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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.man
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.PU
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.TH RASMOL 1 "July 2009"
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.SH NAME
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rasmol \- Molecular Graphics Visualisation Tool v2.7.5
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.SH SYNOPSIS
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.B rasmol
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.RB "[\|" \-nodiplay "\|]"
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.RB "[\|\&[\|" "\-"\c
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.I "format"\c
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.RB "\|]"
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.I filename\c
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\&\|]
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.RB "[\|" "\-script "\c
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.I scriptfile\c
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\&\|]
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.SH FORMATS
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.PD 0
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.TP 12
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.B \-pdb
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Protein Data Bank
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.TP
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.B \-mdl
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MDL's MOL File Format
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.TP
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.B \-mol2
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Tripos' Sybyl MOL2 Format
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.TP
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.B \-xyz
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MSC's XYZ (XMol) Format
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.TP
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.B \-mopac
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MOPAC Input or Output File Format
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.TP
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.B \-alchemy
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Alchemy File Format
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.TP
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.B \-charmm
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CHARMm File Format
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.TP
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.B \-cif
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IUCr CIF or CIF File Format
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.PD
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.SH NOTICES
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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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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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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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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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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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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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Please type the RasMol commands
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.B help copying,
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.B help general,
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.B help IUCR,
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.B help CBFlib,
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and
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.B help CIFPARSE
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for applicable notices. Please type
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.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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.B help oldnotice.
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.SH COPYING
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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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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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89
http://www.gnu.org/licenses/gpl.txt
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or the file GPL or type the command
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.B help GPL
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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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.B help RASLIC
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99
.TP
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.B GPL
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GNU GENERAL PUBLIC LICENSE
102
Version 2, June 1991
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Copyright (C) 1989, 1991 Free Software Foundation, Inc.
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59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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Everyone is permitted to copy and distribute verbatim copies
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of this license document, but changing it is not allowed.
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Preamble
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The licenses for most software are designed to take away your
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freedom to share and change it. By contrast, the GNU General Public
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License is intended to guarantee your freedom to share and change free
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software--to make sure the software is free for all its users. This
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General Public License applies to most of the Free Software
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Foundation's software and to any other program whose authors commit to
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using it. (Some other Free Software Foundation software is covered by
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the GNU Library General Public License instead.) You can apply it to
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your programs, too.
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When we speak of free software, we are referring to freedom, not
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price. Our General Public Licenses are designed to make sure that you
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We protect your rights with two steps: (1) copyright the software, and
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How to Apply These Terms to Your New Programs
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Gnomovision version 69, Copyright (C) year name of author
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Yoyodyne, Inc., hereby disclaims all copyright interest in the program
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`Gnomovision' (which makes passes at compilers) written by James Hacker.
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<signature of Ty Coon>, 1 April 1989
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Ty Coon, President of Vice
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consider it more useful to permit linking proprietary applications with the
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.TP
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.B RASLIC
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If you do not use the GPL, the following license terms apply:
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RasMol License
446
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Even though the authors of the various documents and software found here
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greatly appreciate hearing of any problems you may encounter, the programs
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THE RESPONSIBILITY FOR ANY ADVERSE CONSEQUENCES FROM THE USE OF PROGRAMS OR
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DOCUMENTS OR ANY FILE OR FILES CREATED BY USE OF THE PROGRAMS OR DOCUMENTS
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LIES SOLELY WITH THE USERS OF THE PROGRAMS OR DOCUMENTS OR FILE OR FILES AND
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Subject to your acceptance of the conditions stated above, and your respect
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going to make any modifications or create derived works, you are given
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following:
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1. Either include the complete documentation, especially the file
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NOTICE, with what you distribute or provide a clear indication where
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people can get a copy of the documentation; and
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original authors properly; and
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3. Please do not give anyone the impression that the original
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If you would like to use major pieces of RasMol in some other program,
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are encouraged to do so. In addition to the things we discussed above,
480
please do the following:
481
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4. Please explain in your documentation how what you did differs
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from this version of RasMol; and
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5. Please make your modified source code available.
486
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This version of RasMol is _not_ in the public domain, but it is given
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freely to the community in the hopes of advancing science. If you make
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changes, please make them in a responsible manner, and please offer us
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the opportunity to include those changes in future versions of RasMol.
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.TP
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.B General Notice
494
The following notice applies to this work as a whole and to the works
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* Creative endeavors depend on the lively exchange of ideas. There are laws
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* THE RESPONSIBILITY FOR ANY ADVERSE CONSEQUENCES FROM THE USE OF PROGRAMS
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DOCUMENTS LIES SOLELY WITH THE USERS OF THE PROGRAMS OR DOCUMENTS OR FILE
532
OR FILES AND NOT WITH AUTHORS OF THE PROGRAMS OR DOCUMENTS.
533
534
See the files GPL and RASLIC for two alternate ways to license this
535
package.
536
537
.TP
538
.B RasMol V2.6 Notice
539
The following notice applies to RasMol V 2.6 and older RasMol versions.
540
541
Information in this document is subject to change without notice and
542
does not represent a commitment on the part of the supplier. This package
543
is sold/distributed subject to the condition that it shall not, by way
544
of trade or otherwise, be lent, re-sold, hired out or otherwise
545
circulated without the supplier's prior consent, in any form of
546
packaging or cover other than that in which it was produced. No
547
part of this manual or accompanying software may be reproduced,
548
stored in a retrieval system on optical or magnetic disk, tape or
549
any other medium, or transmitted in any form or by any means,
550
electronic, mechanical, photocopying, recording or otherwise for
551
any purpose other than the purchaser's personal use.
552
553
This product is not to be used in the planning, construction,
554
maintenance, operation or use of any nuclear facility nor the
555
flight, navigation or communication of aircraft or ground support
556
equipment. The author shall not be liable, in whole or in part, for
557
any claims or damages arising from such use, including death,
558
bankruptcy or outbreak of war.
559
560
.TP
561
.B IUCR Policy
562
.B The IUCr Policy for the Protection and the Promotion of the STAR File and
563
.B CIF Standards for Exchanging and Archiving Electronic Data.
564
565
.B Overview
566
567
The Crystallographic Information File (CIF)[1] is a standard for information
568
interchange promulgated by the International Union of Crystallography
569
(IUCr). CIF (Hall, Allen & Brown, 1991) is the recommended method for
570
submitting publications to Acta Crystallographica Section C and reports of
571
crystal structure determinations to other sections of Acta Crystallographica
572
and many other journals. The syntax of a CIF is a subset of the more general
573
STAR File[2] format. The CIF and STAR File approaches are used increasingly
574
in the structural sciences for data exchange and archiving, and are having a
575
significant influence on these activities in other fields.
576
577
.B Statement of intent
578
579
The IUCr's interest in the STAR File is as a general data interchange
580
standard for science, and its interest in the CIF, a conformant derivative
581
of the STAR File, is as a concise data exchange and archival standard for
582
crystallography and structural science.
583
584
.B Protection of the standards
585
586
To protect the STAR File and the CIF as standards for interchanging and
587
archiving electronic data, the IUCr, on behalf of the scientific community,
588
589
* holds the copyrights on the standards themselves,
590
591
* owns the associated trademarks and service marks, and
592
593
* holds a patent on the STAR File.
594
595
These intellectual property rights relate solely to the interchange formats,
596
not to the data contained therein, nor to the software used in the
597
generation, access or manipulation of the data.
598
599
.B Promotion of the standards
600
601
The sole requirement that the IUCr, in its protective role, imposes on
602
software purporting to process STAR File or CIF data is that the following
603
conditions be met prior to sale or distribution.
604
605
* Software claiming to read files written to either the STAR File or the
606
CIF standard must be able to extract the pertinent data from a file
607
conformant to the STAR File syntax, or the CIF syntax, respectively.
608
609
* Software claiming to write files in either the STAR File, or the CIF,
610
standard must produce files that are conformant to the STAR File
611
syntax, or the CIF syntax, respectively.
612
613
* Software claiming to read definitions from a specific data dictionary
614
approved by the IUCr must be able to extract any pertinent definition
615
which is conformant to the dictionary definition language (DDL)[3]
616
associated with that dictionary.
617
618
The IUCr, through its Committee on CIF Standards, will assist any developer
619
to verify that software meets these conformance conditions.
620
621
.B Glossary of terms
622
623
[1] CIF:
624
625
is a data file conformant to the file syntax defined at
626
http://www.iucr.org/iucr-top/cif/spec/index.html
627
628
[2] STAR File:
629
630
is a data file conformant to the file syntax defined at
631
http://www.iucr.org/iucr-top/cif/spec/star/index.html
632
633
[3] DDL:
634
635
is a language used in a data dictionary to define data items in terms
636
of "attributes". Dictionaries currently approved by the IUCr, and the
637
DDL versions used to construct these dictionaries, are listed at
638
http://www.iucr.org/iucr-top/cif/spec/ddl/index.html
639
640
Last modified: 30 September 2000
641
642
IUCr Policy Copyright (C) 2000 International Union of Crystallography
643
644
.TP
645
.B CBFLIB
646
The following Disclaimer Notice applies to CBFlib V0.1, from which this code
647
in part is derived.
648
649
* The items furnished herewith were developed under the sponsorship of the
650
U.S. Government. Neither the U.S., nor the U.S. D.O.E., nor the Leland
651
Stanford Junior University, nor their employees, makes any warranty,
652
express or implied, or assumes any liability or responsibility for
653
accuracy, completeness or usefulness of any information, apparatus, product
654
or process disclosed, or represents that its use will not infringe
655
privately-owned rights. Mention of any product, its manufacturer, or
656
suppliers shall not, nor is it intended to, imply approval, disapproval,
657
or fitness for any particular use. The U.S. and the University at all times
658
retain the right to use and disseminate the furnished items for any purpose
659
whatsoever.
660
661
Notice 91 02 01
662
663
.TP
664
.B CIFPARSE
665
Portions of this software are loosely based on the CIFPARSE software package
666
from the NDB at Rutgers University. See
667
668
http://ndbserver.rutgers.edu/NDB/mmcif/software
669
670
CIFPARSE is part of the NDBQUERY application, a program component of the
671
Nucleic Acid Database Project [ H. M. Berman, W. K. Olson, D. L. Beveridge,
672
J. K. Westbrook, A. Gelbin, T. Demeny, S. H. Shieh, A. R. Srinivasan, and B.
673
Schneider. (1992). The Nucleic Acid Database: A Comprehensive Relational
674
Database of Three-Dimensional Structures of Nucleic Acids. Biophys J., 63,
675
751-759.], whose cooperation is gratefully acknowledged, especially in the
676
form of design concepts created by J. Westbrook.
677
678
Please be aware of the following notice in the CIFPARSE API:
679
680
This software is provided WITHOUT WARRANTY OF MERCHANTABILITY OR FITNESS
681
FOR A PARTICULAR PURPOSE OR ANY OTHER WARRANTY, EXPRESS OR IMPLIED. RUTGERS
682
MAKE NO REPRESENTATION OR WARRANTY THAT THE SOFTWARE WILL NOT INFRINGE ANY
683
PATENT, COPYRIGHT OR OTHER PROPRIETARY RIGHT.
684
685
.SH DESCRIPTION
686
RasMol is a molecular graphics program intended for the visualisation of
687
proteins, nucleic acids and small molecules.
688
The program is aimed at display, teaching and generation of
689
publication quality images. RasMol runs on wide range of architectures
690
and operating systems including Microsoft Windows, Apple
691
Macintosh, UNIX and VMS systems. UNIX and VMS versions require an 8, 24 or
692
32 bit colour X Windows display (X11R4 or later). The X Windows version of
693
RasMol provides optional support for a hardware dials box and accelerated
694
shared memory communication (via the XInput and MIT-SHM extensions)
695
if available on the current X Server.
696
697
The program reads in a
698
molecule coordinate file and interactively displays the molecule on the
699
screen in a variety of colour schemes and molecule representations. Currently
700
available representations include depth-cued wireframes, 'Dreiding' sticks,
701
spacefilling (CPK) spheres, ball and stick, solid and strand biomolecular
702
ribbons, atom labels and dot surfaces.
703
704
Up to 5 molecules may be loaded and displayed at once. Any one or all of
705
the molecules may be rotated and translated.
706
707
The RasMol help facility can be accessed by typing "help <topic>" or "help
708
<topic> <subtopic>" from the command line. A complete list of RasMol commands
709
may be displayed by typing "help commands". A single question mark may also
710
be used to abbreviate the keyword "help". Please type "help notices" for
711
important notices.
712
713
.SH COMMANDS
714
RasMol allows the execution of interactive commands typed at the
715
.B RasMol>
716
prompt in the terminal window. Each command must be given on
717
a separate line. Keywords are case insensitive and may be entered in
718
either upper or lower case letters. All whitespace characters are
719
ignored except to separate keywords and their arguments.
720
721
All commands may be prefixed by a parenthesized
722
.B atom expression
723
to temporarily select certain atoms just for the execution
724
of that one command. After execution of the command, the
725
previous selection is restored except for the commands
726
.B select
727
,
728
.B restrict
729
and
730
.B script.
731
732
The commands/keywords currently recognised by RasMol are given below.
733
734
.TP
735
.B Backbone
736
The RasMol
737
.B backbone
738
command permits the representation of a polypeptide
739
backbone as a series of bonds connecting the adjacent alpha carbons of
740
each amino acid in a chain. The display of these backbone 'bonds' is
741
turned on and off by the command parameter in the same way as with the
742
.B wireframe
743
command. The command
744
.B backbone off
745
turns off the selected 'bonds', and
746
.B backbone on
747
or with a number turns them on. The number can be used
748
to specify the cylinder radius of the representation in either Angstrom
749
or RasMol units. A parameter value of 500 (2.0 Angstroms) or above
750
results in a "Parameter value too large" error. Backbone objects may be
751
coloured using the RasMol
752
.B colour backbone
753
command.
754
755
The reserved word backbone is also used as a predefined set ("help sets")
756
and as a parameter to the
757
.B set hbond
758
and
759
.B set ssbond
760
commands. The
761
RasMol command
762
.B trace
763
renders a smoothed backbone, in contrast to
764
.B backbone
765
which connects alpha carbons with straight lines.
766
767
The backbone may be displayed with dashed lines by use of the
768
.B backbone dash
769
command.
770
771
.TP
772
.B Background
773
The RasMol
774
.B background
775
command is used to set the colour of the "canvas" background. The
776
colour may be given as either a colour name or a comma separated
777
triple of Red, Green and Blue (RGB) components enclosed in square
778
brackets. Typing the command
779
.B help colours
780
will give a list of the predefined colour names recognised by RasMol.
781
When running under X Windows, RasMol also recognises colours in the
782
X server's colour name database.
783
784
The
785
.B background
786
command is synonymous with the RasMol
787
.B set background
788
command.
789
790
.TP
791
.B Bond
792
The RasMol command
793
.B bond <number> <number> +
794
adds the designated bond to the drawing, increasing the bond order
795
if the bond already exists. The command
796
.B bond <number> <number> pick
797
selects the two atoms specified by the atom serial numbers
798
as the two ends of a bond around which the
799
.B rotate bond <angle>
800
command will be applied. If no bond exists, it is created.
801
802
Rotation around a previously picked bond may be specified by the
803
.B rotate bond <angle>
804
command, or may also be controlled with the mouse, using the
805
.B bond rotate on/off
806
or the equivalent
807
.B rotate bond on/off
808
commands.
809
810
.TP
811
.B Bulgarian
812
The RasMol
813
.B Bulgarian
814
command sets the menus and messages to the Bulgarian versions.
815
816
This command may not work correctly unless appropriate fonts
817
have been installed. The commands
818
.B Bulgarian,
819
.B Chinese,
820
.B English,
821
.B French,
822
.B Italian,
823
.B Russian
824
and
825
.B Spanish
826
may be used to select Bulgarian, Chinese, English, French,
827
Italian, Japanese, Russian and Spanish menus and messages if the
828
appropriate fonts have been installed.
829
830
.TP
831
.B Cartoon
832
The RasMol
833
.B cartoon
834
command does a display of a molecule
835
.B ribbons
836
as Richardson (MolScript) style protein
837
.B cartoons,
838
implemented as thick (deep) ribbons. The
839
easiest way to obtain a cartoon representation of a protein is
840
to use the
841
.B Cartoons
842
option on the
843
.B Display
844
menu. The
845
.B cartoon
846
command represents the currently selected residues
847
as a deep ribbon with width specified by the command's argument.
848
Using the command without a parameter results in the ribbon's
849
width being taken from the protein's secondary structure,
850
as described in the
851
.B ribbons
852
command. By default, the C-termini of beta-sheets are displayed
853
as arrow heads. This may be enabled and disabled using the
854
.B set cartoons
855
command.
856
The depth of the cartoon may be adjusted using the
857
.B set cartoons <number>
858
command. The
859
.B set cartoons
860
command without any parameters returns these two options
861
to their default values.
