helvetica,Arial,Times" size=2>
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HR<li><a href=http://www.rasmol.org/software/RasMol_2.7.4.2_Windows_Installer.exe>RasMol
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HR2.7.4.2 Windows Installer</a> <br /> <br />
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HR<li><a href=http://www.rasmol.org/software/RasMol_2.7.4.2.tar.gz>RasMol
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HR2.7.4.2 Source Tarball</a><br /> <br />
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HR<li><a href=http://www.rasmol.org/software/RasMol_2.7.4.2_Manual.html>RasMol
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HR2.7.4.2 Manual</a><br /> <br />
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HR<li><a href=http://www.rasmol.org/software/RasMol_2.7.5_Windows_Installer.exe>RasMol
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HR2.7.5 Windows Installer</a> <br /> <br />
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HR<li><a href=http://www.rasmol.org/software/RasMol_2.7.5.tar.gz>RasMol
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HR2.7.5 Source Tarball</a><br /> <br />
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HR<li><a href=http://www.rasmol.org/software/RasMol_2.7.5_Manual.html>RasMol
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HR2.7.5 Manual</a><br /> <br />
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HR<li><a href=http://www.rasmol.org/donate.shtml>Donate to Support RasMol </a><br />
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HR<li><a href=http://www.rasmol.org/register.shtml>Register your RasMol</a><br />
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HR</ul>
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HR</center>
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HR<H3 ALIGN=CENTER>
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HRMolecular Graphics Visualisation Tool<BR>
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HR19 November 2007 (rev. 17 March 2008)<br />
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HR13 June 2009 (rev. 17 July 2009)<br />
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HR</H3>
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HR</font><font color="#000000">
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HR<CENTER>
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HR<td valign="top">© UC Regents/ModularCHEM<br>Consortium 1995, 1996
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HR<tr><td>Philippe Valadon<td>RasTop 1.3 August 2000<td>© Philippe Valadon 2000
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HR<tr><td valign="top">Herbert J. Bernstein<td>RasMol 2.7.0 March 1999<br>
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HRRasMol 2.7.1 June 1999<br>RasMol 2.7.1.1 January 2001<BR>
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HRRasMol 2.7.2 August 2000<br>RasMol 2.7.2.1 April 2001<BR>
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HRRasMol 2.7.2.1.1 January 2004<br>RasMol 2.7.3 February 2005<BR>
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HRRasMol 2.7.3.1 Apr 06<br>RasMol 2.7.4 November 2007<br>
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HRRasMol 2.7.4.1 January 2008<br>
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HRRasMol 2.7.4.2 March 2008<br>
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HR<td valign="top">© Herbert J. Bernstein 1998-2008
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HRRasMol 2.7.1 June 1999<br />RasMol 2.7.1.1 January 2001<br />
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HRRasMol 2.7.2 August 2000<br />RasMol 2.7.2.1 April 2001<br />
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HRRasMol 2.7.2.1.1 January 2004<br />RasMol 2.7.3 February 2005<br />
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HRRasMol 2.7.3.1 Apr 06<br>RasMol 2.7.4 November 2007<br />
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HRRasMol 2.7.4.1 January 2008<br />
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HRRasMol 2.7.4.2 March 2008<br />
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HRRasMol 2.7.5 June 2009<br />
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HRRasMol 2.7.5.1 July 2009<br />
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HR<td valign="top">© Herbert J. Bernstein 1998-2009
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HR</table>
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HR</CENTER>
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HR<P>
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HR RasMol 2.7.3 incorporates changes by Clarice Chigbo, Ricky Chachra,
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HR and Mamoru Yamanishi. Work on RasMol 2.7.3 supported in part by
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HR grants DBI-0203064, DBI-0315281 and EF-0312612 from the U.S. National
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HR Science Foundation and grant DE-FG02-03ER63601 from the U.S. Department
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HR of Energy. RasMol 2.7.4 incorporates changes by G. Todorov, Nan Jia,
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HR N. Darakev, P. Kamburov, G. McQuillan, J. Jemilawon. Work on RasMol
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HR 2.7.4 supported in part by grant 1R15GM078077-01 from the National
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HR Institute of General Medical Sciences (NIGMS). The content is solely
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HR the responsibility of the authors and does not necessarily represent
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HR the official views of the funding organizations.
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HRRasMol 2.7.5 incorporates changes by T. Ikonen, G. McQuillan, N. Darakev
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HRand L. Andrews (via the neartree package). Work on RasMol 2.7.5
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HRsupported in part by grant 1R15GM078077-01 from the National Institute
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HRof General Medical Sciences (NIGMS), U.S. National Institutes of Health
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HRand by grant ER63601-1021466-0009501 from the Office of Biological &
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HREnvironmental Research (BER), Office of Science, U. S. Department of
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HREnergy. RasMol 2.7.4 incorporated changes by G. Todorov, Nan Jia,
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HRN. Darakev, P. Kamburov, G. McQuillan, and J. Jemilawon. Work on RasMol
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HR2.7.4 supported in part by grant 1R15GM078077-01 from the NIGMS/NIH and
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HRgrant ER63601-1021466-0009501 from BER/DOE. RasMol 2.7.3 incorporates
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HRchanges by Clarice Chigbo, Ricky Chachra, and Mamoru Yamanishi. Work
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HRon RasMol 2.7.3 supported in part by grants DBI-0203064, DBI-0315281
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HRand EF-0312612 from the U.S. National Science Foundation and grant
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HRDE-FG02-03ER63601 from BER/DOE. The content is solely the responsibility
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HRof the authors and does not necessarily represent the official views of
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HRthe funding organizations.
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HR<P>
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HR The code for use of RasMol under GTK in RasMol 2.7.4.2 was written by
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HR Teemu Ikonen.
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HRThe code for use of RasMol under GTK in RasMol 2.7.4.2 was written by
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HRTeemu Ikonen.
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HR<P>
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HR<CENTER>
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HRand Incorporating Translations by
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HRyaya@bernstein-plus-sons.com
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HR</noscript>
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HR<BR>
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HRCopyright © Herbert J. Bernstein 1998-2008<BR>
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HRCopyright © Herbert J. Bernstein 1998-2009<BR>
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HR</CENTER>
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HRThe original RasMol manual was created by Roger Sayle. In July 1996,
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HRJanuary 2008 and March 2008 for RasMol version 2.7.4.