862
863
.TP
864
.B Centre
865
The RasMol
866
.B centre
867
command defines the point about which the
868
.B rotate
869
command and the scroll bars rotate the current molecule. Without a
870
parameter the centre command resets the centre of rotation to be the
871
centre of gravity of the molecule. If an atom expression is specified,
872
RasMol rotates the molecule about the centre of gravity of the set of
873
atoms specified by the expression. Hence, if a single atom is specified
874
by the expression, that atom will remain 'stationary' during rotations.
875
876
Type
877
.B help expression
878
for more information on RasMol atom expressions.
879
880
Alternatively the centring may be given as a comma separated triple of
881
[CenX, CenY, CenZ] offsets in RasMol units (1/250 of an Angstrom) from
882
the centre of gravity. The triple must be enclosed in square brackets.
883
884
The optional forms
885
.B centre ... translate
886
and
887
.B centre ... center
888
may be used to specify use of a translated centre of rotation (not
889
necessarily in the centre of the canvas) or a centre of rotation
890
which is placed at the centre of the canvas. Starting with
891
RasMol 2.7.2, the default is
892
to center the new axis on the canvas.
893
894
.TP
895
.B Chinese
896
The RasMol
897
.B Chinese
898
command sets the menus and messages to the Chinese versions.
899
900
This command may not work correctly unless appropriate fonts
901
have been installed. The commands
902
.B Bulgarian,
903
.B Chinese,
904
.B English,
905
.B French,
906
.B Italian,
907
.B Russian
908
and
909
.B Spanish
910
may be used to select Bulgarian, Chinese, English, French,
911
Italian, Japanese, Russian and Spanish menus and messages if the
912
appropriate fonts have been installed.
913
914
.TP
915
.B Clipboard
916
The RasMol
917
.B clipboard
918
command places a copy of the currently displayed image on the local
919
graphics 'clipboard'. Note: this command is not yet supported on
920
UNIX or VMS machines. It is intended to make transfering images
921
between applications easier under Microsoft Windows or on an Apple
922
Macintosh.
923
924
When using RasMol on a UNIX or VMS system this functionality may be
925
achieved by generating a raster image in a format that can be read
926
by the receiving program using the RasMol
927
.B write
928
command.
929
930
.TP
931
.B Colour
932
Colour the atoms (or other objects) of the selected region. The colour may
933
be given as either a colour name or a comma separated triple of Red, Green
934
and Blue (RGB) components enclosed in square brackets. Typing the command
935
.B help colours
936
will give a list of all the predefined colour names recognised
937
by RasMol.
938
939
Allowed objects are
940
.B atoms,
941
.B bonds,
942
.B backbone,
943
.B ribbons,
944
.B labels,
945
.B dots,
946
.B hbonds,
947
.B map,
948
and
949
.B ssbonds.
950
If no object is specified, the default keyword
951
.B atom
952
is assumed.
953
Some colour schemes are defined for certain object types. The colour scheme
954
.B none
955
can be applied to all objects except atoms and dots, stating that the selected
956
objects have no colour of their own, but use the colour of their associated
957
atoms (i.e. the atoms they connect).
958
.B Atom
959
objects can also be coloured by
960
.B alt,
961
.B amino,
962
.B chain,
963
.B charge,
964
.B cpk,
965
.B group,
966
.B model,
967
.B shapely,
968
.B structure,
969
.B temperature
970
or
971
.B user.
972
Hydrogen bonds can also be coloured by
973
.B type
974
and dot surfaces can also be coloured by
975
.B electrostatic potential.
976
For more information type
977
.B help colour <colour>.
978
Map objects may be coloured by specific color of by nearest atom.
979
980
.TP
981
.B ColourMode
982
ColourMode allows the user to switch between using the new
983
.B colour
984
method. At present, the new coloring technique is the same as
985
the old one, but to preserve compatibility for older scripts
986
it may be wise to add a "colormode on" near the top of your
987
script somewhere, if the script was designed for version 2.7.3
988
of RasMol or earlier. The new color method, when completed,
989
aims to fix a few bugs in the coloring routines.
990
991
.TP
992
.B Connect
993
The RasMol
994
.B connect
995
command is used to force RasMol to (re)calculate the connectivity
996
of the current molecule.
997
If the original input file contained connectivity information, this
998
is discarded. The command
999
.B connect false
1000
uses a fast heuristic
1001
algorithm that is suitable for determining bonding in large
1002
bio-molecules such as proteins and nucleic acids. The command
1003
.B connect true
1004
uses a slower more accurate algorithm based upon
1005
covalent radii that is more suitable to small molecules containing
1006
inorganic elements or strained rings. If no parameters are given,
1007
RasMol determines which algorithm to use based on the number of atoms
1008
in the input file. Greater than 255 atoms causes RasMol to use the
1009
faster implementation. This is the method used to determine bonding,
1010
if necessary, when a molecule is first read in using the
1011
.B load
1012
command.
1013
1014
.TP
1015
.B Defer
1016
The RasMol
1017
.B defer
1018
command adds the command given to the macro with given name,
1019
if no name is given, the command is added to the macro with a
1020
blank name. The command
1021
.B zap
1022
is a special case. In that case the macro is erased. If no name is
1023
given the command must begin with a selection, e.g.
1024
.B defer (selection).spacefill
1025
1026
The deferred commands accumulated under the given name can be executed
1027
using the
1028
.B execute
1029
command
1030
1031
.TP
1032
.B Define
1033
The RasMol
1034
.B define
1035
command allows the user to associate an arbitrary set of atoms with a
1036
unique identifier. This allows the definition of user-defined sets. These
1037
sets are declared statically, i.e. once defined the contents of the set
1038
do not change, even if the expression defining them depends on the
1039
current transformation and representation of the molecule.
1040
1041
.TP
1042
.B Depth
1043
The RasMol
1044
.B depth
1045
command enables, disables or positions the back-clipping plane of the
1046
molecule. The program only draws those portions of the
1047
molecule that are closer to the viewer than the clipping plane.
1048
Integer values range from zero at the very back of the molecule to
1049
100 which is completely in front of the molecule. Intermediate values
1050
determine the percentage of the molecule to be drawn.
1051
1052
This command interacts with the
1053
.B slab <value>
1054
command, which clips to the front of a given z-clipping plane.
1055
1056
.TP
1057
.B Dots
1058
The RasMol
1059
.B dots
1060
command is used to generate a van der Waals' dot surface around the
1061
currently selected atoms. Dot surfaces display regularly spaced points
1062
on a sphere of van der Waals' radius about each selected atom. Dots that
1063
would are 'buried' within the van der Waals' radius of any other atom
1064
(selected or not) are not displayed.
1065
The command
1066
.B dots on
1067
deletes any existing dot surface and generates a dots surface around
1068
the currently selected atom set with a default dot density of 100. The
1069
command
1070
.B dots off
1071
deletes any existing dot surface. The dot density may be
1072
specified by providing a numeric parameter between 1 and 1000. This
1073
value approximately corresponds to the number of dots on the surface
1074
of a medium sized atom.
1075
1076
By default, the colour of each point on a dot surface is the colour
1077
of its closest atom at the time the surface is generated. The colour
1078
of the whole dot surface may be changed using the
1079
.B colour dots
1080
command.
1081
1082
.TP
1083
.B Echo
1084
The RasMol
1085
.B echo
1086
command is used to display a message in the RasMol command/terminal
1087
window. The string parameter may optionally be delimited in double
1088
quote characters. If no parameter is specified, the
1089
.B echo
1090
command displays a blank line. This command is particularly useful
1091
for displaying text from within a RasMol
1092
.B script
1093
file.
1094
1095
.TP
1096
.B English
1097
The RasMol
1098
.B English
1099
command sets the menus and messages to the English versions.
1100
1101
This command may not work correctly unless appropriate fonts
1102
have been installed. The commands
1103
.B Bulgarian,
1104
.B Chinese,
1105
.B English,
1106
.B French,
1107
.B Italian,
1108
.B Russian
1109
and
1110
.B Spanish
1111
may be used to select Bulgarian, Chinese, English, French,
1112
Italian, Japanese, Russian and Spanish menus and messages if the
1113
appropriate fonts have been installed.
1114
1115
.TP
1116
.B Execute
1117
The RasMol
1118
.B execute
1119
command:
1120
1121
1. saves the old poise of the molecule (translation,
1122
rotation and zoom)
1123
1124
2. executes the specified macro suppressing both screen
1125
updates and recording
1126
1127
3. animates motion of the newly rendered molecule linearly
1128
from the old poise to the new poise
1129
1130
The macro must have been previously defined by calls to the
1131
.B defer
1132
command.
1133
1134
The animation of the motion depends on the prior settings of the
1135
.B record
1136
command.
1137
1138
.TP
1139
.B French
1140
The RasMol
1141
.B French
1142
command sets the menus and messages to the French versions.
1143
1144
This command may not work correctly unless appropriate fonts
1145
have been installed. The commands
1146
.B Bulgarian,
1147
.B Chinese,
1148
.B English,
1149
.B French,
1150
.B Italian,
1151
.B Russian
1152
and
1153
.B Spanish
1154
may be used to select Bulgarian, Chinese, English, French,
1155
Italian, Japanese, Russian and Spanish menus and messages if the
1156
appropriate fonts have been installed.
1157
1158
.TP
1159
.B HBonds
1160
The RasMol
1161
.B hbond
1162
command is used to represent the hydrogen bonding of the protein
1163
molecule's backbone. This information is useful in assessing the
1164
protein's secondary structure. Hydrogen bonds are represented as
1165
either dotted lines or cylinders between the donor and acceptor
1166
residues. The first time the
1167
.B hbond
1168
command is used, the program searches the structure of the
1169
molecule to find hydrogen bonded residues and reports the number of bonds
1170
to the user. The command
1171
.B hbonds on
1172
displays the selected 'bonds' as dotted lines, and the
1173
.B hbonds off
1174
turns off their display. The colour of hbond objects may be changed
1175
by the
1176
.B colour hbond
1177
command. Initially, each hydrogen bond has the colours of its connected
1178
atoms.
1179
1180
By default the dotted lines are drawn between the accepting oxygen and
1181
the donating nitrogen. By using the
1182
.B set hbonds
1183
command the alpha carbon positions of the appropriate residues may be
1184
used instead. This is especially useful when examining proteins in
1185
backbone representation.
1186
1187
.TP
1188
.B Help
1189
The RasMol
1190
.B help
1191
command provides on-line help on the given topic.
1192
1193
.TP
1194
.B Italian
1195
The RasMol
1196
.B Italian
1197
command sets the menus and messages to the Italian versions.
1198
1199
This command may not work correctly unless appropriate fonts
1200
have been installed. The commands
1201
.B Bulgarian,
1202
.B Chinese,
1203
.B English,
1204
.B French,
1205
.B Italian,
1206
.B Russian
1207
and
1208
.B Spanish
1209
may be used to select Bulgarian, Chinese, English, French,
1210
Italian, Japanese, Russian and Spanish menus and messages if the
1211
appropriate fonts have been installed.
1212
1213
.TP
1214
.B Japanese
1215
The RasMol
1216
.B Japanese
1217
command sets the menus and messages to the Japanese versions.
1218
1219
This command may not work correctly unless appropriate fonts
1220
have been installed. The commands
1221
.B Bulgarian,
1222
.B Chinese,
1223
.B English,
1224
.B French,
1225
.B Italian,
1226
.B Russian
1227
and
1228
.B Spanish
1229
may be used to select Bulgarian, Chinese, English, French,
1230
Italian, Japanese, Russian and Spanish menus and messages if the
1231
appropriate fonts have been installed.
1232
1233
.TP
1234
.B Label
1235
The RasMol
1236
.B label
1237
command allows an arbitrary formatted text string to be
1238
associated with each currently selected atom. This string may contain
1239
embedded 'expansion specifiers' which display properties of the atom
1240
being labelled. An expansion specifier consists of a '%' character
1241
followed by a single alphabetic character specifying the property to be
1242
displayed.
1243
An actual '%' character may be displayed by using the expansion
1244
specifier '%%'.
1245
1246
Atom labelling for the currently selected atoms may be turned off with
1247
the command
1248
.B label off.
1249
By default, if no string is given as a parameter, RasMol uses labels
1250
appropriate for the current molecule.
1251
1252
The colour of each label may be changed using the
1253
.B colour label
1254
command. By default, each label is drawn in the same colour as the atom
1255
to which it is attached. The size and spacing of the displayed text
1256
may be changed using the
1257
.B set fontsize
1258
command. The width of the strokes in the displayed text may be changed
1259
using the
1260
.B set fontstroke
1261
command.
1262
1263
.TP
1264
.B Load
1265
Load a molecule coordinate file into RasMol. Valid molecule file
1266
formats are
1267
.B pdb
1268
(Protein Data Bank format),
1269
.B mdl
1270
(Molecular Design Limited's MOL file format),
1271
.B alchemy
1272
(Tripos' Alchemy file format),
1273
.B mol2
1274
(Tripos' Sybyl Mol2 file format),
1275
.B charmm
1276
(CHARMm file format),
1277
.B xyz
1278
(MSC's XMol XYZ file format),
1279
.B mopac
1280
(J. P. Stewart's MOPAC file format) or
1281
.B cif
1282
(IUCr CIF or mmCIF file format). If no file format is specified,
1283
.B PDB,
1284
.B CIF,
1285
or
1286
.B mmCIF
1287
is assumed by default. Up to 20 molecules may be loaded at a time.
1288
If CHEM_COMP ligand models are included in an mmCIF file, they will be loaded
1289
as NMR models, first giving the all the NMR models for model
1290
coordinates if specified and then giving all the NMR models for
1291
ideal model coordinates.
1292
1293
To delete a molecule prior to loading another use the RasMol
1294
.B zap
1295
command. To select a molecule for manipulation use the RasMol
1296
.B molecule <n>
1297
command.
1298
1299
The
1300
.B load
1301
command selects all the atoms in the molecule, centres it on the
1302
screen and renders it as a CPK coloured wireframe model. If the molecule
1303
contains no bonds (i.e. contains only alpha carbons), it is drawn as
1304
an alpha carbon backbone. If the file specifies fewer bonds than atoms,
1305
RasMol determines connectivity using the
1306
.B connect
1307
command.
1308
1309
The
1310
.B load inline
1311
command also allows the storing of atom coordinates in scripts
1312
to allow better integration with WWW browsers. A load command
1313
executed inside a script file may specify the keyword
1314
.B inline
1315
instead of a conventional filename. This option specifies that
1316
the coordinates of the molecule to load are stored in the same
1317
file as the currently executing commands.
1318
1319
.TP
1320
.B Map
1321
The RasMol
1322
.B map
1323
commands manipulate electron density maps in coordination
1324
with the display of molecules. These commands are very
1325
memory intensive and may not work on machines with
1326
limited memory. Each molecule may have as many maps
1327
as available memory permits. Maps may be read from
1328
files or generated from Gaussian density distributions
1329
around atoms.
1330
1331
.B map colour,
1332
to colour a map according to a given colour scheme,
1333
.B map generate,
1334
to generate a map from selected atoms based on pseudo-Gaussians,
1335
.B map level,
1336
to set the contouring level for selected maps,
1337
.B map load,
1338
to load a map from a file,
1339
.B map mask
1340
to designate a mask for the selected maps,
1341
.B map resolution,
1342
to set the resolution for contouring selected maps,
1343
.B map restrict,
1344
to select one or more maps and to disable all others,
1345
.B map save,
1346
to save map information to a file,
1347
.B map scale,
1348
.B control the scaling of pseudo-Gaussians when generating maps,
1349
.B map select,
1350
to select one or more maps,
1351
.B map show,
1352
to display information about one or more maps or about the
1353
parameters to be used in generating or loading the next map,
1354
.B map spacing,
1355
to set the spacing betwen contour lines of selected maps,
1356
.B map spread,
1357
to set the variance of the Gaussians for map generation as a fraction
1358
of the atomic radius, and
1359
.B map zap
1360
to delete previously generated or loaded maps.
1361
1362
The effect of
1363
.B map generate
1364
and
1365
.B map load
1366
commands is modified by the
1367
.B map mask
1368
command which limits the portion of the display space
1369
that can be considered for display of maps.
1370
1371
.TP
1372
.B Map colour
1373
The RasMol
1374
.B map colour
1375
command colours the selected maps according to the specified
1376
colour scheme. The colour scheme may be a colour name or
1377
and RBG triple in brackets, or the keyword
1378
.B atom
1379
to cause the map points to be coloured by the color of the
1380
nearest atom.
1381
1382
.TP
1383
.B Map generate
1384
The RasMol
1385
.B map generate
1386
command generates a map from whatever atoms are currently selected,
1387
by summing electron densities approximated by Gaussian distributions.
1388
The height of each Gaussian is determined by the setting of the
1389
.B map scale
1390
command.
1391
In the default of map scale true, each Gaussian has a height proportional
1392
element type of the atom.
1393
If the optional 'LRSurf' parameter is given or if map scale false
1394
has been executed, each Gaussian is scaled so that
1395
the Gaussian contour level 1 is at the van der Waals radius.
1396
In either case a standard deviation determined by the
1397
most recently specified spread or resolution is used. If a non-zero spread has been
1398
given the radius of the atom is multiplied by the spread to find the
1399
standard deviation. The default is 2/3rds. If a resolution
1400
has been given, the spread is inferred as 2/3rds of the resolution.
1401
1402
For example, if the resolution is given as 1., and the atom in question
1403
is a Carbon with a van der Waals radius of 468 RasMol units (1.87 Angstroms),
1404
the inferred spead is .6667, and the standard deviation of the Gaussian
1405
is taken as 1.25 Angstroms.
1406
1407
If the spread has been set to zero, the spread for each atom is determined
1408
from the van der Waals radius and the probe atom radius to simulate the
1409
effect of a Lee-Richards surface.
1410
1411
If no specific map was given by the map selector, the new map is
1412
given the next available map number.
1413
1414
If a specific map was given by the map selector, the new map replaces
1415
that map. If more than one map was given by the map selector, the
1416
new map replaces the lowest numbered of the selected maps. In any
1417
case the new map becomes the currently selected map.
1418
1419
The map is displayed as dots, mesh or a surface, depending on the last
1420
map rendering mode selected or the mode selected on the command itself.
1421
1422
.TP
1423
.B Map level
1424
The RasMol
1425
.B map level
1426
command sets the contour level to be used in creating subsequent
1427
representations of generated or loaded maps. If the keyword MEAN
1428
in used the level is relative to the mean of the map data. Otherwise
1429
the level is absolute.
1430
1431
In general, a lower level results in a map containing more of the
1432
displayed volume, while a higher level results in a map containing
1433
less of the displayed volume.
1434
1435
.TP
1436
.B Map load
1437
The RasMol
1438
.B map load
1439
command loads a map file into RasMol. The valid formats are
1440
CCP4 map format and imgCIF format.
1441
1442
If no specific map was given by the map selector, the new map is
1443
given the next available map number.
1444
1445
If a specific map was given by the map selector, the new map replaces
1446
that map. If more than one map was given by the map selector, the
1447
new map replaces the lowest numbered of the selected maps. In any
1448
case the new map becomes the currently selected map.
1449
1450
The map is displayed as dots, mesh or a surface depending on the
1451
last map rendering mode selected.
1452
1453
.TP
1454
.B Map mask
1455
The RasMol
1456
.B map mask
1457
command specifies a mask to be used to limit the display space
1458
to be used for making representations of other maps or removes
1459
an earlier mask specification.
1460
1461
The 'selected' option indicates that the mask is to be created
1462
from the currently selected atoms. The '<number>' option indicates
1463
that the mask is to be copied from the map of the number specified.
1464
The 'none' option removes the previously specified mask, if any.
1465
1466
The map selector specifies the map or maps to which the specified mask
1467
will the applied. For example, 'map next mask selected' specifies
1468
that the currently selected atoms are to be used to generate a
1469
mask to be applied to any maps created by subsequent 'map load'
1470
or 'map generate' commands.
1471
1472
Any map may be used as a mask. The portions of the mask map greater than
1473
than or equal to the average value of the mask map allow the values of the
1474
map being masked to be used as given. The portions of the mask
1475
map lower than the average value of the mask map cause the values of
1476
the map being masked to be treated as if they were equal to the
1477
lowest data value of the map being masked.
1478
1479
.TP
1480
.B Map resolution
1481
The RasMol
1482
.B map resolution
1483
command specifies the resolution in RasMol units or,
1484
if a number containing a decimal point is given, the
1485
resolution in Angstroms to be used in generating and
1486
in representing maps.
1487
1488
The resolution is used at the map spacing for
1489
representations of maps, indicating the separation
1490
between contour levels (see the
1491
.B map spacing
1492
command) and to infer the map spread to be used in
1493
generated maps from selected atoms (see the
1494
.B map spread
1495
command). The map spread is set to two thirds of
1496
the specified resolution.
1497
1498
.TP
1499
.B Map restrict
1500
The RasMol
1501
.B map restrict
1502
command selects particular maps to make them active for
1503
subsequent map commands. This is similar to the
1504
.B map select
1505
command, but does disables the display of the
1506
maps that were not selected.
1507
1508
.TP
1509
.B Map save
1510
The RasMol
1511
.B map save
1512
command saves an imgCIF map file.
1513
1514
If no specific map was given by the map selector, the currently
1515
selected maps and their masks are written to the file, one
1516
map and mask pair per data block.
1517
1518
.TP
1519
.B Map scale
1520
The RasMol
1521
.B map scale
1522
command selects the scaling of pseudo-Gaussians in the
1523
.B map generate
1524
commands.
1525
In the default of map scale true, each Gaussian has a height proportional
1526
element type of the atom.
1527
If map scale false has been executed, each Gaussian is scaled so that
1528
the Gaussian contour level 1 is at the van der Waals radius.
1529
In either case a standard deviation determined by the
1530
most recently specified spread or resolution is used.
1531
1532
.TP
1533
.B Map select
1534
The RasMol
1535
.B map select
1536
command selects particular maps to make them active for
1537
subsequent map commands. This is similar to the
1538
.B map restrict
1539
command, but does not disable the display of the
1540
maps that were not selected.
1541
1542
If the optional
1543
.B atom
1544
parameter is given, the command selects the atoms with centres closest to the
1545
map points. The radius of the search may be specified by the parameter
1546
.B search_radius.
1547
The default is to look for atoms within 4 Angstroms plus the probe radius.
1548
If the optional
1549
.B within
1550
parameter is given, the new selection is taken from within the currently
1551
selected atoms. If the options
1552
.B add
1553
parameter is given, the new selection is added to the currently selected atoms.
1554
The default is to search within all atoms.
1555
1556
.TP
1557
.B Map show
1558
The RasMol
1559
.B map show
1560
command causes information about the maps specified by
1561
the map selector to be written to the command window.
1562
1563
.TP
1564
.B Map spacing
1565
The RasMol
1566
.B map spacing
1567
command specifies the spacing to be used between contour lines
1568
in creating representations of maps. The spacing is typically
1569
given in Angstroms with a decimal point, but may also be
1570
specified in RasMol units (250ths of an Angstom) as an
1571
integer. For maps loaded in grid coordinates that spacing
1572
is parallel to the cell edges. The default spacing is
1573
one half Angstrom.
1574
1575
.TP
1576
.B Map spread
1577
The RasMol
1578
.B map spread
1579
command specifies the reciprocal of the number of
1580
standard deviations per radius to be used in
1581
generating maps as sums of Gaussians centered
1582
on atomic positions. The default spread is one
1583
two thirds (i.e. each radius covers 1.5 standard deviations).
1584
1585
If the spread has been set to zero, the spread for each atom is determined
1586
from the van der Waals radius and the probe atom radius to simulate the
1587
effect of a Lee-Richards surface.
1588
1589
.TP
1590
.B Map zap
1591
The RasMol
1592
.B map zap
1593
command removes the data and representations of the
1594
maps specified by the map selector. The map numbers
1595
of maps that have not been removed are not changed.
1596
1597
.TP
1598
.B Molecule
1599
The RasMol
1600
.B molecule
1601
command selects one of up to 5 previously loaded molecules
1602
for active manipulation. While all the molcules are displayed
1603
and may be rotated collectively (see the
1604
.B rotate all
1605
command), only one molecule at a time
1606
time is active for manipulation by the commands which
1607
control the details of rendering.
1608
1609
.TP
1610
.B Monitor
1611
The RasMol
1612
.B monitor
1613
command allows the display of distance monitors. A distance
1614
monitor is a dashed (dotted) line between an arbitrary pair
1615
of atoms, optionally labelled by the distance between them.
1616
The RasMol command
1617
.B monitor <number> <number>
1618
adds such a distance monitor between the two atoms specified by the atom
1619
serial numbers given as parameters
1620
1621
Distance monitors are turned off with the command
1622
.B monitors off.
1623
By default, monitors display the
1624
distance between its two end points as a label at the centre of
1625
the monitor. These distance labels may be turned off with the
1626
command
1627
.B set monitors off,
1628
and re-enabled with the command
1629
.B set monitors on.
1630
Like most other representations,
1631
the colour of a monitor is taken from the colour of its end points unless
1632
specified by the
1633
.B colour monitors
1634
command.
1635
1636
Distance monitors may also be added to a molecule interactively with
1637
the mouse, using the
1638
.B set picking monitor
1639
command. Clicking on an atom results
1640
in its being identified on the rasmol command line. In addition
1641
every atom picked increments a modulo counter such that, in monitor
1642
mode, every second atom displays the distance between this atom and
1643
the previous one. The shift key may be used to form distance monitors
1644
between a fixed atom and several consecutive positions. A distance
1645
monitor may also be removed (toggled) by selecting the appropriate
1646
pair of atom end points a second time.
1647
1648
.TP
1649
.B Notoggle
1650
The RasMol
1651
.B NoToggle
1652
command enables or disables the use of the toggle ability
1653
that is used by some of the other RasMol commands.
1654
When no boolean value is specified, NoToggle mode is ENABLED.
1655
When NoToggle mode is ENABLED, all toggle functionality is
1656
DISABLED. To turn it off, one must explicitly set
1657
.B notoggle off.
1658
1659
Some commands which use the toggle feature are:
1660
.B ColourMode.
1661
More functions that utilize this capability may be added
1662
at a later date.
1663
1664
.TP
1665
.B Pause
1666
The RasMol
1667
.B pause
1668
command is used in script files to stop the script file for local
1669
manipulation by a mouse, until any key is pushed to restart the
1670
script file.
1671
.B Wait
1672
is synonymous with
1673
.B pause.
1674
This command may be executed in RasMol script files to suspend
1675
the sequential execution of commands and allow the user to examine
1676
the current image. When RasMol executes a
1677
.B pause
1678
command in a script file, it suspends execution of the rest
1679
of the file, refreshes the image on the screen and allows the
1680
manipulation of the image using the mouse and scroll bars, or
1681
resizing of the graphics window. Once a key is pressed, control
1682
returns to the script file at the line following the
1683
.B pause
1684
command. While a script is suspended the molecule may be rotated,
1685
translated, scaled, slabbed and picked as usual, but all menu
1686
commands are disabled.
1687
1688
.TP
1689
.B Play
1690
The RasMol
1691
.B play
1692
command specifies the recording medium from which to play back a movie.
1693
The playback frame start time is given in seconds to millisecond precision.
1694
Since we are working on computers, the medium is specified as a set of files,
1695
each marked with the playback frame start time in milliseconds as part of the
1696
name. The place in the name at which to look for the playback frame start
1697
time in milliseconds is marked by the characters "ssssss" with an
1698
appropriate number of digits. RasMol accepts either upper or lower case
1699
s's or decimal digits to mark the place for the time. The play off and play
1700
eject commands effectively remove the specified medium from use. If no medium
1701
is specified, play off suspends playing and play on resumes playing.
1702
Normally play starts immediately and runs to the end of the medium. However,
1703
if play off and/or or some combination of play from and play until is entered
1704
before
1705
.B play type medium,
1706
those settings will be used.
1707
1708
As of release 2.7.5, RasMol support play from scripts and data files.
1709
1710
.TP
1711
.B Print
1712
The RasMol
1713
.B print
1714
command sends the currently displayed image to the local default printer
1715
using the operating system's native printer driver. Note: this command
1716
is not yet supported under UNIX or VMS. It is intended to take advantage
1717
of Microsoft Windows and Apple Macintosh printer drivers. For example,
1718
this allows images to be printed directly on a dot matrix printer.
1719
1720
When using RasMol on a UNIX or VMS system this functionality may be
1721
achieved by either generating a PostScript file using the RasMol
1722
.B write ps
1723
or
1724
.B write vectps
1725
commands and printing that or generating a raster image file and using a
1726
utility to dump that to the local printer.
1727
1728
.TP
1729
.B Quit
1730
Exit from the RasMol program. The RasMol commands
1731
.B exit
1732
and
1733
.B quit
1734
are synonymous, except within nested scripts. In that case,
1735
.B exit
1736
terminates only the current level, while
1737
.B quit
1738
terminates all nested levels of scripts.
1739
1740
.TP
1741
.B Record
1742
The RasMol
1743
.B record
1744
command specifies the recording medium to hold the movie. Since we are
1745
working on computers, the medium is specified as a template for a set of
1746
files, each marked with the playback frame start time in milliseconds
1747
(rather than as seconds to avoid embedding a decimal point) as part of
1748
the name. The place in the name to be replaced with the playback frame
1749
start time in milliseconds is marked by the characters "ssssss" with
1750
an appropriate number of digits. RasMol accepts either upper or lower case
1751
s's or decimal digits to mark the place for the time. The record off
1752
commands remove the specified medium from use. If no medium is specified,
1753
record off suspends recording and record on resumes recording with the
1754
next available time on the same medium. The screen is the default medium
1755
and is, by default, on. Writing to disk must be explicitly specified so
1756
that the disk does not get filled up unintentionally. The type of a
1757
recording medium may be an image type such as gif, pict or png to record
1758
the actual screen images or script to record the RasMol commands used to
1759
generate the frames.
1760
1761
Normally recording starts at playback frame start time 0 seconds.
1762
A non-zero starting time in seconds can be specified with the
1763
.B record from
1764
command as in
1765
.B record from 25
1766
or
1767
.B record from 37.25
1768
to help in organizing scenes of movies to be assembled later in an
1769
appropriate order.
1770
The
1771
.B record until
1772
command allows an upper limit to be set on recording time in seconds.
1773
The default is to have no limit. Issuing the commands
1774
1775
.B record from 600
1776
1777
.B record until 1800
1778
1779
would result in a 20 minute movie segment intended to start 10
1780
minutes into a longer movie.
1781
These commands allow control over rewriting selected time segments.
1782
1783
.TP
1784
.B Refresh
1785
The RasMol
1786
.B refresh
1787
command redraws the current image. This is useful in scripts
1788
to ensure application of a complex list of parameter changes.
1789
1790
.TP
1791
.B Renumber
1792
The RasMol
1793
.B renumber
1794
command sequentially numbers the residues in a macromolecular chain.
1795
The optional parameter specifies the value of the first residue in the
1796
sequence. By default, this value is one. For proteins,
1797
each amino acid is numbered consecutively from the N terminus to the C
1798
terminus. For nucleic acids, each base is numbered from the 5' terminus
1799
to the 3' terminus. All chains in the current database are renumbered and gaps
1800
in the original sequence are ignored. The starting value for numbering may
1801
be negative.
1802
1803
.TP
1804
.B Reset
1805
The RasMol
1806
.B reset
1807
command restores the original viewing transformation
1808
and centre of rotation. The scale is set to its default value,
1809
.B zoom 100,
1810
the centre of rotation is set to the geometric centre of the currently
1811
loaded molecule,
1812
.B centre all,
1813
this centre is translated to the middle of the screen and
1814
the viewpoint set to the default orientation.
1815
1816
This command should not be mistaken for the RasMol
1817
.B zap
1818
command which deletes the currently stored molecule, returning the
1819
program to its initial state.
1820
1821
.TP
1822
.B Restrict
1823
The RasMol
1824
.B restrict
1825
command both defines the currently selected region of the
1826
molecule and disables the representation of (most of) those parts of the
1827
molecule no longer selected. All subsequent RasMol commands that modify
1828
a molecule's colour or representation affect only the currently selected
1829
region. The parameter of a
1830
.B restrict
1831
command is a RasMol atom expression that is evaluated for every atom
1832
of the current molecule. This command is very similar to the RasMol
1833
.B select
1834
command, except
1835
.B restrict
1836
disables the
1837
.B wireframe,
1838
.B spacefill
1839
and
1840
.B backbone
1841
representations in the non-selected region.
1842
1843
Type "help expression" for more information on RasMol atom expressions or
1844
see section
1845
.B Atom Expressions.
1846
1847
.TP
1848
.B Ribbons
1849
The RasMol
1850
.B ribbons
1851
command displays the currently loaded protein or nucleic acid as a
1852
smooth solid "ribbon" surface passing along the backbone of the protein.
1853
The ribbon is drawn between each amino acid whose alpha carbon is
1854
currently selected. The colour of the ribbon is changed by the RasMol
1855
.B colour ribbon
1856
command. If the current ribbon colour is
1857
.B none
1858
(the default), the colour is taken from the alpha carbon at each
1859
position along its length.
1860
1861
The width of the ribbon at each position is determined by the optional
1862
parameter in the usual RasMol units. By default the width of the ribbon
1863
is taken from the secondary structure of the protein or a constant value
1864
of 720 (2.88 Angstroms) for nucleic acids.