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HR<CENTER>Documentation Last Updated 12 November 2007<br>
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HR<CENTER>Documentation Last Updated 17 July 2009<br>
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HREdited by Herbert J. Bernstein and Frances C. Bernstein
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HR</CENTER>
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HR<H2 ALIGN=CENTER>IMPORTANT</H2>
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HRThis version is based directly on RasMol version 2.7.4,
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HRThis version is based directly on RasMol version 2.7.4.2,
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HRon RasMol version 2.7.4.1,
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HRon RasMol version 2.7.4,
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HRon RasMol version 2.7.3.1,
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HRon RasMol vesion 2.7.3, on RasMol version 2.7.2.1.1,
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HRon RasMol version 2.7.2, on RasMol version 2.7.1, on RasMol
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HR<td><a href="#connect">Connect</a>
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HR<td><a href="#spacefill">CPK</a>
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HR<td><a href="#cpknew">CPKnew</a>
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HR<td><a href="#defer">Defer</a>
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HR<td><a href="#define">Define</a>
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HR<td><a href="#depth">Depth</a>
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HR<td><a href="#dots">Dots</a>
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HR<tr><td><a href="#echo">Echo</a>
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HR<td><a href="#execute">Execute</a>
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HR<td><a href="#quit">Exit</a>
625
662
HR<td><a href="#french">French</a>
626
663
HR<td><a href="#hbonds">HBonds</a>
627
664
HR<td><a href="#help">Help</a>
628
HR<td><a href="#italian">Italian</a>
665
666
HR<tr><td><a href="#italian">Italian</a>
629
667
HR<td><a href="#japanese">Japanese</a>
630
631
HR<tr><td><a href="#label">Label</a>
668
HR<td><a href="#label">Label</a>
632
669
HR<td><a href="#load">Load</a>
633
670
HR<td><a href="#map">Map</a>
634
671
HR<td><a href="#molecule">Molecule</a>
635
672
HR<td><a href="#monitor">Monitor</a>
636
673
HR<td><a href="#notoggle">NoToggle</a>
637
HR<td><a href="#pause">Pause</a>
674
675
HR<tr><td><a href="#pause">Pause</a>
676
HR<td><a href="#play">Play</a>
638
677
HR<td><a href="#print">Print</a>
639
640
HR<tr><td><a href="#quit">Quit</a>
678
HR<td><a href="#quit">Quit</a>
679
HR<td><a href="#record">Record</a>
641
680
HR<td><a href="#refresh">Refresh</a>
642
681
HR<td><a href="#renumber">Renumber</a>
643
682
HR<td><a href="#reset">Reset</a>
644
HR<td><a href="#restrict">Restrict</a>
683
684
HR<tr><td><a href="#restrict">Restrict</a>
645
685
HR<td><a href="#ribbons">Ribbons</a>
646
686
HR<td><a href="#rotate">Rotate</a>
647
687
HR<td><a href="#save">Save</a>
648
649
HR<tr><td><a href="#script">Script</a>
688
HR<td><a href="#script">Script</a>
650
689
HR<td><a href="#select">Select</a>
651
690
HR<td><a href="#set">Set</a>
652
691
HR<td><a href="#show">Show</a>
653
HR<td><a href="#slab">Slab</a>
692
693
HR<tr><td><a href="#slab">Slab</a>
654
694
HR<td><a href="#script">Source</a>
655
695
HR<td><a href="#spacefill">Spacefill</a>
656
696
HR<td><a href="#spanish">Spanish</a>
657
658
HR<tr><td><a href="#ssbonds">SSBonds</a>
697
HR<td><a href="#ssbonds">SSBonds</a>
659
698
HR<td><a href="#star">Star</a>
660
699
HR<td><a href="#stereo">Stereo</a>
661
700
HR<td><a href="#strands">Strands</a>
662
HR<td><a href="#structure">Structure</a>
701
702
HR<tr><td><a href="#structure">Structure</a>
663
703
HR<td><a href="#surface">Surface</a>
664
704
HR<td><a href="#trace">Trace</a>
665
705
HR<td><a href="#translate">Translate</a>
666
667
HR<tr><td><a href="#unbond">UnBond</a>
706
HR<td><a href="#unbond">UnBond</a>
668
707
HR<td><a href="#wireframe">Wireframe</a>
669
708
HR<td><a href="#write">Write</a>
670
709
HR<td><a href="#zap">Zap</a>
671
HR<td><a href="#zoom">Zoom</a>
672
HR<td colspan=1>
710
711
HR<tr><td><a href="#zoom">Zoom</a>
712
HR<td colspan=7>
673
713
HR</table>
674
714
675
715
HR</center>
676
716
HR<li><a href="#chsetopt">Internal Parameters</a>
677
717
HR<center><table BORDER CELLPADDING=2>
718
678
719
HR<TR><TD><a href="#setambient">Ambient</a>
679
720
HR<TD><a href="#setaxes">Axes</a>
680
721
HR<TD><a href="#setbackground">Background</a>
683
724
HR<TD><a href="#setbonds">Bonds</a>
684
725
HR<TD><a href="#setboundbox">BoundBox</a>
685
726
HR<TD><a href="#setcartoon">Cartoon</a>
727
686
728
HR<TR><TD><a href="#setcisangle">CisAngle</A>
687
729
HR<TD><a href="#setdisplay">Display</a>
688
730
HR<TD><a href="#setfontsize">FontSize</a>
691
733
HR<TD><a href="#sethetero">Hetero</a>
692
734
HR<TD><a href="#sethourglass">HourGlass</a>
693
735
HR<TD><a href="#sethydrogen">Hydrogen</a>
736
694
737
HR<TR><TD><a href="#setkinemage">Kinemage</a>
695
738
HR<TD><a href="#setmenus">Menus</a>
696
739
HR<TD><a href="#setmonitor">Monitor</a>
697
740
HR<TD><a href="#setmouse">Mouse</a>
698
741
HR<TD><a href="#setpicking">Picking</a>
742
HR<TD><a href="#setplay">Play...</a>
699
743
HR<TD><a href="#setradius">Radius</a>
700
HR<TD><a href="#setshadepower">ShadePower</a>
744
HR<TD><a href="#setrecord">Record...</a>
745
746
HR<TR><TD><a href="#setshadepower">ShadePower</a>
701
747
HR<TD><a href="#setshadow">Shadow</a>
702
HR<TR><TD><a href="#setslabmode">SlabMode</a>
748
HR<TD><a href="#setslabmode">SlabMode</a>
703
749
HR<TD><a href="#setsolvent">Solvent</a>
704
750
HR<TD><a href="#setspecular">Specular</a>
705
751
HR<TD><a href="#setspecpower">SpecPower</a>
706
752
HR<TD><a href="#setstereo">Stereo</a>
707
753
HR<TD><a href="#setssbonds">SSBonds</a>
708
HR<TD><a href="#setstrands">Strands</a>
754
755
HR<TR><TD><a href="#setstrands">Strands</a>
709
756
HR<TD><a href="#settransparent">Transparent</a>
710
HR<TR><TD><a href="#setunitcell">UnitCell</a>