1865
The default width of protein alpha helices and beta sheets is 380 (1.52
1866
Angstroms) and 100 (0.4 Angstroms) for turns and random coil. The
1867
secondary structure assignment is either from the PDB file or calculated
1868
using the DSSP algorithm as used by the
1869
.B structure
1870
command. This command is similar to the RasMol command
1871
.B strands
1872
which renders the biomolecular ribbon as parallel depth-cued curves.
1873
1874
.TP
1875
.B Rotate
1876
Rotate the molecule about the specified axis.
1877
Permitted values for the axis parameter are
1878
"x", "y", "z" and "bond".
1879
The integer parameter states the angle in degrees for the structure to
1880
be rotated. For the X and Y axes, positive values move the closest point
1881
up and right, and negative values move it down and left, respectively. For
1882
the Z axis, a positive rotation acts clockwise and a negative angle
1883
anti-clockwise.
1884
1885
Alternatively, this command may be used to specify which rotations
1886
the mouse or dials will control. If
1887
.B rotate bond true
1888
is selected, the horizontal scroll bar will control rotation around
1889
the axis selected by the
1890
.B bond src dst pick
1891
command. If
1892
.B rotate all true
1893
is selected, and multiple molecules have been loaded, then all molecules
1894
will rotate together. In all other cases, the mouseand dials control the
1895
the rotation of the molecule selected by the
1896
.B molecule n
1897
command.
1898
1899
.TP
1900
.B Russian
1901
The RasMol
1902
.B Russian
1903
command sets the menus and messages to the Russian versions.
1904
1905
This command may not work correctly unless appropriate fonts
1906
have been installed. The commands
1907
.B Bulgarian,
1908
.B Chinese,
1909
.B English,
1910
.B French,
1911
.B Italian,
1912
.B Russian
1913
and
1914
.B Spanish
1915
may be used to select Bulgarian, Chinese, English, French,
1916
Italian, Japanese, Russian and Spanish menus and messages if the
1917
appropriate fonts have been installed.
1918
1919
.TP
1920
.B Save
1921
Save the currently selected set of atoms in a Protein
1922
Data Bank (PDB), MDL, Alchemy(tm) or XYZ format file.
1923
The distinction between this command and the RasMol
1924
.B write
1925
command has been dropped. The only difference is that without a format
1926
specifier the
1927
.B save
1928
command generates a
1929
.B PDB
1930
file and the
1931
.B write
1932
command generates a
1933
.B GIF
1934
image.
1935
1936
.TP
1937
.B Script
1938
The RasMol
1939
.B script
1940
command reads a set of RasMol commands sequentially from a
1941
text file and executes them. This allows sequences of commonly used
1942
commands to be stored and performed by single command. A RasMol script
1943
file may contain a further script command up to a maximum "depth" of 10,
1944
allowing complicated sequences of actions to be executed. RasMol
1945
ignores all characters after the first '#' character on each line
1946
allowing the scripts to be annotated. Script files are often also
1947
annotated using the RasMol
1948
.B echo
1949
command.
1950
1951
The most common way to generate a RasMol script file is to use the
1952
.B write script
1953
or
1954
.B write rasmol
1955
commands to output the sequence of commands that are needed to
1956
regenerate the current view, representation and colouring of the
1957
currently displayed molecule.
1958
1959
The RasMol command
1960
.B source
1961
is synonymous with the
1962
.B script
1963
command.
1964
1965
.TP
1966
.B Select
1967
Define the currently selected region of the molecule. All subsequent RasMol
1968
commands that manipulate a molecule or modify its colour or representation
1969
only affect the currently selected region. The parameter of a
1970
.B select
1971
command is a RasMol expression that is evaluated for every atom of the
1972
current molecule. The currently selected (active) region of the molecule
1973
are those atoms that cause the expression to evaluate true. To select
1974
the whole molecule use the RasMol command
1975
.B select all.
1976
The behaviour of the
1977
.B select
1978
command without any parameters is determined by the RasMol
1979
.B hetero
1980
and
1981
.B hydrogen
1982
parameters.
1983
1984
Type "help expression" for more information on RasMol atom expressions or
1985
see section
1986
.B Atom Expressions.
1987
1988
.TP
1989
.B Set
1990
The RasMol
1991
.B set
1992
command allows the user to alter various internal program parameters
1993
such as those controlling rendering options. Each parameter has its
1994
own set or permissible parameter options. Typically, omitting the
1995
paramter option resets that parameter to its default value. A list of
1996
valid parameter names is given below.
1997
1998
.TP
1999
.B Show
2000
The RasMol
2001
.B show
2002
command display details of the status of the currently
2003
loaded molecule. The command
2004
.B show information
2005
lists the molecule's name,
2006
classification, PDB code and the number of atoms, chains, groups it contains.
2007
If hydrogen bonding, disulphide bridges or secondary structure have been
2008
determined, the number of hbonds, ssbonds, helices, ladders and turns
2009
are also displayed, respectively. The command
2010
.B show centre
2011
shows any non-zero centering values selected by the
2012
.B centre [CenX, CenY, CenZ]
2013
command. The command
2014
.B show phipsi
2015
shows the phi and psi angles of the currently selected residues and
2016
the omega angles of cis peptide bonds. The command
2017
.B show RamPrint
2018
(or 'show RPP' or 'show RamachandranPrinterPlot') shows a simple
2019
Ramachandran printer plot in the style of Frances Bernstein's fisipl
2020
program. The command
2021
.B show rotation
2022
(or 'show rot' or 'show 'rotate') shows the currently selected values
2023
of z, y, x and bond rotations, if any.
2024
The command
2025
.B show selected
2026
(or 'show selected group' or 'show selected chain' or 'show selected atom' )
2027
shows the groups (default), chains or atoms of the current selection.
2028
The command
2029
.B show sequence
2030
lists the residues that comprise each chain of the molecule. The command
2031
.B show symmetry
2032
shows the space group and unit cell of the molecule. The command
2033
.B show translation
2034
shows any non-zero translation values selected by the
2035
.B translate <axis> <value>
2036
command. The command
2037
.B show zoom
2038
shows any non-zero zoom value selected by the
2039
.B zoom <value>
2040
command.
2041
2042
.TP
2043
.B Slab
2044
The RasMol
2045
.B slab
2046
command enables, disables or positions the z-clipping plane of the
2047
molecule. The program only draws those portions of the
2048
molecule that are further from the viewer than the slabbing plane.
2049
Integer values range from zero at the very back of the molecule to
2050
100 which is completely in front of the molecule. Intermediate values
2051
determine the percentage of the molecule to be drawn.
2052
2053
This command interacts with the
2054
.B depth <value>
2055
command, which clips to the rear of a given z-clipping plane.
2056
2057
.TP
2058
.B Spacefill
2059
The RasMol
2060
.B spacefill
2061
command is used to represent all of the currently selected atoms as solid
2062
spheres. This command is used to produce both union-of-spheres and
2063
ball-and-stick models of a molecule. The command,
2064
.B spacefill true,
2065
the default, represents each atom as a sphere of van der Waals radius.
2066
The command
2067
.B spacefill off
2068
turns off the representation of the selected atom as spheres. A sphere
2069
radius may be specified as an integer in RasMol units (1/250th Angstrom)
2070
or a value containing a decimal point. A value of 500 (2.0
2071
Angstroms) or greater results in a "Parameter value too large" error.
2072
2073
The
2074
.B temperature
2075
option sets the radius of each sphere to the value stored in its temperature
2076
field. Zero or negative values have no effect and values greater than
2077
2.0 are truncated to 2.0. The
2078
.B user
2079
option allows the radius of each sphere to be specified by additional lines
2080
in the molecule's PDB file using Raster 3D's COLOUR record extension.
2081
2082
The RasMol command
2083
.B cpk
2084
is synonymous with the
2085
.B spacefill
2086
command.
2087
2088
The RasMol command
2089
.B cpknew
2090
is synonymous with the
2091
.B spacefill
2092
command, except that a slightly different set of colours is used.
2093
2094
.TP
2095
.B Spanish
2096
The RasMol
2097
.B Spanish
2098
command sets the menus and messages to the Spanish versions.
2099
2100
This command may not work correctly unless appropriate fonts
2101
have been installed. The commands
2102
.B Bulgarian,
2103
.B Chinese,
2104
.B English,
2105
.B French,
2106
.B Italian,
2107
.B Russian
2108
and
2109
.B Spanish
2110
may be used to select Bulgarian, Chinese, English, French,
2111
Italian, Japanese, Russian and Spanish menus and messages if the
2112
appropriate fonts have been installed.
2113
2114
.TP
2115
.B SSBonds
2116
The RasMol
2117
.B ssbonds
2118
command is used to represent the disulphide bridges of the protein
2119
molecule as either dotted lines or cylinders between the connected
2120
cysteines. The first time that the
2121
.B ssbonds
2122
command is used, the program searches the structure of the protein to
2123
find half-cysteine pairs (cysteines whose sulphurs are within 3 Angstroms
2124
of each other) and reports the number of bridges to the user. The command
2125
.B ssbonds on
2126
displays the selected "bonds" as dotted lines, and the command
2127
.B ssbonds off
2128
disables the display of ssbonds in the currently selected area. Selection
2129
of disulphide bridges is identical to normal bonds, and may be adjusted
2130
using the RasMol
2131
.B set bondmode
2132
command. The colour of disulphide bonds may be changed using the
2133
.B colour ssbonds
2134
command. By default, each disulphide bond has the colours of its connected
2135
atoms.
2136
2137
By default disulphide bonds are drawn between the sulphur atoms within
2138
the cysteine groups. By using the
2139
.B set ssbonds
2140
command the position of the cysteine's alpha carbons may be used instead.
2141
2142
.TP
2143
.B Star
2144
The RasMol
2145
.B star
2146
command is used to represent all of the currently selected atoms as
2147
stars (six strokes, one each in the x, -x, y, -y, z and -z directions).
2148
The commands
2149
.B select not bonded
2150
followed by
2151
.B star 75
2152
are useful to mark unbonded atoms in a
2153
.B wireframe
2154
display with less overhead than provided by
2155
.B spacefill 75.
2156
This can be done automatically for all subsequent wireframe
2157
displays with the command
2158
.B set bondmode not bonded.
2159
2160
The command
2161
.B star true,
2162
the default, represents each atom as a star with strokes
2163
length equal to van der Waals radius.
2164
The command
2165
.B star off
2166
turns off the representation of the selected atom as stars. A star
2167
stroke length may be specified as an integer in RasMol units
2168
(1/250th Angstrom)
2169
or a value containing a decimal point. A value of 500 (2.0
2170
Angstroms) or greater results in a "Parameter value too large" error.
2171
2172
The
2173
.B temperature
2174
option sets the stroke length of each star to the value stored
2175
in its temperature
2176
field. Zero or negative values have no effect and values greater than
2177
2.0 are truncated to 2.0. The
2178
.B user
2179
option allows the stroke length of each star to be specified by
2180
additional lines
2181
in the molecule's PDB file using Raster 3D's COLOUR record extension.
2182
2183
The RasMol
2184
.B spacefill
2185
command can be used for more artistic rendering of atoms as spheres.
2186
2187
.TP
2188
.B Stereo
2189
The RasMol
2190
.B stereo
2191
command provides side-by-side stereo display of images. Stereo
2192
viewing of a molecule may be turned on (and off) either by
2193
selecting
2194
.B Stereo
2195
from the
2196
.B Options
2197
menu, or by
2198
typing the commands
2199
.B stereo on
2200
or
2201
.B stereo off.
2202
2203
Starting with RasMol version 2.7.2.1, the
2204
.B Stereo
2205
menu selection and the command
2206
.B stereo
2207
without arguments cycle from the initial state of
2208
.B stereo off
2209
to
2210
.B stereo on
2211
in cross-eyed mode to
2212
.B stereo on
2213
in wall-eyed mode and then back to
2214
.B stereo off.
2215
2216
The separation angle between
2217
the two views may be adjusted with the
2218
.B set stereo [-] <number>
2219
command, where positive values result in crossed eye
2220
viewing and negative values in relaxed (wall-eyed) viewing.
2221
The inclusion of
2222
.B [-] <number>
2223
in the
2224
.B stereo
2225
command, as for example in
2226
.B stereo 3
2227
or
2228
.B stereo -5,
2229
also controls angle and direction.
2230
2231
The stereo command is only partially
2232
implemented. When stereo is turned on, the image is not properly
2233
recentred. (This can be done with a
2234
.B translate x -<number>
2235
command.)
2236
It is not supported in vector PostScript output files, is not
2237
saved by the
2238
.B write script
2239
command, and in
2240
general is not yet properly interfaced with several other
2241
features of the program.
2242
2243
.TP
2244
.B Strands
2245
The RasMol
2246
.B strands
2247
command displays the currently loaded protein or nucleic acid as a
2248
smooth "ribbon" of depth-cued curves passing along the backbone of the
2249
protein. The ribbon is composed of a number of strands that run parallel
2250
to one another along the peptide plane of each residue. The ribbon is
2251
drawn between each amino acid whose alpha carbon is currently selected.
2252
The colour of the ribbon is changed by the RasMol
2253
.B colour ribbon
2254
command. If the current ribbon colour is
2255
.B none
2256
(the default), the colour is taken from the alpha carbon at each
2257
position along its length. The central and outermost
2258
strands may be coloured independently using the
2259
.B colour ribbon1
2260
and
2261
.B colour ribbon2
2262
commands, respectively. The number of strands in the ribbon may be
2263
altered using the RasMol
2264
.B set strands
2265
command.
2266
2267
The width of the ribbon at each position is determined by the optional
2268
parameter in the usual RasMol units. By default the width of the ribbon
2269
is taken from the secondary structure of the protein or a constant value
2270
of 720 for nucleic acids (which produces a ribbon 2.88 Angstroms wide).
2271
The default width of protein alpha helices and beta sheets is 380 (1.52
2272
Angstroms) and 100 (0.4 Angstroms) for turns and random coil. The
2273
secondary structure assignment is either from the PDB file or calculated
2274
using the DSSP algorithm as used by the
2275
.B structure
2276
command. This command is similar to the RasMol command
2277
.B ribbons
2278
which renders the biomolecular ribbon as a smooth shaded surface.
2279
2280
.TP
2281
.B Structure
2282
The RasMol
2283
.B structure
2284
command calculates secondary structure assignments
2285
for the currently loaded protein. If the original PDB file contained
2286
structural assignment records (HELIX, SHEET and TURN) these are discarded.
2287
Initially, the hydrogen bonds of the current molecule are found, if this
2288
hasn't been done already. The secondary structure is then determined using
2289
Kabsch and Sander's DSSP algorithm. Once finished the program reports the
2290
number of helices, strands and turns found.
2291
2292
.TP
2293
.B Surface
2294
The RasMol
2295
.B surface
2296
command renders a Lee-Richards molecular surface resulting
2297
from rolling a probe atom on the selected atoms.
2298
The value given specifies the radius of the probe.
2299
If given in the first form, the evolute of the surface
2300
of the probe is shown (the solvent excluded surface).
2301
If given in the second form, the envelope of the
2302
positions of the center of the probe is shown
2303
(the solvent accessible surface).
2304
2305
.TP
2306
.B Trace
2307
The RasMol
2308
.B trace
2309
command displays a smooth spline between consecutive alpha
2310
carbon positions. This spline does not pass exactly through
2311
the alpha carbon position of each residue, but follows the
2312
same path as
2313
.B ribbons,
2314
.B strands
2315
and
2316
.B cartoons.
2317
Note that residues may be displayed as
2318
.B ribbons,
2319
.B strands,
2320
.B cartoons
2321
or as a
2322
.B trace.
2323
Enabling one of these
2324
representations disables the others. However, a residue
2325
may be displayed simultaneously as backbone and as one of
2326
the above representations. This may change in future
2327
versions of RasMol. Prior to version 2.6,
2328
.B trace
2329
was synonymous with
2330
.B backbone.
2331
2332
.B Trace temperature
2333
displays the backbone as a wider cylinder
2334
at high temperature factors and thinner at lower. This
2335
representation is useful to X-ray crystallographers and NMR spectroscopists.
2336
2337
.TP
2338
.B Translate
2339
The RasMol
2340
.B translate
2341
command moves the position of the centre of the molecule on the
2342
screen. The axis parameter specifies along which axis the molecule
2343
is to be moved and the integer parameter specifies the absolute
2344
position of the molecule centre from the middle of the screen.
2345
Permitted values for the axis parameter are
2346
"x", "y" and "z".
2347
Displacement values must be between -100 and 100 which correspond to
2348
moving the current molecule just off the screen. A positive
2349
"x"
2350
displacement moves the molecule to the right, and a positive
2351
"y"
2352
displacement moves the molecule down the screen. The pair of commands
2353
.B translate x 0
2354
and
2355
.B translate y 0
2356
centres the molecule on the screen.
2357
2358
.TP
2359
.B UnBond
2360
The RasMol command
2361
.B unbond <number> <number>
2362
removes the designated bond from the drawing.