757
HR<TD><a href="#setunitcell">UnitCell</a>
711
758
HR<TD><a href="#setvectps">VectPS</a>
712
759
HR<TD><a href="#setwrite">Write</a>
713
HR<TD CELLSPAN=5>
760
HR<TD CELLSPAN=3>
714
761
HR</table></center>
715
762
716
763
HR<li><a href="#chexprs">Atom Expressions</a>
732
779
NRUC Regents/ModularCHEM Consortium 1995, 1996
733
780
NRRasTop 1.3 Copyright (C) Philippe Valadon 2000
734
781
NRVersion 2.7.0, 2.7.1, 2.7.1.1, 2.7.2, 2.7.2.1,
735
NR2.7.2.1.1, 2.7.3, 2.7.4, 2.7.4.1, 2.7.4.2 Mods
736
NRCopyright (C) Herbert J. Bernstein 1998-2008
782
NR2.7.2.1.1, 2.7.3, 2.7.4, 2.7.4.1, 2.7.4.2
783
NR2.7.5, 2.7.5.1 Mods
784
NRCopyright (C) Herbert J. Bernstein 1998-2009
737
785
NRrasmol@bernstein-plus-sons.com
738
786
RTRasMol Copyright \'a9 Roger Sayle 1992-1999\par
739
787
RTVersion 2.6x1 Mods Copyright \'a9 Arne Mueller 1998\par
740
788
RTVersions 2.5-ucb and 2.6-ucb Mods Copyright \'a9\par
741
789
RTUC Regents/ModularCHEM Consortium 1995, 1996\par
742
790
RTRasTop 1.3 Copyright \'a9 Philippe Valadon 2000\par
743
RTVersion 2.7.0, 2.7.1, 2.7.1.1, 2.7.2, 2.7.2.1, 2.7.2.1.1, 2.7.3, 2.7.3.1, 2.7.4, 2.7.4.1, 2.7.4.2 Mods\par
744
RTCopyright \'a9 Herbert J. Bernstein 1998-2008\par
791
RTVersion 2.7.0, 2.7.1, 2.7.1.1, 2.7.2, 2.7.2.1, 2.7.2.1.1\par
792
RT2.7.3, 2.7.3.1, 2.7.4, 2.7.4.1, 2.7.4.2, 2.7.5, 2.7.5.1 Mods\par
793
RTCopyright \'a9 Herbert J. Bernstein 1998-2009\par
745
794
RTrasmol@bernstein-plus-sons.com\par
746
795
HR<P><BR>RasMol Copyright © Roger Sayle 1992-1999
747
796
HR<BR>Version 2.6x1 Mods Copyright © Arne Mueller 1998
748
797
HR<BR>Versions 2.5-ucb and 2.6-ucb Mods Copyright ©
749
798
HRUC Regents/ModularCHEM Consortium 1995, 1996
750
799
HR<BR>RasTop 1.3 Copyright © Philippe Valadon 2000
751
HR<BR>Version 2.7.0, 2.7.1, 2.7.1.1, 2.7.2, 2.7.2.1, 2.7.2.1.1, 2.7.3, 2.7.3.1, 2.7.4, 2.7.4.1, 2.7.4.2 Mods
752
HRCopyright © Herbert J. Bernstein 1998-2008
800
HR<BR>Version 2.7.0, 2.7.1, 2.7.1.1, 2.7.2, 2.7.2.1, 2.7.2.1.1,
801
HR2.7.3, 2.7.3.1, 2.7.4, 2.7.4.1, 2.7.4.2, 2.7.5, 2.7.5.1 Mods
802
HRCopyright © Herbert J. Bernstein 1998-2009
753
803
HR<BR><address><a href="mailto:rasmol@rasmol.org">rasmol@rasmol.org</a></address>
754
804
AP
755
805
890
940
AB
891
941
892
942
NSCopyright
893
NR RasMol 2.7.4.2
943
NR RasMol 2.7.5
894
944
NR Molecular Graphics Visualisation Tool
895
NR 19 November 2007 (rev. 17 March 2008)
945
NR 13 June 2009 (rev. 17 July 2009)
896
946
NR
897
947
NR Based on RasMol 2.6 by Roger Sayle
898
948
NR Biomolecular Structures Group,Glaxo Wellcome Research & Development
921
971
NR RasMol 2.7.4 Nov 07
922
972
NR RasMol 2.7.4.1 Jan 08
923
973
NR RasMol 2.7.4.2 Mar 08
924
NR
925
NR RasMol 2.7.3 incorporates changes by Clarice Chigbo, Ricky Chachra,
926
NR and Mamoru Yamanishi. Work on RasMol 2.7.3 supported in part by
927
NR grants DBI-0203064, DBI-0315281 and EF-0312612 from the U.S. National
928
NR Science Foundation and grant DE-FG02-03ER63601 from the U.S. Department
929
NR of Energy. RasMol 2.7.4 incorporates changes by G. Todorov, Nan Jia,
930
NR N. Darakev, P. Kamburov, G. McQuillan, J. Jemilawon. Work on RasMol
931
NR 2.7.4 supported in part by grant 1R15GM078077-01 from the National
932
NR Institute of General Medical Sciences (NGMS). The content is solely
933
NR the responsibility of the authors and does not necessarily represent
934
NR the official views of the funding organizations.
935
NR
936
NR The code for use of RasMol under GTK in RasMol 2.7.4.2 was written by
937
NR Teemu Ikonen.
974
NR RasMol 2.7.5 Jun 09
975
NR RasMol 2.7.5.1 Jul 09
976
NR
977
NR RasMol 2.7.5 incorporates changes by T. Ikonen, G. McQuillan, N. Darakev
978
NR and L. Andrews (via the neartree package). Work on RasMol 2.7.5
979
NR supported in part by grant 1R15GM078077-01 from the National Institute
980
NR of General Medical Sciences (NIGMS), U.S. National Institutes of Health
981
NR and by grant ER63601-1021466-0009501 from the Office of Biological &
982
NR Environmental Research (BER), Office of Science, U. S. Department of
983
NR Energy. RasMol 2.7.4 incorporated changes by G. Todorov, Nan Jia,
984
NR N. Darakev, P. Kamburov, G. McQuillan, and J. Jemilawon. Work on RasMol
985
NR 2.7.4 supported in part by grant 1R15GM078077-01 from the NIGMS/NIH and
986
NR grant ER63601-1021466-0009501 from BER/DOE. RasMol 2.7.3 incorporates
987
NR changes by Clarice Chigbo, Ricky Chachra, and Mamoru Yamanishi. Work
988
NR on RasMol 2.7.3 supported in part by grants DBI-0203064, DBI-0315281
989
NR and EF-0312612 from the U.S. National Science Foundation and grant
990
NR DE-FG02-03ER63601 from BER/DOE. The content is solely the responsibility
991
NR of the authors and does not necessarily represent the official views of
992
NR the funding organizations.
993
NR
994
NR The code for use of RasMol under GTK in RasMol 2.7.4.2 was written by
995
NR Teemu Ikonen.
938
996
NR
939
997
NR and Incorporating Translations by
940
998
NR
959
1017
NR This Release by
960
1018
NR Herbert J. Bernstein, Bernstein + Sons, P.O. Box 177, Bellport, NY, USA
961
1019
NR yaya@bernstein-plus-sons.com
962
NR Copyright (C) Herbert J. Bernstein 1998-2008
1020
NR Copyright (C) Herbert J. Bernstein 1998-2009
963
1021
964
1022
RB
965
1023
977
1035
HR<a name="chcopying"><h2>Copying</h2></a>
978
1036
XR2 Copying
979
1037
AP
980
ATThis version is based directly on RasMol version 2.7.4.
1038
ATThis version is based directly on RasMol version 2.7.4.2,
1039
ATon RasMol verion 2.7.4.2, on RasMol version 2.7.4,
981
1040
ATon RasMol version 2.7.3.1, on RasMol version 2.7.3,
982
1041
ATon RasMol version 2.7.2.1.1, Rasmol version 2.7.2, RasMol
983
1042
ATversion 2.7.1.1 and RasTop version 1.3 and indirectly on
984
1043
ATthe RasMol 2.5-ucb and 2.6-ucb versions and version
985
1044
AT2.6_CIF.2, RasMol 2.6x1 and RasMol_2.6.4.
986
1045
AP
987
ATRasMol 2.7.4.2 may be distributed under the terms of the GNU
1046
ATRasMol 2.7.5 may be distributed under the terms of the GNU
988
1047
ATGeneral Public License (the GPL), see
989
1048
AP
990
1049
AT http://www.gnu.org/licenses/gpl.txt
992
1051
ATor the file GPL or type the command
993
1052
AXGPL help GPL
994
1053
AP
995
ATor RasMol 2.7.4.2 may be distributed under the RASMOL license.
1054
ATor RasMol 2.7.5 may be distributed under the RASMOL license.