2363
2364
The command
2365
.B unbond
2366
without arguments removes a bond previously picked by the
2367
.B bond <number> <number> pick
2368
command.
2369
2370
.TP
2371
.B Wireframe
2372
The RasMol
2373
.B wireframe
2374
command represents each bond within the selected region of the molecule
2375
as a cylinder, a line or a depth-cued vector. The display of bonds
2376
as depth-cued vectors (drawn darker the further away from the viewer)
2377
is turned on by the command
2378
.B wireframe
2379
or
2380
.B wireframe on.
2381
The selected bonds are displayed as cylinders by specifying a radius
2382
either as an integer in RasMol units or containing a decimal point as
2383
a value in Angstroms. A parameter value of 500 (2.0 Angstroms) or
2384
above results in an "Parameter value too large" error. Bonds may be
2385
coloured using the
2386
.B colour bonds
2387
command.
2388
2389
If the selected bonds involved atoms of alternate conformers then
2390
the bonds are narrowed in the middle to a radius of .8 of the specified
2391
radius (or to the radius specifed as the optional second parameter).
2392
2393
Non-bonded atoms, which could become invisible in an
2394
ordinary
2395
.B wireframe
2396
display can be marked by a preceding
2397
.B set bondmode not bonded
2398
command. If nearly co-linear bonds to atoms cause them to be
2399
difficult to see in a wireframe display, the
2400
.B set bondmode all
2401
command will add markers for
2402
.B all
2403
atoms in subsequent
2404
.B wireframe
2405
command executions.
2406
2407
.TP
2408
.B Write
2409
Write the current image to a file in a standard format. Currently
2410
supported image file formats include
2411
.B bmp
2412
(Microsoft bitmap) and
2413
.B gif
2414
(Compuserve GIF),
2415
.B iris
2416
(IRIS RGB),
2417
.B ppm
2418
(Portable Pixmap),
2419
.B ras
2420
(Sun rasterfile),
2421
.B ps
2422
and
2423
.B epsf
2424
(Encapsulated PostScript),
2425
.B monops
2426
(Monochrome Encapsulated PostScript),
2427
.B pict
2428
(Apple PICT),
2429
.B vectps
2430
(Vector Postscript). The
2431
.B write
2432
command may also be used to generate command scripts for other graphics
2433
programs. The format
2434
.B script
2435
writes out a file containing the RasMol
2436
.B script
2437
commands to reproduce the current image. The format
2438
.B molscript
2439
writes out the commands required to render the current view of the
2440
molecule as ribbons in Per Kraulis' Molscript program and the format
2441
.B kinemage
2442
the commands for David Richardson's program Mage. The following
2443
formats are useful for further processing:
2444
.B povray
2445
(POVRay 2),
2446
.B povray3
2447
(POVRay 3 -- under development),
2448
.B vrml
2449
(VRML file).
2450
Finally, several
2451
formats are provided to provide phi-psi data for listing or for
2452
.B phipsi
2453
(phi-psi data as an annotated list with cis omegas),
2454
.B ramachan
2455
and
2456
.B RDF
2457
and
2458
.B RamachandranDataFile
2459
(phi-psi data as columns of numbers for gnuplot),
2460
.B RPP
2461
and
2462
.B RamachandranPrinterPlot
2463
(phi-psi data as a printer plot).
2464
2465
The distinction between this command and the RasMol
2466
.B save
2467
command has been dropped. The only difference is that without a format
2468
specifier the
2469
.B save
2470
command generates a
2471
.B PDB
2472
file and the
2473
.B write
2474
command generates a
2475
.B GIF
2476
image.
2477
2478
.TP
2479
.B Zap
2480
Deletes the contents of the current database and resets parameter
2481
variables to their initial default state.
2482
2483
.TP
2484
.B Zoom
2485
Change the magnification of the currently displayed image. Boolean
2486
parameters either magnify or reset the scale of current molecule. An
2487
integer parameter specifies the desired magnification as a percentage
2488
of the default scale. The minimum parameter value is 10; the maximum
2489
parameter value is dependent upon the size of the molecule being
2490
displayed. For medium sized proteins this is about 500.
2491
2492
.SH SET PARAMETERS
2493
RasMol has a number of internal parameters that may be modified using the
2494
.B set
2495
command. These parameters control a number of program options such as
2496
rendering options and mouse button mappings.
2497
2498
picking play.fps radius record.aps
2499
2500
.TP
2501
.B Set Ambient
2502
The RasMol
2503
.B ambient
2504
parameter is used to control the amount of ambient (or surrounding)
2505
light in the scene. The
2506
.B ambient
2507
value must be between 0 and 100. It controls the percentage intensity
2508
of the darkest shade of an object. For a solid object, this is the
2509
intensity of surfaces facing away from the light source or in shadow.
2510
For depth-cued objects this is the intensity of objects furthest from
2511
the viewer.
2512
2513
This parameter is commonly used to correct for monitors with different
2514
"gamma values" (brightness), to change how light or dark a hardcopy
2515
image appears when printed or to alter the feeling of depth for
2516
wireframe or ribbon representations.
2517
2518
.TP
2519
.B Set Axes
2520
The RasMol
2521
.B axes
2522
parameter controls the display of orthogonal coordinate axes on
2523
the current display. The coordinate axes are those used in the
2524
molecule data file, and the origin is the centre of the molecule's
2525
bounding box. The
2526
.B set axes
2527
command is similar to the commands
2528
.B set boundbox
2529
and
2530
.B set unitcell
2531
that display the bounding box and the crystallographic unit cell,
2532
respectively.
2533
2534
.TP
2535
.B Set Backfade
2536
The RasMol
2537
.B backfade
2538
parameter is used to control backfade to the specified background
2539
colour, rather than black. This is controlled by the commands
2540
.B set backfade on
2541
and
2542
.B set backfade off.
2543
For example, this may be used to generate depth-cued images that
2544
fade to white, rather than black.
2545
2546
.TP
2547
.B Set Background
2548
The RasMol
2549
.B background
2550
parameter is used to set the colour of the "canvas" background. The
2551
colour may be given as either a colour name or a comma separated
2552
triple of Red, Green, Blue (RGB) components enclosed in square
2553
brackets. Typing the command
2554
.B help colours
2555
will give a list of the predefined colour names recognised by RasMol.
2556
When running under X Windows, RasMol also recognises colours in the
2557
X server's colour name database.
2558
2559
The command
2560
.B set background
2561
is synonymous with the RasMol command
2562
.B background.
2563
2564
.TP
2565
.B Set BondMode
2566
The RasMol
2567
.B set bondmode
2568
command controls the mechanism used to select individual bonds
2569
and modifies the display of bonded and non-bonded atoms by subsequent
2570
.B wireframe
2571
commands.
2572
2573
When using the
2574
.B select
2575
and
2576
.B restrict
2577
commands, a given bond will be selected if i) the bondmode is
2578
.B or
2579
and either of the connected atoms is selected, or ii) the bondmode is
2580
.B and
2581
and both atoms connected by the bond are selected. Hence an individual
2582
bond may be uniquely identified by using the command
2583
.B set bondmode and
2584
and then uniquely selecting the atoms at both ends.
2585
2586
The
2587
.B bondmode [all | none | not bonded]
2588
commands add
2589
.B star 75
2590
or
2591
.B spacefill 75
2592
markers for the designated atoms to
2593
.B wireframe
2594
displays. Stars are used when the specified wireframe radius is zero.
2595
2596
.TP
2597
.B Set Bonds
2598
The RasMol
2599
.B bonds
2600
parameter is used to control display of double and triple bonds as
2601
multiple lines or cylinders. Currently bond orders are only read
2602
from MDL Mol files, Sybyl Mol2 format files, Tripos Alchemy format
2603
files, CIF and mmCIF, and suitable PDB files. Double (and triple) bonds
2604
are specified in some PDB files by specifying a given bond twice (and
2605
three times) in CONECT records. The command
2606
.B set bonds on
2607
enables the display of bond orders, and the command
2608
.B set bonds off
2609
disables them.
2610
2611
.TP
2612
.B Set BoundBox
2613
The RasMol
2614
.B boundbox
2615
parameter controls the display of the current molecule's bounding box
2616
on the display. The bounding box is orthogonal to the data file's
2617
original coordinate axes. The
2618
.B set boundbox
2619
command is similar to the commands
2620
.B set axes
2621
and
2622
.B set unitcell
2623
that display orthogonal coordinate axes and the bounding box,
2624
respectively.
2625
2626
.TP
2627
.B Set Cartoon
2628
The RasMol
2629
.B cartoon
2630
parameter is used to control display of the cartoon version of the
2631
.B ribbons
2632
display. By default, the C-termini of beta-sheets are displayed as
2633
arrow heads. This may be enabled and disabled using the
2634
.B set cartoons <boolean>
2635
command. The depth of the cartoon may be adjusted using the
2636
.B cartoons <number>
2637
command. The
2638
.B set cartoons
2639
command without any parameters returns these two options to
2640
their default values.
2641
2642
.TP
2643
.B Set CisAngle
2644
The RasMol
2645
.B cisangle
2646
parameter controls the cutoff angle for identifying cis peptide
2647
bonds. If no value is given, the cutoff is set to 90 degrees.
2648
2649
.TP
2650
.B Set Display
2651
This command controls the display mode within RasMol. By default,
2652
.B set display normal,
2653
RasMol displays the molecule in the representation specified by the
2654
user. The command
2655
.B set display selected
2656
changes the display mode such that the molecule is temporarily drawn
2657
so as to indicate currently selected portion of the molecule. The
2658
user specified colour scheme and representation remains unchanged.
2659
In this representation all selected atoms are shown in yellow and
2660
all non selected atoms are shown in blue. The colour of the background
2661
is also changed to a dark grey to indicate the change of display mode.
2662
This command is typically only used by external Graphical User
2663
Interfaces (GUIs).
2664
2665
.TP
2666
.B Set FontSize
2667
The RasMol
2668
.B set fontsize
2669
command is used to control the size of the characters that
2670
form atom labels. This value corresponds to the height of
2671
the displayed character in pixels. The maximum value of
2672
.B fontsize
2673
is 48 pixels, and the default value is 8 pixels high.
2674
Fixed or proportional spacing may be selected by appending the
2675
"FS" or "PS" modifiers, respectively. The default is "FS".
2676
To display atom labels on the screen use the RasMol
2677
.B label
2678
command and to change the colour of displayed labels, use
2679
the
2680
.B colour labels
2681
command.
2682
2683
.TP
2684
.B Set FontStroke
2685
The RasMol
2686
.B set fontstroke
2687
command is used to control the size of the stroke width of the
2688
characters that form atom labels. This value is the radius in
2689
pixels of cylinders used to form the strokes. The special value
2690
of "0" is the default used for the normal single pixel stroke width,
2691
which allows for rapid drawing and rotation of the image.
2692
Non-zero values are provided to allow for more artistic atom
2693
labels for publication at the expense of extra time in rendering
2694
the image.
2695
2696
When wider strokes are used, a larger font size is recommend, e.g.
2697
by using the RasMol
2698
.B set fontsize 24 PS
2699
command, followed by
2700
.B set fontstroke 2
2701
2702
To display atom labels on the screen use the RasMol
2703
.B label
2704
command, and to change the colour of displayed labels use
2705
the
2706
.B colour labels
2707
command.
2708
2709
.TP
2710
.B Set HBonds
2711
The RasMol
2712
.B hbonds
2713
parameter determines whether hydrogen bonds are drawn between
2714
the donor and acceptor atoms of the hydrogen bond,
2715
.B set hbonds sidechain
2716
or between the alpha carbon atoms of the protein backbone and between
2717
the phosphorous atoms of the nucleic acid backbone,
2718
.B set hbonds backbone.
2719
The actual display of hydrogen bonds is controlled by the
2720
.B hbonds
2721
command. Drawing hydrogen bonds between protein alpha carbons or
2722
nucleic acid phosphorous atoms is useful when the rest of the molecule
2723
is shown in only a schematic representation such as
2724
.B backbone,
2725
.B ribbons
2726
or
2727
.B strands.
2728
This parameter is similar to the RasMol
2729
.B ssbonds
2730
parameter.
2731
2732
.TP
2733
.B Set Hetero
2734
The RasMol
2735
.B hetero
2736
parameter is used to modify the 'default' behaviour of the RasMol
2737
.B select
2738
command, i.e. the behaviour of
2739
.B select
2740
without any parameters. When this value is
2741
.B false,
2742
the default
2743
.B select
2744
region does not include any heterogeneous atoms (refer to the
2745
predefined set
2746
.B hetero
2747
). When this value is
2748
.B true,
2749
the default
2750
.B select
2751
region may contain hetero atoms. This parameter is similar to
2752
the RasMol
2753
.B hydrogen
2754
parameter which determines whether hydrogen atoms should be
2755
included in the default set. If both
2756
.B hetero
2757
and
2758
.B hydrogen
2759
are
2760
.B true,
2761
.B select
2762
without any parameters is equivalent to
2763
.B select all.
2764
2765
.TP
2766
.B Set HourGlass
2767
The RasMol
2768
.B hourglass
2769
parameter allows the user to enable and disable the use of the 'hour
2770
glass' cursor used by RasMol to indicate that the program is currently
2771
busy drawing the next frame. The command
2772
.B set hourglass on
2773
enables the indicator, whilst
2774
.B set hourglass off
2775
prevents RasMol from changing the cursor. This is useful when spinning
2776
the molecule, running a sequence of commands from a script file or
2777
using interprocess communication to execute complex sequences of
2778
commands. In these cases a 'flashing' cursor may be distracting.
2779
2780
.TP
2781
.B Set Hydrogen
2782
The RasMol
2783
.B hydrogen
2784
parameter is used to modify the "default" behaviour of the RasMol
2785
.B select
2786
command, i.e. the behaviour of
2787
.B select
2788
without any parameters. When this value is
2789
.B false,
2790
the default
2791
.B select
2792
region does not include any hydrogen, deuterium or tritium atoms (refer
2793
to the predefined set
2794
.B hydrogen
2795
). When this value is
2796
.B true,
2797
the default
2798
.B select
2799
region may contain hydrogen atoms. This parameter is similar to
2800
the RasMol
2801
.B hetero
2802
parameter which determines whether heterogeneous atoms should be
2803
included in the default set. If both
2804
.B hydrogen
2805
and
2806
.B hetero
2807
are
2808
.B true,
2809
.B select
2810
without any parameters is equivalent to
2811
.B select all.
2812
2813
.TP
2814
.B Set Kinemage
2815
The RasMol
2816
.B set kinemage
2817
command controls the amount of detail stored in a Kinemage output
2818
file generated by the RasMol
2819
.B write kinemage
2820
command. The output kinemage files are intended to be displayed by
2821
David Richardson's Mage program.
2822
.B set kinemage false,
2823
the default, only stores the currently displayed representation in
2824
the generated output file. The command
2825
.B set kinemage true,
2826
generates a more complex Kinemage that contains both the wireframe
2827
and backbone representations as well as the coordinate axes,
2828
bounding box and crystal unit cell.
2829
2830
.TP
2831
.B Set Menus
2832
The RasMol
2833
.B set menus
2834
command enables the canvas window's menu buttons or menu bar. This
2835
command is typically only used by graphical user interfaces or to
2836
create as large an image as possible when using Microsoft Windows.
2837
2838
.TP
2839
.B Set Monitor
2840
The RasMol
2841
.B set monitor
2842
command enables
2843
.B monitors.
2844
The distance monitor labels may be turned off with the command
2845
.B set monitor off,
2846
and re-enabled with the command
2847
.B set monitor on.
2848
2849
2850
.TP
2851
.B Set Mouse
2852
The RasMol
2853
.B set mouse
2854
command sets the rotation, translation, scaling and zooming mouse
2855
bindings. The default value is
2856
.B rasmol
2857
which is suitable for two button mice (for three button mice the
2858
second and third buttons are synonymous); X-Y rotation is controlled
2859
by the first button, and X-Y translation by the second. Additional
2860
functions are controlled by holding a modifier key on the keyboard.
2861
[Shift] and the first button performs scaling, [shift] and the second
2862
button performs Z-rotation, and [control] and the first mouse button
2863
controls the clipping plane. The
2864
.B insight
2865
and
2866
.B quanta
2867
options provide the same mouse bindings as other packages for experienced
2868
users.
2869
2870
.TP
2871
.B Set Picking
2872
The RasMol
2873
.B set picking
2874
series of commands affects how a user may interact with a
2875
molecule displayed on the screen in RasMol.
2876
2877
.B Enabling/Disabling Atom Identification Picking:
2878
Clicking on an atom with the mouse results in identification and
2879
the display of its residue name, residue number, atom name, atom serial
2880
number and chain in the command window. This behavior may be disabled
2881
with the command
2882
.B set picking none
2883
and restored with the command
2884
.B set picking ident.
2885
The command
2886
.B set picking coord
2887
adds the atomic coordinates of the atom to the display.