996
1055
ATSee the file NOTICE
997
1056
ATor type the command
998
1057
AXRASLIC help RASLIC
1677
1736
NR Copyright (C) UC Regents/ModularCHEM Consortium 1995, 1996
1678
1737
NRRasTop 1.3 Copyright (C) Philippe Valadon 2000
1679
1738
NRVersion 2.7.0, 2.7.1, 2.7.1.1, 2.7.2, 2.7.2.1, 2.7.2.1.1,
1680
NR 2.7.3, 2.7.3.1, 2.7.4, 2.7.4.1, 2.7.4.2 Mods
1681
NR Copyright (C) Herbert J. Bernstein 1998-2008
1739
NR 2.7.3, 2.7.3.1, 2.7.4, 2.7.4.1, 2.7.4.2,
1740
NR 2.7.5, 2.7.5.1 Mods
1741
NR Copyright (C) Herbert J. Bernstein 1998-2009
1682
1742
NR (yaya@bernstein-plus-sons.com)
1683
1743
AB
1684
1744
2312
2372
ATignored except to separate keywords and their arguments.
2313
2373
AP
2314
2374
2375
ATAll commands may be prefixed by a parenthesized
2376
AXchexprs atom expression
2377
ATto temporarily select certain atoms just for the execution
2378
ATof that one command. After execution of the command, the
2379
ATprevious selection is restored except for the commands
2380
AXselect select
2381
AT,
2382
AXrestrict restrict
2383
ATand
2384
AXscript script.
2385
AP
2386
2315
2387
ATThe commands/keywords currently recognised by RasMol are given below.
2316
2388
PRType "help <command>" for more information on each RasMol function.
2317
2389
AP
2347
2419
HR<td><a href="#connect">Connect</a>
2348
2420
HR<td><a href="#spacefill">CPK</a>
2349
2421
HR<td><a href="#cpknew">CPKnew</a>
2422
HR<td><a href="#defer">Defer</a>
2350
2423
HR<td><a href="#define">Define</a>
2351
2424
HR<td><a href="#depth">Depth</a>
2352
HR<td><a href="#dots">Dots</a>
2353
2425
2354
HR<tr><td><a href="#echo">Echo</a>
2426
HR<tr><td><a href="#dots">Dots</a>
2427
HR<td><a href="#echo">Echo</a>
2355
2428
HR<td><a href="#english">English</a>
2429
HR<td><a href="#execute">Execute</a>
2356
2430
HR<td><a href="#quit">Exit</a>
2357
2431
HR<td><a href="#french">French</a>
2358
2432
HR<td><a href="#hbonds">HBonds</a>
2359
2433
HR<td><a href="#help">Help</a>
2360
HR<td><a href="#italian">Italian</a>
2361
HR<td><a href="#Japanese">Japanese</a>
2362
2434
2363
HR<tr><td><a href="#label">Label</a>
2435
HR<tr><td><a href="#italian">Italian</a>
2436
HR<td><a href="#japanese">Japanese</a>
2437
HR<td><a href="#label">Label</a>
2364
2438
HR<td><a href="#load">Load</a>
2365
2439
HR<td><a href="#map">Map</a>
2366
2440
HR<td><a href="#molecule">Molecule</a>
2367
2441
HR<td><a href="#monitor">Monitor</a>
2368
2442
HR<td><a href="#notoggle">NoToggle</a>
2369
HR<td><a href="#pause">Pause</a>
2443
2444
HR<tr><td><a href="#pause">Pause</a>
2445
HR<td><a href="#play">Play</a>
2370
2446
HR<td><a href="#print">Print</a>
2371
2372
HR<tr><td><a href="#quit">Quit</a>
2447
HR<td><a href="#quit">Quit</a>
2448
HR<td><a href="#record">Record</a>
2373
2449
HR<td><a href="#refresh">Refresh</a>
2374
2450
HR<td><a href="#renumber">Renumber</a>
2375
2451
HR<td><a href="#reset">Reset</a>
2376
HR<td><a href="#restrict">Restrict</a>
2452
2453
HR<tr><td><a href="#restrict">Restrict</a>
2377
2454
HR<td><a href="#ribbons">Ribbons</a>
2378
2455
HR<td><a href="#rotate">Rotate</a>
2379
2456
HR<td><a href="#save">Save</a>
2380
2381
HR<tr><td><a href="#script">Script</a>
2457
HR<td><a href="#script">Script</a>
2382
2458
HR<td><a href="#select">Select</a>
2383
2459
HR<td><a href="#set">Set</a>
2384
2460
HR<td><a href="#show">Show</a>
2385
HR<td><a href="#slab">Slab</a>
2461
2462
HR<tr><td><a href="#slab">Slab</a>
2386
2463
HR<td><a href="#script">Source</a>
2387
2464
HR<td><a href="#spacefill">Spacefill</a>
2388
2465
HR<td><a href="#spanish">Spanish</a>
2389
2390
HR<tr><td><a href="#ssbonds">SSBonds</a>
2466
HR<td><a href="#ssbonds">SSBonds</a>
2391
2467
HR<td><a href="#star">Star</a>
2392
2468
HR<td><a href="#stereo">Stereo</a>
2393
2469
HR<td><a href="#strands">Strands</a>
2394
HR<td><a href="#structure">Structure</a>
2470
2471
HR<tr><td><a href="#structure">Structure</a>
2395
2472
HR<td><a href="#surface">Surface</a>
2396
2473
HR<td><a href="#trace">Trace</a>
2397
2474
HR<td><a href="#translate">Translate</a>
2398
2399
HR<tr><td><a href="#unbond">UnBond</a>
2475
HR<td><a href="#unbond">UnBond</a>
2400
2476
HR<td><a href="#wireframe">Wireframe</a>
2401
2477
HR<td><a href="#write">Write</a>
2402
2478
HR<td><a href="#zap">Zap</a>
2403
HR<td><a href="#zoom">Zoom</a>
2479
2480
HR<tr><td><a href="#zoom">Zoom</a>
2481
HR<td colspan=7>
2404
2482
HR</table>
2405
2483
2406
2484
HR</center><hr>
2427
2505
RR\row\intbl
2428
2506
2429
2507
RR{\uldb cpknew}{\v cpknew}\cell
2508
RR{\uldb defer}{\v defer}\cell
2430
2509
RR{\uldb define}{\v define}\cell
2431
2510
RR{\uldb depth}{\v depth}\cell
2511
RR\row\intbl
2512
2513
2432
2514
RR{\uldb dots}{\v dots}\cell
2433
RR\row\intbl
2434
2435
2515
RR{\uldb echo}{\v echo}\cell
2436
2516
RR{\uldb english}{\v english}\cell
2517
RR{\uldb execute}{\v execute}\cell
2518
RR\row\intbl
2519
2437
2520
RR{\uldb exit}{\v exit}\cell
2438
2521
RR{\uldb french}{\v french}\cell
2439
RR\row\intbl
2440
2441
2522
RR{\uldb hbonds}{\v hbonds}\cell
2442
2523
RR{\uldb help}{\v help}\cell
2524
RR\row\intbl
2525
2443
2526
RR{\uldb italian}{\v italian}\cell
2444
2527
RR{\uldb japanese}{\v japanese}\cell
2445
RR\row\intbl
2446
2447
2528
RR{\uldb label}{\v label}\cell
2448
2529
RR{\uldb load}{\v load}\cell
2530
RR\row\intbl
2531
2449
2532
RR{\uldb map}{\v map}\cell
2450
2533
RR{\uldb molecule}{\v molecule}\cell
2451
RR\row\intbl
2452
2453
2534
RR{\uldb monitor}{\v pause}\cell
2454
2535
RR{\uldb notoggle}{\v notoggle}\cell
2536
RR\row\intbl
2537
2455
2538
RR{\uldb pause}{\v pause}\cell
2539
RR{\uldb pause}{\v play}\cell
2456
2540
RR{\uldb print}{\v print}\cell
2457
RR\row\intbl
2458
2459
2541
RR{\uldb quit}{\v quit}\cell
2542
RR\row\intbl
2543
2544
RR{\uldb record}{\v record}\cell
2460
2545
RR{\uldb refresh}{\v refresh}\cell
2461
2546
RR{\uldb renumber}{\v renumber}\cell
2462
2547
RR{\uldb reset}{\v reset}\cell
2840
2925
AXribbons ribbons,
2841
2926
AXlabel labels,
2842
2927
AXdots dots,
2843
AXhbonds hbonds
2928
AXhbonds hbonds,
2929
AXmap map,
2844
2930
ATand
2845
2931
AXssbonds ssbonds.