2888
2889
Disabling picking, by using
2890
.B set picking off
2891
is useful when executing the
2892
.B pause
2893
command in RasMol scripts as it prevents the display of
2894
spurious message on the command line while the script is suspended.
2895
2896
.B Measuring Distances, Angles and Torsions:
2897
Interactive measurement of distances, angles and torsions
2898
is achieved using the commands:
2899
.B set picking distance,
2900
.B set picking monitor,
2901
.B set picking angle
2902
and
2903
.B set picking torsion,
2904
respectively. In these modes, clicking on an atom results in it
2905
being identified on the rasmol command line. In addition every
2906
atom picked increments a modulo counter such that in distance
2907
mode, every second atom displays the distance (or distance monitor)
2908
between this atom and the previous one. In angle mode, every
2909
third atom displays the angle between the previous three atoms
2910
and in torsion mode every fourth atom displays the torsion between
2911
the last four atoms. By holding down the shift key while picking an
2912
atom, this modulo counter is not incremented and allows, for
2913
example, the distances of consecutive atoms from a fixed atom to
2914
be displayed. See the
2915
.B monitor
2916
command for how to control the display of distance monitor lines and labels.
2917
2918
.B Labelling Atoms with the Mouse:
2919
The mouse may also be used to toggle the display of an atom label
2920
on a given atom. The RasMol command
2921
.B set picking label
2922
removes a label from a picked atom if it already has one or
2923
displays a concise label at that atom position otherwise.
2924
2925
.B Centring Rotation with the Mouse:
2926
A molecule may be centred on a specified atom position using the
2927
RasMol commands
2928
.B set picking centre
2929
or
2930
.B set picking center.
2931
In this mode, picking an atom causes all futher rotations to be
2932
about that point.
2933
2934
.B Picking a Bond as a Rotation Axis:
2935
Any bond may be picked as an axis of rotation for the portion of
2936
the molecule beyond the second atom selected. This feature should
2937
be used with caution, since, naturally, it changes the conformation
2938
of the molecule. After executing
2939
.B set picking bond
2940
or using the equivalent "Pick Bond" in the "Settings" menu,
2941
a bond to be rotated is picked with the same sort of mouse clicks
2942
as are used for picking atoms for a distance measurement. Normally
2943
this should be done where a bond exists, but if no bond exists, it
2944
will be added. The bond cannot be used for rotation if it is part
2945
of a ring of any size. All bonds selected for rotation are remembered
2946
so that they can be properly reported when writing a script, but
2947
only the most recently selected bond may be actively rotated.
2948
2949
.B Enabling Atom/Group/Chain Selection Picking:
2950
Atoms, groups and chains may be selected (as if with the
2951
.B select
2952
command), with the
2953
.B set picking atom,
2954
.B set picking group,
2955
.B set picking chain
2956
commands. For each of these commands, the shift key may be used to
2957
have a new selection added to the old, and the control key may be
2958
used to have a new selection deleted from the old. When the
2959
.B set picking atom
2960
command is given, the mouse can be used to pick or to drag a box around
2961
the atoms for which selection is desired. When the
2962
.B set picking group
2963
command is given, picking any an atom will cause selection
2964
of all atoms which agree in residue number with the picked atom,
2965
even if in different chains.
2966
When the
2967
.B set picking chain
2968
command is given, picking any atom will cause selection
2969
of all atoms which agree in chain identifier with the picked atom.
2970
2971
.TP
2972
.B Set Play
2973
The RasMol
2974
.B set play.fps
2975
command gives the number of frames per second for playback by the
2976
.B play
2977
command (default 24 frames per second).
2978
2979
In the current release of RasMol, the play timing is not controlled
2980
by this parameter.
2981
2982
.TP
2983
.B Set Radius
2984
The RasMol
2985
.B set radius
2986
command is used to alter the behaviour of the RasMol
2987
.B dots
2988
command depending upon the value of the
2989
.B solvent
2990
parameter.
2991
When
2992
.B solvent
2993
is
2994
.B true,
2995
the
2996
.B radius
2997
parameter controls whether a true van der Waals' surface
2998
is generated by the
2999
.B dots
3000
command. If the value of
3001
.B radius
3002
is anything other than zero, that value is used as the
3003
radius of each atom instead of its true vdW value. When
3004
the value of
3005
.B solvent
3006
is
3007
.B true,
3008
this parameter determines the 'probe sphere' (solvent) radius.
3009
The parameter may be given as an integer in rasmol units or
3010
containing a decimal point in Angstroms. The default value of
3011
this parameter is determined by the value of
3012
.B solvent
3013
and changing
3014
.B solvent
3015
resets
3016
.B radius
3017
to its new default value.
3018
3019
.TP
3020
.B Set Record
3021
The RasMol
3022
.B set record.aps
3023
gives the maximum on-screen velocity in Angstroms per second in animating
3024
translations, rotations and zooms (default 10 A/second).
3025
3026
The RasMol
3027
.B set record.aps
3028
command gives number of frames per second for recording by the
3029
.B record
3030
command (default 24 frames per second).
3031
3032
The RasMol
3033
.B set record.dwell
3034
command sets the time in seconds to dwell on a change in appearance
3035
(default .5 sec).
3036
3037
.TP
3038
.B Set ShadePower
3039
The
3040
.B shadepower
3041
parameter (adopted from RasTop) determines the shade repartition (the contrast)
3042
used in rendering solid objects. This value between 0 and 100 adjusts
3043
shading on an object surface oriented along the direction to the
3044
light source. Changing the shadepower parameter does not change the
3045
maximum or the minimum values of this shading, as does changing the
3046
.B ambient
3047
parameter. A value of 100 concentrates the light on the top of spheres,
3048
giving a highly specular, glassy rendering (see the
3049
.B specpower
3050
parameter).
3051
A value of 0 distributes the light on the entire object.
3052
3053
This implementation of shadepower differs from the one in RasTop
3054
only in the choice of range (0 to 100 versus -20 to 20 in RasTop).
3055
3056
.TP
3057
.B Set Shadow
3058
The RasMol
3059
.B set shadow
3060
command enables and disables ray-tracing of the currently rendered image.
3061
Currently only the spacefilling representation is shadowed or can cast
3062
shadows. Enabling shadowing will automatically disable the Z-clipping
3063
(slabbing) plane using the command
3064
.B slab off.
3065
Ray-tracing typically takes about several seconds for a moderately sized protein.
3066
It is recommended that shadowing be normally disabled whilst the
3067
molecule is being transformed or manipulated, and only enabled once
3068
an appropiate viewpoint is selected, to provide a greater impression
3069
of depth.
3070
3071
.TP
3072
.B Set SlabMode
3073
The RasMol
3074
.B slabmode
3075
parameter controls the rendering method of objects cut by the
3076
slabbing (z-clipping) plane. Valid slabmode parameters are
3077
"reject", "half", "hollow", "solid" and "section".
3078
3079
.TP
3080
.B Set Solvent
3081
The RasMol
3082
.B set solvent
3083
command is used to control the behaviour of the RasMol
3084
.B dots
3085
command. Depending upon the value of the
3086
.B solvent
3087
parameter, the
3088
.B dots
3089
command either generates a van der Waals' or a solvent
3090
accessible surface around the currently selected set of
3091
atoms. Changing this parameter automatically resets the
3092
value of the RasMol
3093
.B radius
3094
parameter.
3095
The command
3096
.B set solvent false,
3097
the default value, indicates that a van der Waals' surface
3098
should be generated and resets the value of
3099
.B radius
3100
to zero. The command
3101
.B set solvent true
3102
indicates that a 'Connolly' or 'Richards' solvent
3103
accessible surface should be drawn and sets the
3104
.B radius
3105
parameter, the solvent radius, to 1.2 Angstroms (or 300
3106
RasMol units).
3107
3108
.TP
3109
.B Set Specular
3110
The RasMol
3111
.B set specular
3112
command enables and disables the display of specular highlights on
3113
solid objects drawn by RasMol. Specular highlights appear as white
3114
reflections of the light source on the surface of the object. The
3115
current RasMol implementation uses an approximation function to
3116
generate this highlight.
3117
3118
The specular highlights on the surfaces of solid objects may be
3119
altered by using the specular reflection coefficient, which is
3120
altered using the RasMol
3121
.B set specpower
3122
command.
3123
3124
.TP
3125
.B Set SpecPower
3126
The
3127
.B specpower
3128
parameter determines the shininess of solid objects rendered by
3129
RasMol. This value between 0 and 100 adjusts the reflection
3130
coefficient used in specular highlight calculations. The specular
3131
highlights are enabled and disabled by the RasMol
3132
.B set specular
3133
command. Values around 20 or 30 produce plastic looking surfaces.
3134
High values represent more shiny surfaces such as metals, while
3135
lower values produce more diffuse/dull surfaces.
3136
3137
.TP
3138
.B Set SSBonds
3139
The RasMol
3140
.B ssbonds
3141
parameter determines whether disulphide bridges are drawn between
3142
the sulphur atoms in the sidechain (the default) or between the alpha
3143
carbon atoms in the backbone of the cysteines residues. The actual
3144
display of disulphide bridges is controlled by the
3145
.B ssbonds
3146
command. Drawing disulphide bridges between alpha carbons is useful
3147
when the rest of the protein is shown in only a schematic
3148
representation such as
3149
.B backbone,
3150
.B ribbons
3151
or
3152
.B strands.
3153
This parameter is similar to the RasMol
3154
.B hbonds
3155
parameter.
3156
3157
.TP
3158
.B Set Stereo
3159
The RasMol
3160
.B set stereo
3161
parameter controls the separation between the left and
3162
right images. Turning stereo on and off doesn't reposition
3163
the centre of the molecule.
3164
3165
Stereo viewing of a molecule may be turned on (and off) either
3166
by selecting
3167
.B Stereo
3168
from the
3169
.B Options
3170
menu, or by typing the commands
3171
.B stereo on
3172
or
3173
.B stereo off.
3174
3175
The separation angle between the two views may be adjusted with the
3176
.B set stereo [-] <number>
3177
command, where positive values result in crossed eye viewing and
3178
negative values in relaxed (wall-eyed) viewing. Currently, stereo viewing
3179
is not supported in
3180
.B vector PostScript
3181
output files.
3182
3183
.TP
3184
.B Set Strands
3185
The RasMol
3186
.B strands
3187
parameter controls the number of parallel strands that are displayed
3188
in the ribbon representations of proteins. The permissible values for
3189
this parameter are 1, 2, 3, 4, 5 and 9. The default value is 5. The
3190
number of strands is constant for all ribbons being displayed.
3191
However, the ribbon width (the separation between strands) may be
3192
controlled on a residue by residue basis using the RasMol
3193
.B ribbons
3194
command.
3195
3196
.TP
3197
.B Set Transparent
3198
The RasMol
3199
.B transparent
3200
parameter controls the writing of transparent GIFs by the
3201
.B write gif <filename>
3202
command. This may be controlled by the
3203
.B set transparent on
3204
and
3205
.B set transparent off
3206
commands.
3207
3208
.TP
3209
.B Set UnitCell
3210
The RasMol
3211
.B unitcell
3212
parameter controls the display of the crystallographic unit cell on
3213
the current display. The crystal cell is only enabled if the appropriate
3214
crystal symmetry information is contained in the PDB, CIF or mmCIF data
3215
file. The
3216
RasMol command
3217
.B show symmetry
3218
display details of the crystal's space group and unit cell axes. The
3219
.B set unitcell
3220
command is similar to the commands
3221
.B set axes
3222
and
3223
.B set boundbox
3224
that display orthogonal coordinate axes and the bounding box,
3225
respectively.
3226
3227
.TP
3228
.B Set VectPS
3229
The RasMol
3230
.B vectps
3231
parameter is use to control the way in which the RasMol
3232
.B write
3233
command generates vector PostScript output files. The command
3234
.B set vectps on
3235
enables the use of black outlines around spheres and cylinder bonds
3236
producing "cartoon-like" high resolution output. However, the current
3237
implementation of RasMol incorrectly cartoons spheres that are intersected
3238
by more than one other sphere. Hence "ball and stick" models are rendered
3239
correctly but not large spacefilling spheres models. Cartoon outlines
3240
can be disabled, the default, by the command
3241
.B set vectps off.
3242
3243
.TP
3244
.B Set Write
3245
The RasMol
3246
.B write
3247
parameter controls the use of the
3248
.B save
3249
and
3250
.B write
3251
commands within scripts, but it may only be executed from the
3252
command line. By default, this value is
3253
.B false,
3254
prohibiting the generation of files in any scripts executed at
3255
start-up (such as those launched from a WWW browser). However,
3256
animators may start up RasMol interactively: type
3257
.B set write on
3258
and then execute a script to generate each frame using the
3259
source command.
3260
3261
.SH ATOM EXPRESSIONS
3262
RasMol atom expressions uniquely identify an arbitrary group of atoms
3263
within a molecule. Atom expressions are composed of either primitive
3264
expressions,
3265
predefined sets,
3266
comparison operators,
3267
.B within
3268
expressions,
3269
or logical (boolean) combinations of the above expression types.
3270
3271
The logical operators allow complex queries to be constructed out of
3272
simpler ones using the standard boolean connectives
3273
.B and,
3274
.B or
3275
and
3276
.B not.
3277
These may be abbreviated by the symbols
3278
"&", "|" and "!",
3279
respectively. Parentheses (brackets) may be used to alter the
3280
precedence of the operators. For convenience, a comma may also
3281
be used for boolean disjunction.
3282
3283
The atom expression is evaluated for each atom, hence
3284
.B protein and backbone
3285
selects protein backbone atoms, not the protein and [nucleic] acid
3286
backbone atoms!
3287
3288
.TP
3289
.B Primitive Expressions
3290
RasMol primitive expressions are the fundamental building blocks
3291
of atom expressions. There are two types of primitive expression.
3292
The first type is used to identify a given residue number or range
3293
of residue numbers. A single residue is identified by its number
3294
(position in the sequence), and a range is specified by lower and
3295
upper bounds separated by a hyphen character. For example
3296
.B select 5,6,7,8
3297
is also
3298
.B select 5-8.
3299
Note that this selects the given residue numbers in all macromolecule
3300
chains.
3301
3302
The second type of primitive expression specifies a sequence of fields
3303
that must match for a given atom. The first part specifies a residue
3304
(or group of residues) and an optional second part specifies the atoms
3305
within those residues. The first part consists of a residue name,
3306
optionally followed by a residue number and/or chain identifier.
3307
3308
The second part consists of a period character followed by an atom
3309
name. An atom name may be up to four alphabetic or numeric characters.
3310
An optional semicolon followed by an alternate conformation
3311
identifier may be appended. An optional slash followed by a
3312
model number may also be appended.
3313
3314
An asterisk may be used as a wild card for a whole field and a
3315
question mark as a single character wildcard.
3316
3317
.TP
3318
.B Comparison Operators
3319
Parts of a molecule may also be distinguished using equality,
3320
inequality and ordering operators on their properties. The format
3321
of such comparison expression is a property name, followed by a
3322
comparison operator and then an integer value.
3323
3324
The atom properties that may be used in RasMol are
3325
.B atomno
3326
for the atom serial number,
3327
.B elemno
3328
for the atom's atomic number (element),
3329
.B resno
3330
for the residue number,
3331
.B radius
3332
for the spacefill radius in RasMol units (or zero if not represented
3333
as a sphere) and
3334
.B temperature
3335
for the PDB isotropic temperature value.
3336
3337
The equality operator is denoted either
3338
"=" or "==".
3339
The inequality operator as either
3340
"<>", "!=" or "/=".
3341
The ordering operators are
3342
"<"
3343
for less than,
3344
"<="
3345
for less than or equal to,
3346
">"
3347
for greater than, and
3348
">"
3349
for greater than or equal to.
3350
3351
.TP
3352
.B Within Expressions
3353
A RasMol
3354
.B within
3355
expression allows atoms to be selected on their proximity to
3356
another set of atoms. A
3357
.B within
3358
expression takes two parameters separated by a comma and surrounded
3359
by parentheses. The first argument is an integer value called the
3360
"cut-off" distance of the within expression and the second argument
3361
is any valid atom expression. The cut-off distance is expressed in
3362
either integer RasMol units or Angstroms containing a decimal point.
3363
An atom is selected if it is within the cut-off distance of any of
3364
the atoms defined by the second argument. This allows complex
3365
expressions to be constructed containing nested
3366
.B within
3367
expressions.
3368
3369
For example, the command
3370
.B select within(3.2,backbone)
3371
selects any atom within a 3.2 Angstrom radius of any atom in a
3372
protein or nucleic acid backbone.
3373
.B Within
3374
expressions are particularly useful for selecting the atoms
3375
around an active site.
3376
3377
.TP
3378
.B Predefined Sets
3379
RasMol atom expressions may contain predefined sets. These sets
3380
are single keywords that represent portions of a molecule of interest.
3381
Predefined sets are often abbreviations of primitive atom expressions.
3382
In some cases the use of predefined sets allows selection of areas of
3383
a molecule that could not otherwise be distinguished.
3384
A list of the currently predefined sets
3385
is given below.
3386
In addition to the sets listed here, RasMol also treats element names
3387
(and their plurals) as predefined sets containing all atoms of that
3388
element type, i.e. the command
3389
.B select oxygen
3390
is equivalent to the command
3391
.B select elemno=8.
3392
3393
.SH Predefined Sets
3394
.TP
3395
.B AT Set
3396
This set contains the atoms in the complementary nucleotides
3397
adenosine and thymidine (A and T, respectively). All nucleotides
3398
are classified as either the set
3399
.B at
3400
or the set
3401
.B cg
3402
This set is equivalent to the RasMol atom expressions
3403
.B a,t,
3404
and
3405
.B nucleic and not cg.
3406
3407
.TP
3408
.B Acidic Set
3409
The set of acidic amino acids.
3410
These are the residue types Asp and Glu.
3411
All amino acids are classified as either
3412
.B acidic,
3413
.B basic
3414
.B or
3415
.B neutral.
3416
This set is equivalent to the RasMol atom expressions
3417
.B asp, glu
3418
and
3419
.B amino and not (basic or neutral).
3420
3421
.TP
3422
.B Acyclic Set
3423
The set of atoms in amino acids not containing a cycle or
3424
ring. All amino acids are classified as either
3425
.B cyclic
3426
or
3427
.B acyclic.
3428
This set is equivalent to the RasMol atom expression
3429
.B amino and not cyclic.
3430
3431
.TP
3432
.B Aliphatic Set
3433
This set contains the aliphatic amino acids.
3434
These are the amino acids Ala, Gly, Ile, Leu and Val.
3435
This set is equivalent to the RasMol atom expression
3436
.B ala, gly, ile, leu, val.
3437
3438
.TP
3439
.B Alpha Set
3440
The set of alpha carbons in the protein molecule. This set is
3441
approximately equivalent to the RasMol atom expression
3442
.B *.CA.
3443
This command should not be confused with the predefined set
3444
.B helix
3445
which contains the atoms in the amino acids of the protein's
3446
alpha helices.
3447
3448
.TP
3449
.B Amino Set
3450
This set contains all the atoms contained in amino acid residues.
3451
This is useful for distinguishing the protein from the nucleic
3452
acid and heterogeneous atoms in the current molecule database.
3453
3454
.TP
3455
.B Aromatic Set
3456
The set of atoms in amino acids containing aromatic rings.
3457
These are the amino acids His, Phe, Trp and Tyr.
3458
Because they contain aromatic rings all members of this
3459
set are member of the predefined set
3460
.B cyclic.
3461
This set is equivalent to the RasMol atom expressions
3462
.B his, phe, trp, tyr
3463
and
3464
.B cyclic and not pro.
3465
3466
.TP
3467
.B Backbone Set
3468
This set contains the four atoms of each amino acid that form the
3469
polypeptide N-C-C-O backbone of proteins, and the atoms of the sugar
3470
phosphate backbone of nucleic acids.
3471
Use the RasMol predefined sets
3472
.B protein
3473
and
3474
.B nucleic
3475
to distinguish between the two forms of backbone.
3476
Atoms in nucleic acids and proteins are either
3477
.B backbone
3478
or
3479
.B sidechain.
3480
This set is equivalent to the RasMol expression
3481
.B (protein or nucleic) and not sidechain.
3482
3483
The predefined set
3484
.B mainchain
3485
is synonymous with the set
3486
.B backbone.
3487
3488
.TP
3489
.B Basic Set
3490
The set of basic amino acids.
3491
These are the residue types Arg, His and Lys.
3492
All amino acids are classified as either
3493
.B acidic,
3494
.B basic
3495
or
3496
.B neutral.
3497
This set is equivalent to the RasMol atom expressions
3498
.B arg, his, lys
3499
and
3500
.B amino and not (acidic or neutral).
3501
3502
.TP
3503
.B Bonded Set
3504
This set contain all the atoms in the current molecule database that
3505
are bonded to at least one other atom.
3506
3507
.TP
3508
.B Buried Set
3509
This set contains the atoms in those amino acids that tend
3510
(prefer) to be buried inside protein, away from contact with
3511
solvent molecules. This set refers to the amino acids
3512
preference and not the actual solvent accessibility for
3513
the current protein.
3514
All amino acids are classified as either
3515
.B surface
3516
or
3517
.B buried.
3518
This set is equivalent to the RasMol atom expression
3519
.B amino and not surface.
3520
3521
.TP
3522
.B CG Set
3523
This set contains the atoms in the complementary nucleotides
3524
cytidine and guanosine (C and G, respectively). All nucleotides
3525
are classified as either the set
3526
.B at
3527
or the set
3528
.B cg
3529
This set is equivalent to the RasMol atom expressions
3530
.B c,g
3531
and
3532
.B nucleic and not at.
3533
3534
.TP
3535
.B Charged Set
3536
This set contains the charged amino acids. These are the amino
3537
acids that are either
3538
.B acidic
3539
or
3540
.B basic.
3541
Amino acids are classified as being either
3542
.B charged
3543
or
3544
.B neutral.
3545
This set is equivalent to the RasMol atom expressions
3546
.B acidic or basic
3547
and
3548
.B amino and not neutral.
3549
3550
.TP
3551
.B Cyclic Set
3552
The set of atoms in amino acids containing a cycle or rings.
3553
All amino acids are classified as either
3554
.B cyclic
3555
or
3556
.B acyclic.
3557
This set consists of the amino acids His, Phe, Pro, Trp and Tyr.
3558
The members of the predefined set
3559
.B aromatic
3560
are members of this set.
3561
The only cyclic but non-aromatic amino acid is proline.
3562
This set is equivalent to the RasMol atom expressions
3563
.B his, phe, pro, trp, tyr
3564
and
3565
.B aromatic or pro
3566
and
3567
.B amino and not acyclic.
3568
3569
.TP
3570
.B Cystine Set
3571
This set contains the atoms of cysteine residues that form part
3572
of a disulphide bridge, i.e. half cystines. RasMol automatically
3573
determines disulphide bridges, if neither the predefined set
3574
.B cystine
3575
nor the RasMol
3576
.B ssbonds
3577
command have been used since the molecule was loaded. The set of
3578
free cysteines may be determined using the RasMol atom expression
3579
.B cys and not cystine.
3580
3581
.TP
3582
.B Helix Set
3583
This set contains all atoms that form part of a protein alpha
3584
helix as determined by either the PDB file author or Kabsch and
3585
Sander's DSSP algorithm. By default, RasMol uses the secondary
3586
structure determination given in the PDB file if it exists.
3587
Otherwise, it uses the DSSP algorithm as used by the RasMol
3588
.B structure
3589
command.
3590
3591
This predefined set should not be confused with the predefined set
3592
.B alpha
3593
which contains the alpha carbon atoms of a protein.
3594
3595
.TP
3596
.B Hetero Set
3597
This set contains all the heterogeneous atoms in the molecule. These
3598
are the atoms described by HETATM entries in the PDB file. These
3599
typically contain water, cofactors and other solvents and ligands. All
3600
.B hetero
3601
atoms are classified as either
3602
.B ligand
3603
or
3604
.B solvent
3605
atoms. These heterogeneous
3606
.B solvent
3607
atoms are further classified as either
3608
.B water
3609
or
3610
.B ions.
3611
3612
.TP
3613
.B Hydrogen Set
3614
This predefined set contains all the hydrogen, deuterium and tritium atoms
3615
of the current molecule. This predefined set is equivalent to the
3616
RasMol atom expression
3617
.B elemno=1.
3618
3619
.TP
3620
.B Hydrophobic Set
3621
This set contains all the hydrophobic amino acids.
3622
These are the amino acids Ala, Leu, Val, Ile, Pro, Phe, Met and Trp.
3623
All amino acids are classified as either
3624
.B hydrophobic
3625
or
3626
.B polar.
3627
This set is equivalent to the RasMol atom expressions
3628
.B ala, leu, val, ile, pro, phe, met, trp
3629
and
3630
.B amino and not polar.
3631
3632
.TP
3633
.B Ions Set
3634
This set contains all the heterogeneous phosphate and sulphate ions in
3635
the current molecule data file. A large number of these ions are
3636
sometimes associated with protein and nucleic acid structures determined
3637
by X-ray crystallography. These atoms tend to clutter an image. All
3638
.B hetero
3639
atoms are classified as either
3640
.B ligand
3641
or
3642
.B solvent
3643
atoms. All
3644
.B solvent
3645
atoms are classified as either
3646
.B water
3647
or
3648
.B ions.
3649
3650
.TP
3651
.B Large Set
3652
All amino acids are classified as either
3653
.B small,
3654
.B medium
3655
or
3656
.B large.
3657
This set is equivalent to the RasMol atom expression
3658
.B amino and not (small or medium).
3659
3660
.TP
3661
.B Ligand Set
3662
This set contains all the heterogeneous cofactor and ligand moieties that
3663
are contained in the current molecule data file. This set is defined
3664
to be all
3665
.B hetero
3666
atoms that are not
3667
.B solvent
3668
atoms. Hence this set is equivalent to the RasMol atom expression
3669
.B hetero and not solvent.
3670
3671
.TP
3672
.B Medium Set
3673
All amino acids are classified as either
3674
.B small,
3675
.B medium
3676
or
3677
.B large.
3678
This set is equivalent to the RasMol atom expression
3679
.B amino and not (large or small).
3680
3681
.TP
3682
.B Neutral Set
3683
The set of neutral amino acids.
3684
All amino acids are classified as either
3685
.B acidic,
3686
.B basic
3687
or
3688
.B neutral.
3689
This set is equivalent to the RasMol atom expression
3690
.B amino and not (acidic or basic).
3691
3692
.TP
3693
.B Nucleic Set
3694
The set of all atoms in nucleic acids, which consists of the four
3695
nucleotide bases adenosine, cytidine, guanosine and thymidine (A,
3696
C, G and T, respectively). All neucleotides are classified as either
3697
.B purine
3698
or
3699
.B pyrimidine.
3700
This set is equivalent to the RasMol atom expressions
3701
.B a,c,g,t
3702
and
3703
.B purine or pyrimidine.
3704
The symbols for RNA nucleotides (U, +U, I, 1MA, 5MC, OMC,
3705
1MG, 2MG, M2G, 7MG, OMG, YG, H2U, 5MU, and PSU) are also
3706
recognized as members of this set.
3707
3708
.TP
3709
.B Polar Set
3710
This set contains the polar amino acids.
3711
All amino acids are classified as either
3712
.B hydrophobic
3713
or
3714
.B polar.
3715
This set is equivalent to the RasMol atom expression
3716
.B amino and not hydrophobic.
3717
3718
.TP
3719
.B Protein Set
3720
The set of all atoms in proteins. This consists of the RasMol
3721
predefined set
3722
.B amino
3723
and common post-translation modifications.
3724
3725
.TP
3726
.B Purine Set
3727
The set of purine nucleotides.
3728
These are the bases adenosine and guanosine (A and G, respectively).
3729
All nucleotides are either
3730
.B purines
3731
or
3732
.B pyrimidines.
3733
This set is equivalent to the RasMol atom expressions
3734
.B a,g
3735
and
3736
.B nucleic and not pyrimidine.
3737
3738
.TP
3739
.B Pyrimidine Set
3740
The set of pyrimidine nucleotides.
3741
These are the bases cytidine and thymidine (C and T, respectively).
3742
All nucleotides are either
3743
.B purines
3744
or
3745
.B pyrimidines.
3746
This set is equivalent to the RasMol atom expressions
3747
.B c,t
3748
and
3749
.B nucleic and not purine.
3750
3751
.TP
3752
.B Selected Set
3753
This set contains the set of atoms in the currently selected
3754
region. The currently selected region is defined by the preceding
3755
.B select
3756
or
3757
.B restrict
3758
command and not the atom expression containing the
3759
.B selected
3760
keyword.
3761
3762
.TP
3763
.B Sheet Set
3764
This set contains all atoms that form part of a protein beta
3765
sheet as determined by either the PDB file author or Kabsch and
3766
Sander's DSSP algorithm. By default, RasMol uses the secondary
3767
structure determination given in the PDB file if it exists.
3768
Otherwise, it uses the DSSP algorithm as used by the RasMol
3769
.B structure
3770
command.
3771
3772
.TP
3773
.B Sidechain Set
3774
This set contains the functional sidechains of any amino acids
3775
and the base of each nucleotide. These are the atoms not part of
3776
the polypeptide N-C-C-O backbone of proteins or the sugar
3777
phosphate backbone of nucleic acids.
3778
Use the RasMol predefined sets
3779
.B protein
3780
and
3781
.B nucleic
3782
to distinguish between the two forms of sidechain.
3783
Atoms in nucleic acids and proteins are either
3784
.B backbone
3785
or
3786
.B sidechain.
3787
This set is equivalent to the RasMol expression
3788
.B (protein or nucleic) and not backbone.
3789
3790
.TP
3791
.B Small Set
3792
All amino acids are classified as either
3793
.B small,
3794
.B medium
3795
or
3796
.B large.
3797
This set is equivalent to the RasMol atom expression
3798
.B amino and not (medium or large).
3799
3800
.TP
3801
.B Solvent Set
3802
This set contains the solvent atoms in the molecule coordinate file.
3803
These are the heterogeneous water molecules, phosphate and sulphate
3804
ions. All
3805
.B hetero
3806
atoms are classified as either
3807
.B ligand
3808
or
3809
.B solvent
3810
atoms. All
3811
.B solvent
3812
atoms are classified as either
3813
.B water
3814
or
3815
.B ions.
3816
This set is equivalent to the RasMol atom expressions
3817
.B hetero and not ligand
3818
and
3819
.B water or ions.
3820
3821
.TP
3822
.B Surface Set
3823
This set contains the atoms in those amino acids that tend
3824
(prefer) to be on the surface of proteins, in contact with
3825
solvent molecules. This set refers to the amino acids
3826
preference and not the actual solvent accessibility for
3827
the current protein.
3828
All amino acids are classified as either
3829
.B surface
3830
or
3831
.B buried.
3832
This set is equivalent to the RasMol atom expression
3833
.B amino and not buried.
3834
3835
.TP
3836
.B Turn Set
3837
This set contains all atoms that form part of a protein turns
3838
as determined by either the PDB file author or Kabsch and
3839
Sander's DSSP algorithm. By default, RasMol uses the secondary
3840
structure determination given in the PDB file if it exists.
3841
Otherwise, it uses the DSSP algorithm as used by the RasMol
3842
.B structure
3843
command.
3844
3845
.TP
3846
.B Water Set
3847
This set contains all the heterogeneous water molecules in the current
3848
database. A large number of water molecules are sometimes associated
3849
with protein and nucleic acid structures determined by X-ray
3850
crystallography. These atoms tend to clutter an image.
3851
All
3852
.B hetero
3853
atoms are classified as either
3854
.B ligand
3855
or
3856
.B solvent
3857
atoms. The
3858
.B solvent
3859
atoms are further classified as either
3860
.B water
3861
or
3862
.B ions.
3863
3864
.TP
3865
.B Set Summary
3866
The table below summarises RasMol's classification of the common amino acids.
3867
3868
.SH COLOUR SCHEMES
3869
The RasMol
3870
.B colour
3871
command allows different objects (such as atoms, bonds and ribbon segments)
3872
to be given a specified colour. Typically this colour is either a RasMol
3873
predefined colour name or an RGB triple. Additionally RasMol also supports
3874
.B alt,
3875
.B amino,
3876
.B chain,
3877
.B charge,
3878
.B cpk,
3879
.B group,
3880
.B model,
3881
.B shapely,
3882
.B structure,
3883
.B temperature
3884
or
3885
.B user
3886
colour schemes for atoms, and
3887
.B hbond type
3888
colour scheme for hydrogen bonds and
3889
.B electrostatic potential
3890
colour scheme for dot surfaces.
3891
The 24 currently predefined colour
3892
names are
3893
Black, Blue, BlueTint, Brown, Cyan, Gold, Grey, Green,
3894
GreenBlue, GreenTint, HotPink, Magenta, Orange, Pink,
3895
PinkTint, Purple, Red, RedOrange, SeaGreen, SkyBlue,
3896
Violet, White, Yellow and YellowTint
3897
3898
If you frequently wish to use a colour not predefined, you can write
3899
a one-line script. For example, if you make the file
3900
.B grey.col
3901
containing the line,
3902
.B colour [180,180,180] #grey,
3903
then the command
3904
.B script grey.col
3905
colours the currently selected atom set grey.
3906
3907
.TP
3908
.B Alt Colours
3909
The RasMol
3910
.B alt
3911
(Alternate Conformer)
3912
colour scheme codes the base
3913
structure with one colour and applies a limited number of colours to each
3914
alternate conformer. In a RasMol built for 8-bit colour systems, 4 colours
3915
are allowed for alternate conformers. Otherwise, 8 colours are available.