2846
2932
ATIf no object is specified, the default keyword
2872
2958
AXpotentialcolours electrostatic potential.
2873
2959
ATFor more information type
2874
2960
AXchcolours help colour <colour>.
2961
ATMap objects may be coloured by specific color of by nearest atom.
2875
2962
AB
2876
2963
2877
2964
PR?colourmode
2937
3024
AB
2938
3025
2939
3026
3027
ASDefer
3028
NRSyntax: defer <name> <command to defer>
3029
NR
3030
HR<pre>
3031
HRSyntax: defer <name> <command to defer>
3032
HR</pre><p>
3033
RR\tx1200
3034
RR{\f2\b Syntax:\tab
3035
RRdefer <name> <command to defer>\par
3036
RR}\pard\par
3037
3038
ATThe RasMol
3039
ACdefer
3040
ATcommand adds the command given to the macro with given name,
3041
ATif no name is given, the command is added to the macro with a
3042
ATblank name. The command
3043
ACzap
3044
ATis a special case. In that case the macro is erased. If no name is
3045
ATgiven the command must begin with a selection, e.g.
3046
AC'defer (selection).spacefill'
3047
AP
3048
ATThe deferred commands accumulated under the given name can be executed
3049
ATusing the
3050
AXexecute execute
3051
ATcommand
3052
3053
AB
3054
3055
3056
2940
3057
ASDefine
2941
3058
NRSyntax: define <identifier> <expression>
2942
3059
NR
3084
3201
AB
3085
3202
3086
3203
3204
ASExecute
3205
NRSyntax: execute <name>
3206
NR
3207
HR<pre>
3208
HRSyntax: execute <name>
3209
HR</pre><p>
3210
RR\tx1200
3211
RR{\f2\b Syntax:\tab
3212
RRexecute <name>\par
3213
RR}\pard\par
3214
3215
ATThe RasMol
3216
ACexecute
3217
ATcommand:
3218
AP
3219
AT1. saves the old poise of the molecule (translation,
3220
ATrotation and zoom)
3221
AP
3222
AT2. executes the specified macro suppressing both screen
3223
ATupdates and recording
3224
AP
3225
AT3. animates motion of the newly rendered molecule linearly
3226
ATfrom the old poise to the new poise
3227
AP
3228
ATThe macro must have been previously defined by calls to the
3229
AXdefer defer
3230
ATcommand.
3231
AP
3232
ATThe animation of the motion depends on the prior settings of the
3233
AXrecord record
3234
ATcommand.
3235
3236
3237
AB
3238
3087
3239
ASFrench
3088
3240
NRSyntax: French
3089
3241
NR
3380
3532
ACCIF,
3381
3533
ATor
3382
3534
ACmmCIF
3383
ATis assumed by default. Up to 5 molecules may be loaded at a time.
3535
ATis assumed by default. Up to 20 molecules may be loaded at a time.
3536
ATIf CHEM_COMP ligand models are included in an mmCIF file, they will be loaded
3537
ATas NMR models, first giving the all the NMR models for model
3538
ATcoordinates if specified and then giving all the NMR models for
3539
ATideal model coordinates.
3540
AP
3384
3541
ATTo delete a molecule prior to loading another use the RasMol
3385
3542
AXzap zap
3386
3543
ATcommand. To select a molecule for manipulation use the RasMol
3451
3608
all, next and new (or none) may also be used as map selectors.
3452
3609
AP
3453
3610
The map subcommands are
3611
AXmapcolour map colour,
3612
ATto colour a map according to a given colour scheme,
3454
3613
AXmapgenerate map generate,
3455
ATto generate a map from selected atoms,
3614
ATto generate a map from selected atoms based on pseudo-Gaussians,
3456
3615
AXmaplevel map level,
3457
3616
ATto set the contouring level for selected maps,
3458
3617
AXmapload map load,
3465
3624
ATto select one or more maps and to disable all others,
3466
3625
AXmapsave map save,
3467
3626
ATto save map information to a file,
3627
AXmapscale map scale,
3628
AXto control the scaling of pseudo-Gaussians when generating maps,
3468
3629
AXmapselect map select,
3469
3630
ATto select one or more maps,
3470
3631
AXmapshow map show,
3490
3651
3491
3652
AB
3492
3653
3654
PR?mapcolour
3655
ASMap colour
3656
NRSyntax: map {<map_selector>} colour <colour_scheme>
3657
NR
3658
HR<pre>
3659
HRSyntax: map {<map_selector>} colour <colour_scheme>
3660
HR
3661
HR</pre><p>
3662
RR\tx1200
3663
RR{\f2\b Syntax:\tab
3664
RRmap \{<map_selector>\} colour <colour_scheme>
3665
RR}\pard\par
3666
3667
ATThe RasMol
3668
ACmap colour
3669
ATcommand colours the selected maps according to the specified
3670
ATcolour scheme. The colour scheme may be a colour name or
3671
ATand RBG triple in brackets, or the keyword
3672
ACatom
3673
ATto cause the map points to be coloured by the color of the
3674
ATnearest atom.
3675
AB
3676
3677
3493
3678
PR?mapgenerate
3494
3679
ASMap generate
3495
NRSyntax: map {<map_selector>} generate dots
3496
NR map {<map_selector>} generate mesh
3497
NR map {<map_selector>} generate surface
3680
NRSyntax: map {<map_selector>} generate {LRsurf} dots
3681
NR map {<map_selector>} generate {LRsurf} mesh
3682
NR map {<map_selector>} generate {LRsurf} surface
3498
3683
NR
3499
3684
HR<pre>
3500
HRSyntax: map {<map_selector>} generate dots
3501
HR map {<map_selector>} generate mesh
3502
HR map {<map_selector>} generate surface
3685
HRSyntax: map {<map_selector>} generate {LRsurf} dots
3686
HR map {<map_selector>} generate {LRsurf} mesh
3687
HR map {<map_selector>} generate {LRsurf} surface
3503
3688
HR
3504
3689
HR</pre><p>
3505
3690
RR\tx1200
3506
3691
RR{\f2\b Syntax:\tab
3507
RRmap \{<map_selector>\} generate dots\line\tab
3508
RRmap \{<map_selector>\} generate mesh\line\tab
3509
RRmap \{<map_selector>\} generate surface
3692
RRmap \{<map_selector>\} generate \{LRsurf\} dots\line\tab
3693
RRmap \{<map_selector>\} generate \{LRsurf\} mesh\line\tab
3694
RRmap \{<map_selector>\} generate \{LRsurf\} surface
3510
3695
RR}\pard\par
3511
3696
3512
3697
ATThe RasMol
3513
3698
ACmap generate
3514
3699
ATcommand generates a map from whatever atoms are currently selected,
3515
3700
ATby summing electron densities approximated by Gaussian distributions.
3516
ATEach Gaussian has a height proportional to the atomic number of the
3517
ATelement type of the atom and a standard deviation determined by the
3518
ATmost recently specified spread or resolution. If a spread has been
3701
ATThe height of each Gaussian is determined by the setting of the
3702
AXmapscale map scale
3703
ATcommand.
3704
ATIn the default of map scale true, each Gaussian has a height proportional
3705
to the atomic number of the
3706
ATelement type of the atom.
3707
ATIf the optional 'LRSurf' parameter is given or if map scale false
3708
AThas been executed, each Gaussian is scaled so that
3709
ATthe Gaussian contour level 1 is at the van der Waals radius.
3710
ATIn either case a standard deviation determined by the
3711
ATmost recently specified spread or resolution is used. If a non-zero spread has been
3519
3712
ATgiven the radius of the atom is multiplied by the spread to find the
3520
3713
ATstandard deviation. The default is 2/3rds. If a resolution
3521
3714
AThas been given, the spread is inferred as 2/3rds of the resolution.
3715
AP
3522
3716
ATFor example, if the resolution is given as 1., and the atom in question
3523
3717
ATis a Carbon with a van der Waals radius of 468 RasMol units (1.87 Angstroms),
3524
3718
ATthe inferred spead is .6667, and the standard deviation of the Gaussian
3525
3719
ATis taken as 1.25 Angstroms.
3526
3720
AP
3721
ATIf the spread has been set to zero, the spread for each atom is determined
3722
ATfrom the van der Waals radius and the probe atom radius to simulate the
3723
ATeffect of a Lee-Richards surface.
3724
AP
3527
3725
ATIf no specific map was given by the map selector, the new map is
3528
3726
ATgiven the next available map number.
3529
3727
AP
3715
3913
ATmap and mask pair per data block.
3716
3914
AB
3717
3915
3916
PR?mapscale
3917
ASMap scale
3918
NRSyntax: map {<map_selector>} scale <boolean>
3919
NR
3920
HR<pre>
3921
HRSyntax: map {<map_selector>} scale <boolean>
3922
HR
3923
HR</pre><p>
3924
RR\tx1200
3925
RR{\f2\b Syntax:\tab
3926
RRmap \{<map_selector>\} scale <boolean>
3927
RR}\pard\par
3928
3929
ATThe RasMol
3930
ACmap scale
3931
ATcommand selects the scaling of pseudo-Gaussians in the
3932
AXmapgenerate map generate
3933
ATcommands.
3934
ATIn the default of map scale true, each Gaussian has a height proportional
3935
to the atomic number of the
3936
ATelement type of the atom.
3937
ATIf map scale false has been executed, each Gaussian is scaled so that
3938
ATthe Gaussian contour level 1 is at the van der Waals radius.
3939
ATIn either case a standard deviation determined by the
3940
ATmost recently specified spread or resolution is used.
3941
AB
3942
3943
3944
3718
3945
PR?mapselect
3719
3946
ASMap select
3720
NRSyntax: map {<map_selector>} select
3947
NRSyntax: map {<map_selector>} select {atom {within} {add} {<search_radius>}}
3721
3948
NR
3722
3949
HR<pre>
3723
HRSyntax: map {<map_selector>} select
3950
HRSyntax: map {<map_selector>} select {atom {within} {add} {search_radius}}
3724
3951
HR
3725
3952
HR</pre><p>
3726
3953
RR\tx1200
3727
3954
RR{\f2\b Syntax:\tab
3728
RRmap \{<map_selector>\} select
3955
RRmap \{<map_selector>\} select \{atom \{within\} \{add\} \{search_radius\}\}
3729
3956
RR}\pard\par
3730
3957
3731
3958
ATThe RasMol
3735
3962
AXmaprestrict map restrict
3736
3963
ATcommand, but does not disable the display of the
3737
3964
ATmaps that were not selected.
3965
AP
3966
ATIf the optional
3967
ACatom
3968
ATparameter is given, the command selects the atoms with centres closest to the
3969
ATmap points. The radius of the search may be specified by the parameter
3970
ACsearch_radius.
3971
ATThe default is to look for atoms within 4 Angstroms plus the probe radius.
3972
ATIf the optional
3973
ACwithin
3974
ATparameter is given, the new selection is taken from within the currently
3975
ATselected atoms. If the options
3976
ACadd
3977
ATparameter is given, the new selection is added to the currently selected atoms.
3978
ATThe default is to search within all atoms.
3979
3980
3738
3981
AB
3739
3982
3740
3983
3800
4043
ATcommand specifies the reciprocal of the number of
3801
4044
ATstandard deviations per radius to be used in
3802
4045
ATgenerating maps as sums of Gaussians centered
3803
ATon atomic positions. The default spead is one
4046
ATon atomic positions. The default spread is one
3804
4047
ATtwo thirds (i.e. each radius covers 1.5 standard deviations).
4048
AP
4049
ATIf the spread has been set to zero, the spread for each atom is determined
4050
ATfrom the van der Waals radius and the probe atom radius to simulate the
4051
ATeffect of a Lee-Richards surface.
3805
4052
AB
3806
4053
3807
4054
3980
4227
HTwhilst a script is suspended at a pause.
3981
4228
AB
3982
4229
4230
ASPlay
4231
NRSyntax: play {from <time>} {until <time>} {{on|off|eject} {<type>} <medium>}
4232
NR
4233
HR<pre>
4234
HRSyntax: play {from <time>} {until <time>} {{on|off|eject} {<type>} <medium>}
4235
HR</pre><p>
4236
RR\tx1200
4237
RR{\f2\b Syntax:\tab
4238
RRprint play \{from <time>\} \{until <time>\} \{\{on|off|eject\} \{<type>\} <medium>\}\par
4239
RR}\pard\par
4240
4241
ATThe RasMol
4242
ACplay
4243
ATcommand specifies the recording medium from which to play back a movie.
4244
ATThe playback frame start time is given in seconds to millisecond precision.
4245
ATSince we are working on computers, the medium is specified as a set of files,
4246
ATeach marked with the playback frame start time in milliseconds as part of the
4247
ATname. The place in the name at which to look for the playback frame start
4248
ATtime in milliseconds is marked by the characters "ssssss" with an
4249
ATappropriate number of digits. RasMol accepts either upper or lower case
4250
ATs's or decimal digits to mark the place for the time. The play off and play
4251
ATeject commands effectively remove the specified medium from use. If no medium
4252
ATis specified, play off suspends playing and play on resumes playing.
4253
ATNormally play starts immediately and runs to the end of the medium. However,
4254
ATif play off and/or or some combination of play from and play until is entered
4255
ATbefore
4256
AC'play type medium',
4257
ATthose settings will be used.
4258
AP
4259
ATAs of release 2.7.5, RasMol support play from scripts and data files.
4260
4261
AB
4262
4263
3983
4264
ASPrint
3984
4265
NRSyntax: print
3985
4266
NR
4036
4317
ATterminates all nested levels of scripts.
4037
4318
AB
4038
4319
4320
ASRecord
4321
NRSyntax: record {from <time>} {until <time>} {{on|off} {<type>} <medium>}
4322
NR record {mouse|motion|appearance} {on|off}
4323
NR
4324
HR<pre>
4325
HRSyntax: record {from <time>} {until <time>} {{on|off} {<type>} <medium>}
4326
HR record {mouse|motion|appearance} {on|off}
4327
HR</pre><p>
4328
RR\tx1200
4329
RR{\f2\b Syntax:\tab
4330
RRprint record \{from <time>\} \{until <time>\} \{\{on|off\} \{<type>\} <medium>\}\par
4331
RR\tab record \{mouse|motion|appearance\} \{on|off\}
4332
RR}\pard\par
4333
4334
ATThe RasMol
4335
ACrecord
4336
ATcommand specifies the recording medium to hold the movie. Since we are
4337
ATworking on computers, the medium is specified as a template for a set of
4338
ATfiles, each marked with the playback frame start time in milliseconds
4339
AT(rather than as seconds to avoid embedding a decimal point) as part of
4340
ATthe name. The place in the name to be replaced with the playback frame
4341
ATstart time in milliseconds is marked by the characters "ssssss" with
4342
ATan appropriate number of digits. RasMol accepts either upper or lower case
4343
ATs's or decimal digits to mark the place for the time. The record off
4344
ATcommands remove the specified medium from use. If no medium is specified,
4345
ATrecord off suspends recording and record on resumes recording with the
4346
ATnext available time on the same medium. The screen is the default medium
4347
ATand is, by default, on. Writing to disk must be explicitly specified so
4348
ATthat the disk does not get filled up unintentionally. The type of a
4349
ATrecording medium may be an image type such as gif, pict or png to record
4350
ATthe actual screen images or script to record the RasMol commands used to
4351
ATgenerate the frames.
4352
AP
4353
ATNormally recording starts at playback frame start time 0 seconds.
4354
ATA non-zero starting time in seconds can be specified with the
4355
AC'record from'
4356
ATcommand as in
4357
AC'record from 25'
4358
ATor
4359
AC'record from 37.25'
4360
ATto help in organizing scenes of movies to be assembled later in an
4361
ATappropriate order.
4362
ATThe
4363
AC'record until'
4364
ATcommand allows an upper limit to be set on recording time in seconds.
4365
ATThe default is to have no limit. Issuing the commands
4366
AP
4367
ACrecord from 600
4368
AP
4369
ACrecord until 1800
4370
AP
4371
ATwould result in a 20 minute movie segment intended to start 10
4372
ATminutes into a longer movie.
4373
ATThese commands allow control over rewriting selected time segments.
4374
AB
4375
4376
4377
4039
4378
ASRefresh
4040
4379
NRSyntax: refresh
4041
4380
NR
4140
4479
ATrepresentations in the non-selected region.
4141
4480
AP
4142
4481
4143
ATType "help expression" for more information on RasMol atom expressions.
4482
ATType "help expression" for more information on RasMol atom expressions or
4483
ATsee section
4484
AXchexprs Atom Expressions.
4144
4485
AB
4145
4486
4146
4487
4377
4718
ATparameters.
4378
4719
AP
4379
4720
4380
ATType "help expression" for more information on RasMol atom expressions.
4721
ATType "help expression" for more information on RasMol atom expressions or
4722
ATsee section
4723
AXchexprs Atom Expressions.
4381
4724
AB
4382
4725
4383
4726
ASSet
4421
4764
HR<TD><a href="#setbonds">Bonds</a>
4422
4765
HR<TD><a href="#setboundbox">BoundBox</a>
4423
4766
HR<TD><a href="#setcartoon">Cartoon</a>
4767
4424
4768
HR<TR><TD><a href="#setcisangle">CisAngle</A>
4425
4769
HR<TD><a href="#setdisplay">Display</a>
4426
4770
HR<TD><a href="#setfontsize">FontSize</a>
4429
4773
HR<TD><a href="#sethetero">Hetero</a>
4430
4774
HR<TD><a href="#sethourglass">HourGlass</a>
4431
4775
HR<TD><a href="#sethydrogen">Hydrogen</a>
4776
4432
4777
HR<TR><TD><a href="#setkinemage">Kinemage</a>
4433
4778
HR<TD><a href="#setmenus">Menus</a>
4434
4779
HR<TD><a href="#setmonitor">Monitor</a>
4435
4780
HR<TD><a href="#setmouse">Mouse</a>
4436
4781
HR<TD><a href="#setpicking">Picking</a>
4782
HR<TD><a href="#setplay">Play...</a>
4437
4783
HR<TD><a href="#setradius">Radius</a>
4438
HR<TD><a href="#setshadepower">ShadePower</a>
4784
HR<TD><a href="#setrecord">Record...</a>
4785
4786
HR<TR><TD><a href="#setshadepower">ShadePower</a>
4439
4787
HR<TD><a href="#setshadow">Shadow</a>
4440
HR<TR><TD><a href="#setslabmode">SlabMode</a>
4788
HR<TD><a href="#setslabmode">SlabMode</a>
4441
4789
HR<TD><a href="#setsolvent">Solvent</a>
4442
4790
HR<TD><a href="#setspecular">Specular</a>
4443
4791
HR<TD><a href="#setspecpower">SpecPower</a>
4444
4792
HR<TD><a href="#setstereo">Stereo</a>
4445
4793
HR<TD><a href="#setssbonds">SSBonds</a>
4446
HR<TD><a href="#setstrands">Strands</a>
4794
4795
HR<TR><TD><a href="#setstrands">Strands</a>
4447
4796
HR<TD><a href="#settransparent">Transparent</a>
4448
HR<TR><TD><a href="#setunitcell">UnitCell</a>
4797
HR<TD><a href="#setunitcell">UnitCell</a>
4449
4798
HR<TD><a href="#setvectps">VectPS</a>
4450
4799
HR<TD><a href="#setwrite">Write</a>
4451
HR<TD CELLSPAN=5>
4800
HR<TD CELLSPAN=3>
4452
4801
HR</table></center>
4453
4802
4454
4803
4480
4829
RR{\uldb mouse}{\v setmouse}\cell
4481
4830
RR\row\intbl
4482
4831
RR{\uldb picking}{\v setpicking}\cell
4832
RR{\uldb play...}{\v setplay}\cell
4483
4833
RR{\uldb radius}{\v setradius}\cell
4834
RR{\uldb record...}{\v setrecord}\cell
4835
RR\row\intbl
4484
4836
RR{\uldb shadepower}{\v setshadepower}\cell
4485
4837
RR{\uldb shadow}{\v setshadow}\cell
4486
RR\row\intbl
4487
4838
RR{\uldb slabmode}{\v setslabmode}\cell
4488
4839
RR{\uldb solvent}{\v setsolvent}\cell
4840
RR\row\intbl
4489
4841
RR{\uldb specular}{\v setspecular}\cell
4490
4842
RR{\uldb specpower}{\v setspecpower}\cell
4491
RR\row\intbl
4492
4843
RR{\uldb ssbonds}{\v setssbonds}\cell
4493
4844
RR{\uldb stereo}{\v setstereo}\cell
4845
RR\row\intbl
4494
4846
RR{\uldb strands}{\v setstrands}\cell
4495
4847
RR{\uldb transparent}{\v settransparent}\cell
4496
RR\row\intbl
4497
4848
RR{\uldb unitcell}{\v setunitcell}\cell
4498
4849
RR{\uldb vectps}{\v setvectps}\cell
4850
RR\row\intbl
4499
4851
RR{\uldb write}{\v setwrite}\cell
4500
4852
RR\cell
4853
RR\cell
4854
RR\cell
4501
4855
RR\row}
4502
4856
RR\pard\par\trowd
4503
4857
AB
5317
5671
NR cisangle display fontsize fontstroke
5318
5672
NR hbond hetero hourglass hydrogen
5319
5673
NR kinemage menus monitor mouse
5320
NR picking radius shadow slabmode
5674
MR picking play.fps radius record.aps
5675
NR record.dwell record.fps shadow slabmode
5321
5676
NR solvent specular specpower stereo
5322
5677
NR ssbonds strands transparent unitcell
5323
5678
NR vectps write
5331
5686
HR<TD><a href="#setbonds">Bonds</a>
5332
5687
HR<TD><a href="#setboundbox">BoundBox</a>
5333
5688
HR<TD><a href="#setcartoon">Cartoon</a>
5689
5334
5690
HR<TR><TD><a href="#setcisangle">CisAngle</A>
5335
5691
HR<TD><a href="#setdisplay">Display</a>
5336
5692
HR<TD><a href="#setfontsize">FontSize</a>
5339
5695
HR<TD><a href="#sethetero">Hetero</a>
5340
5696
HR<TD><a href="#sethourglass">HourGlass</a>
5341
5697
HR<TD><a href="#sethydrogen">Hydrogen</a>
5698
5342
5699
HR<TR><TD><a href="#setkinemage">Kinemage</a>
5343
5700
HR<TD><a href="#setmenus">Menus</a>
5344
5701
HR<TD><a href="#setmonitor">Monitor</a>
5345
5702
HR<TD><a href="#setmouse">Mouse</a>
5346
5703
HR<TD><a href="#setpicking">Picking</a>
5704
HR<TD><a href="#setplay">Play...</a>
5347
5705
HR<TD><a href="#setradius">Radius</a>
5348
HR<TD><a href="#setshadepower">ShadePower</a>
5706
HR<TD><a href="#setrecord">Record...</a>
5707
5708
HR<TR><TD><a href="#setshadepower">ShadePower</a>
5349
5709
HR<TD><a href="#setshadow">Shadow</a>
5350
HR<TR><TD><a href="#setslabmode">SlabMode</a>
5710
HR<TD><a href="#setslabmode">SlabMode</a>
5351
5711
HR<TD><a href="#setsolvent">Solvent</a>
5352
5712
HR<TD><a href="#setspecular">Specular</a>
5353
5713
HR<TD><a href="#setspecpower">SpecPower</a>
5354
5714
HR<TD><a href="#setstereo">Stereo</a>
5355
5715
HR<TD><a href="#setssbonds">SSBonds</a>
5356
HR<TD><a href="#setstrands">Strands</a>
5716
5717
HR<TR><TD><a href="#setstrands">Strands</a>
5357
5718
HR<TD><a href="#settransparent">Transparent</a>
5358
HR<TR><TD><a href="#setunitcell">UnitCell</a>
5719
HR<TD><a href="#setunitcell">UnitCell</a>
5359
5720
HR<TD><a href="#setvectps">VectPS</a>
5360
5721
HR<TD><a href="#setwrite">Write</a>
5361
HR<TD CELLSPAN=5>
5722
HR<TD CELLSPAN=3>
5362
5723
HR</table></center>
5363
5724
5364
5725
5391
5752
RR{\uldb mouse}{\v setmouse}\cell
5392
5753
RR\row\intbl
5393
5754
RR{\uldb picking}{\v setpicking}\cell
5755
RR{\uldb play...}{\v setplay}\cell
5394
5756
RR{\uldb radius}{\v setradius}\cell
5757
RR{\uldb record...}{\v setrecord}\cell
5758
RR\row\intbl
5395
5759
RR{\uldb shadepower}{\v setshadepower}\cell
5396
5760
RR{\uldb shadow}{\v setshadow}\cell
5397
RR\row\intbl
5398
5761
RR{\uldb slabmode}{\v setslabmode}\cell
5399
5762
RR{\uldb solvent}{\v setsolvent}\cell
5763
RR\row\intbl
5400
5764
RR{\uldb specular}{\v setspecular}\cell
5401
5765
RR{\uldb specpower}{\v setspecpower}\cell
5402
RR\row\intbl
5403
5766
RR{\uldb ssbonds}{\v setssbonds}\cell
5404
5767
RR{\uldb stereo}{\v setstereo}\cell
5768
RR\row\intbl
5405
5769
RR{\uldb strands}{\v setstrands}\cell
5406
5770
RR{\uldb transparent}{\v settransparent}\cell
5407
RR\row\intbl
5408
5771
RR{\uldb unitcell}{\v setunitcell}\cell
5409
5772
RR{\uldb vectps}{\v setvectps}\cell
5773
RR\row\intbl
5410
5774
RR{\uldb write}{\v setwrite}\cell
5411
5775
RR\cell
5776
RR\cell
5777
RR\cell
5412
5778
RR\row}
5413
5779
RR\pard\par\trowd
5414
5780
6243
6609
AB
6244
6610
6245
6611
6612
PR?setplay
6613
ASSet Play
6614
RRK{\footnote play}
6615
NRSyntax: set play.fps {<value>}
6616
NR
6617
HR<pre>
6618
HRSyntax: set play.fps {<value>}
6619
HR</pre><p>
6620
RR\tx1200
6621
RR{\f2\b Syntax:\tab
6622
RRset play.fps \{<value>\}\par
6623
RR}\pard\par
6624
6625
ATThe RasMol
6626
ACset play.fps
6627
ATcommand gives the number of frames per second for playback by the
6628
AXplay play
6629
ATcommand (default 24 frames per second).
6630
AP
6631
ATIn the current release of RasMol, the play timing is not controlled
6632
ATby this parameter.
6633
AB
6634
6635
6246
6636
PR?radius
6247
6637
ASSet Radius
6248
6638
RRK{\footnote radius}
6292
6682
ATto its new default value.
6293
6683
AB
6294
6684
6685
PR?setrecord
6686
ASSet Record
6687
RRK{\footnote play}
6688
NRSyntax: set record.aps {<value>}
6689
NR set record.fps {<value>}
6690
NR set record.dwell {<value>}
6691
NR
6692
HR<pre>
6693
HRSyntax: set record.aps {<value>}
6694
HR set record.fps {<value>}
6695
HR set record.dwell {<value>}
6696
HR</pre><p>
6697
RR\tx1200
6698
RR{\f2\b Syntax:\tab
6699
RRset record.aps \{<value>\}\par
6700
RR\tab set record.fps \{<value>\}
6701
RR\tab set record.dwell \{<value>\}
6702
RR}\pard\par
6703
6704
ATThe RasMol
6705
ACset record.aps
6706
ATgives the maximum on-screen velocity in Angstroms per second in animating
6707
ARtranslations, rotations and zooms (default 10 A/second).
6708
AP
6709
ATThe RasMol
6710
ACset record.aps
6711
ATcommand gives number of frames per second for recording by the
6712
AXrecord record
6713
ATcommand (default 24 frames per second).
6714
AP
6715
ATThe RasMol
6716
ACset record.dwell
6717
ATcommand sets the time in seconds to dwell on a change in appearance
6718
AT(default .5 sec).
6719
AB
6720
6295
6721
6296
6722
PR?shadepower
6297
6723
ASSet ShadePower
10596
11022
HR<br />
10597
11023
HR</CENTER>
10598
11024
HR<HR>
10599
HRUpdated 18 March 2008.<BR>
11025
HRUpdated 21 July 2009.<BR>
10600
11026
HRHerbert J. Bernstein<BR>
10601
11027
HRBernstein + Sons, 5 Brewster Lane, Bellport, NY 11713-2803, USA<BR>
10602
11028
HR<script language="javascript" type="text/javascript">
Loggerhead is a web-based interface for Breezy
Version: 2.0.1