3916
3917
.TP
3918
.B Amino Colours
3919
The RasMol
3920
.B amino
3921
colour scheme colours amino acids according to traditional amino acid
3922
properties. The purpose of colouring is to identify amino acids in an
3923
unusual or surprising environment. The outer parts of a protein that are
3924
polar are visible (bright) colours and non-polar residues darker. Most
3925
colours are hallowed by tradition. This colour scheme is similar to the
3926
.B shapely
3927
scheme.
3928
3929
.TP
3930
.B Chain Colours
3931
The RasMol
3932
.B chain
3933
colour scheme assigns each macromolecular chain a unique colour. This
3934
colour scheme is particularly useful for distinguishing the parts of
3935
multimeric structure or the individual 'strands' of a DNA chain.
3936
.B Chain
3937
can be selected from the RasMol
3938
.B Colours
3939
menu.
3940
3941
.TP
3942
.B Charge Colours
3943
The RasMol
3944
.B charge
3945
colour scheme colour codes each atom according to the charge value
3946
stored in the input file (or beta factor field of PDB files). High
3947
values are coloured in blue (positive) and lower values coloured in
3948
red (negative). Rather than use a fixed scale this scheme determines
3949
the maximum and minimum values of the charge/temperature field and
3950
interpolates from red to blue appropriately. Hence, green cannot be
3951
assumed to be 'no net charge' charge.
3952
3953
The difference between the
3954
.B charge
3955
and
3956
.B temperature
3957
colour schemes is that increasing temperature values proceed from blue
3958
to red, whereas increasing charge values go from red to blue.
3959
3960
If the charge/temperature field stores reasonable values it is possible
3961
to use the RasMol
3962
.B colour dots potential
3963
command to colour code a dot surface (generated by the
3964
.B dots
3965
command) by electrostatic potential.
3966
3967
.TP
3968
.B CPK Colours
3969
The RasMol
3970
.B cpk
3971
colour scheme is based upon the colours of the popular plastic
3972
spacefilling models which were developed by Corey, Pauling and later
3973
improved by Kultun. This colour scheme colours 'atom' objects by the
3974
atom (element) type. This is the scheme conventionally used by chemists.
3975
The assignment of the most commonly used element types to colours is
3976
given below.
3977
3978
.TP
3979
.B Group Colours
3980
The RasMol
3981
.B group
3982
colour scheme colour codes residues by their position in a macromolecular
3983
chain. Each chain is drawn as a smooth spectrum from blue through green,
3984
yellow and orange to red. Hence the N terminus of proteins and 5' terminus
3985
of nucleic acids are coloured red and the C terminus of proteins and 3'
3986
terminus of nucleic acids are drawn in blue. If a chain has a large number
3987
of heterogeneous molecules associated with it, the macromolecule may not be
3988
drawn in the full 'range' of the spectrum.
3989
.B Group
3990
can be selected from the RasMol
3991
.B Colours
3992
menu.
3993
3994
If a chain has a large number of heterogeneous molecules associated with it,
3995
the macromolecule may not be drawn in the full range of the spectrum. When
3996
RasMol performs group colouring it decides the range of colours it uses from
3997
the residue numbering given in the PDB file. Hence the lowest residue
3998
number is displayed in blue and the highest residue number is displayed as
3999
red. Unfortunately, if a PDB file contains a large number of heteroatoms,
4000
such as water molecules, that occupy the high residue numbers, the protein
4001
is displayed in the blue-green end of the spectrum and the waters in the
4002
yellow-red end of the spectrum. This is aggravated by there typically being
4003
many more water molecules than amino acid residues. The solution to this
4004
problem is to use the command
4005
.B set hetero off
4006
before applying the group
4007
colour scheme. This can also be achieved by toggling
4008
.B Hetero Atoms
4009
on the
4010
.B Options
4011
menu before selecting
4012
.B Group
4013
on the
4014
.B Colour
4015
menu. This command
4016
instructs RasMol to only use non-hetero residues in the group colour scaling.
4017
4018
.TP
4019
.B NMR Model Colours
4020
The RasMol
4021
.B model
4022
colour scheme codes each NMR model with a distinct
4023
colour. The NMR model number is taken as a numeric value. High values
4024
are coloured in blue and lower values coloured in red. Rather than use a
4025
fixed scale this scheme determines the maximum value of the
4026
NMR model number and interpolates from red to blue appropriately.
4027
4028
.TP
4029
.B Shapely Colours
4030
The RasMol
4031
.B shapely
4032
colour scheme colour codes residues by amino acid property. This scheme
4033
is based upon Bob Fletterick's "Shapely Models". Each amino acid and
4034
nucleic acid residue is given a unique colour. The
4035
.B shapely
4036
colour scheme is used by David Bacon's Raster3D program. This colour
4037
scheme is similar to the
4038
.B amino
4039
colour scheme.
4040
4041
.TP
4042
.B Structure Colours
4043
The RasMol
4044
.B structure
4045
colour scheme colours the molecule by protein secondary structure.
4046
Alpha helices are coloured magenta, [240,0,128], beta sheets are
4047
coloured yellow, [255,255,0], turns are coloured pale blue, [96,128,255]
4048
and all other residues are coloured white. The secondary structure
4049
is either read from the PDB file (HELIX, SHEET and TURN records), if available,
4050
or determined using Kabsch and Sander's DSSP algorithm. The RasMol
4051
.B structure
4052
command may be used to force DSSP's structure assignment to be used.
4053
4054
.TP
4055
.B Temperature Colours
4056
The RasMol
4057
.B temperature
4058
colour scheme colour codes each atom according to the anisotropic
4059
temperature (beta) value stored in the PDB file. Typically this gives
4060
a measure of the mobility/uncertainty of a given atom's position. High
4061
values are coloured in warmer (red) colours and lower values in colder
4062
(blue) colours. This feature is often used to associate a "scale" value
4063
[such as amino acid variability in viral mutants] with each atom in a
4064
PDB file, and colour the molecule appropriately.
4065
4066
The difference between the
4067
.B temperature
4068
and
4069
.B charge
4070
colour schemes is that increasing temperature values proceed from blue
4071
to red, whereas increasing charge values go from red to blue.
4072
4073
.TP
4074
.B User Colours
4075
The RasMol
4076
.B user
4077
colour scheme allows RasMol to use the colour scheme stored in the
4078
PDB file. The colours for each atom are stored in COLO records placed
4079
in the PDB data file. This convention was introduced by David Bacon's
4080
Raster3D program.
4081
4082
.TP
4083
.B HBond Type Colours
4084
The RasMol
4085
.B type
4086
colour scheme applies only to hydrogen bonds, hence is used in the command
4087
.B colour hbonds type.
4088
This scheme colour codes each hydrogen bond according to the
4089
distance along a protein chain between hydrogen bond donor and acceptor.
4090
This schematic representation was introduced by Belhadj-Mostefa and
4091
Milner-White. This representation gives a good insight into protein
4092
secondary structure (hbonds forming alpha helices appear red, those
4093
forming sheets appear yellow and those forming turns appear magenta).
4094
4095
.TP
4096
.B Potential Colours
4097
The RasMol
4098
.B potential
4099
colour scheme applies only to dot surfaces, hence is used in the command
4100
.B colour dots potential.
4101
This scheme colours each currently displayed dot by the electrostatic
4102
potential at that point in space. This potential is calculated using
4103
Coulomb's law taking the temperature/charge field of the input file to
4104
be the charge assocated with that atom. This is the same interpretation
4105
used by the
4106
.B colour charge
4107
command. Like the
4108
.B charge
4109
colour scheme low values are blue/white and high values are red.
4110
4111
.TP
4112
.B Amino Acid Codes
4113
The following table lists the names, single letter and three letter
4114
codes of each of the amino acids.
4115
4116
.TP
4117
.B Booleans
4118
A boolean parameter is a truth value. Valid boolean values are 'true' and
4119
'false', and their synonyms 'on' and 'off'. Boolean parameters are commonly
4120
used by RasMol to either enable or disable a representation or option.
4121
4122
.SH FILE FORMATS
4123
4124
.B Protein Data Bank Files
4125
4126
If you do not have the PDB documentation, you may find the
4127
following summary of the PDB file format useful. The Protein Data Bank
4128
is a computer-based archival database for macromolecular structures.
4129
The database was established in 1971 by Brookhaven National
4130
Laboratory, Upton, New York, as a public domain repository for resolved
4131
crystallographic structures. The Bank uses a uniform format to store
4132
atomic coordinates and partial bond connectivities as derived from
4133
crystallographic studies. In 1999 the Protein Data Bank moved
4134
to the Research Collaboratory for Structural Biology.
4135
4136
PDB file entries consist of records of 80 characters each. Using the
4137
punched card analogy, columns 1 to 6 contain a record-type identifier,
4138
the columns 7 to 70 contain data. In older entries, columns 71 to 80
4139
are normally blank,
4140
but may contain sequence information added by library management
4141
programs. In new entries conforming to the 1996 PDB format, there
4142
is other information in those columns. The first four characters of
4143
the record identifier are
4144
sufficient to identify the type of record uniquely, and the syntax of
4145
each record is independent of the order of records within any entry for
4146
a particular macromolecule.
4147
4148
The only record types that are of major interest to the RasMol program
4149
are the ATOM and HETATM records which describe the position of each
4150
atom. ATOM/HETATM records contain standard atom names and residue
4151
abbreviations, along with sequence identifiers, coordinates in
4152
Angstrom units, occupancies and thermal motion factors. The exact
4153
details are given below as a FORTRAN format statement. The "fmt"
4154
column indicates use of the field in all PDB formats,
4155
in the 1992 and earlier formats or in the 1996 and later formats.
4156
4157
Residues occur in order starting from the N-terminal residue
4158
for proteins and
4159
5'-terminus for nucleic acids. If the residue sequence is known,
4160
certain atom serial numbers may be omitted to allow for future insertion
4161
of any missing atoms. Within each residue, atoms are ordered in a
4162
standard manner, starting with the backbone (N-C-C-O for proteins) and
4163
proceeding in increasing remoteness from the alpha carbon, along the
4164
side chain.
4165
4166
HETATM records are used to define post-translational modifications and
4167
cofactors associated with the main molecule. TER records are
4168
interpreted as breaks in the main molecule's backbone.
4169
4170
If present, RasMol also inspects HEADER, COMPND, HELIX, SHEET, TURN,
4171
CONECT, CRYST1, SCALE, MODEL, ENDMDL, EXPDTA and END records. Information such as the
4172
name, database code, revision date and classification of the molecule
4173
are extracted from HEADER and COMPND records, initial secondary
4174
structure assignments are taken from HELIX, SHEET and TURN records, and
4175
the end of the file may be indicated by an END record.
4176
4177
.TP
4178
.B RasMol Interpretation of PDB fields
4179
Atoms located at 9999.000, 9999.000, 9999.000 are assumed to be Insight
4180
pseudo atoms and are ignored by RasMol. Atom names beginning ' Q' are
4181
also assumed to be pseudo atoms or position markers.
4182
4183
When a data file contains an NMR structure, multiple conformations may
4184
be placed in a single PDB file delimited by pairs of MODEL and ENDMDL
4185
records. RasMol displays all the NMR models contained in the file.
4186
4187
Residue names "CSH", "CYH" and "CSM" are considered pseudonyms for
4188
cysteine "CYS". Residue names "WAT", "H20", "SOL" and "TIP" are
4189
considered pseudonyms for water "HOH". The residue name "D20" is
4190
consider heavy water "DOD". The residue name "SUL" is considered a
4191
sulphate ion "SO4". The residue name "CPR" is considered to be
4192
cis-proline and is translated as "PRO". The residue name "TRY" is
4193
considered a pseudonym for tryptophan "TRP".
4194
4195
RasMol uses the HETATM fields to define the sets hetero, water, solvent
4196
and ligand. Any group with the name "HOH", "DOD", "SO4" or "PO4" (or
4197
aliased to one of these names by the preceding rules) is considered a
4198
solvent and is considered to be defined by a HETATM field.
4199
4200
RasMol only respects CONECT connectivity records in PDB files containing
4201
fewer than 256 atoms. This is explained in more detail in the section on
4202
determining molecule connectivity. CONECT records that define a bond
4203
more than once are interpreted as specifying the bond order of that
4204
bond, i.e. a bond specified twice is a double bond and a bond specified
4205
three (or more) times is a triple bond. This is not a standard PDB feature.
4206
4207
.TP
4208
.B PDB Colour Scheme Specification
4209
RasMol also accepts the supplementary COLO record type in the PDB
4210
files. This record format was introduced by David Bacon's Raster3D
4211
program for specifying the colour scheme to be used when rendering the
4212
molecule. This extension is not currently supported by the PDB. The
4213
COLO record has the same basic record type as the ATOM and HETATM
4214
records described above.
4215
4216
Colours are assigned to atoms using a matching process. The Mask field
4217
is used in the matching process as follows. First RasMol reads in and
4218
remembers all the ATOM, HETATM and COLO records in input order. When the
4219
user-defined ('User') colour scheme is selected, RasMol goes through
4220
each remembered ATOM/HETATM record in turn, and searches for a COLO
4221
record that matches in all of columns 7 through 30. The first such COLO
4222
record to be found determines the colour and radius of the atom.
4223
4224
Note that the Red, Green and Blue components are in the same positions
4225
as the X, Y, and Z components of an ATOM or HETA record, and the van
4226
der Waals radius goes in the place of the Occupancy. The Red, Green and
4227
Blue components must all be in the range 0 to 1.
4228
4229
In order that one COLO record can provide colour and radius
4230
specifications for more than one atom (e.g. based on residue, atom
4231
type, or any other criterion for which labels can be given somewhere in
4232
columns 7 through 30), a 'don't-care' character, the hash mark "#"
4233
(number or sharp sign) is used. This character, when found in a COLO
4234
record, matches any character in the corresponding column in a
4235
ATOM/HETATM record. All other characters must match identically to count
4236
as a match. As an extension to the specification, any atom that fails
4237
to match a COLO record is displayed in white.
4238
4239
.TP
4240
.B Multiple NMR Models
4241
RasMol loads all of the NMR models from a PDB file no matter which
4242
command is used:
4243
.B load pdb <filename>
4244
or
4245
.B load nmrpdb <filename>
4246
4247
Once multiple NMR conformations have been loaded they may be
4248
manipulated with the atom expression extensions described in
4249
.B Primitive Expressions.
4250
In particular, the command
4251
.B restrict */1
4252
will restrict the display to the first model only.
4253
4254
.TP
4255
.B CIF and mmCIF Format Files
4256
CIF is the IUCr standard for presentation of small molecules and mmCIF
4257
is intended as the replacement for the fixed-field PDB format for
4258
presentation of macromolecular structures. RasMol can accept data sets
4259
in either format.
4260
4261
There are many useful sites on the World Wide Web where information
4262
tools and software related to CIF, mmCIF and the PDB can be found. The
4263
following are good starting points for exploration:
4264
4265
The International Union of Crystallography (IUCr) provides access to
4266
software, dictionaries, policy statements and documentation relating to
4267
CIF and mmCIF at: IUCr, Chester, England (www.iucr.org/iucr-top/cif/)
4268
with many mirror sites.
4269
4270
The Nucleic Acid Database Project provides access to its entries,
4271
software and documentation, with an mmCIF page giving access to the
4272
dictionary and mmCIF software tools at Rutgers University, New Jersey,
4273
USA (http://ndbserver.rutgers.edu/NDB/mmcif) with many mirror sites.
4274
4275
This version of RasMol restricts CIF or mmCIF tag values to essentially
4276
the same conventions as are used for the fixed-field PDB format. Thus
4277
chain identifiers and alternate conformation identifiers are limited to
4278
a single character, atom names are limited to 4 characters, etc. RasMol
4279
interprets the following CIF and mmCIF tags:
4280
A search is made through multiple data blocks for the desired tags, so
4281
a single dataset may be composed from multiple data blocks, but
4282
multiple data sets may not be stacked in the same file.
4283
4284
.SH MACHINE-SPECIFIC SUPPORT
4285
4286
In the following sections, support for
4287
.B Monochrome X-Windows,
4288
.B Tcl/Tk IPC,
4289
.B UNIX sockets based IPC,
4290
.B Compiling RasWin with Borland and MetroWerks
4291
are described.
4292
4293
.TP
4294
.B Monochrome X-Windows Support
4295
RasMol supports the many
4296
monochrome UNIX workstations typically found in academia, such as low-end
4297
SUN workstations and NCD X-terminals. The X11 version of RasMol (when
4298
compiled in 8 bit mode) now detects black and white X-Windows displays and
4299
enables dithering automatically. The use of run-time error diffusion dithering
4300
means that all display modes of RasMol are available when in monochrome
4301
mode. For best results, users should experiment with the set ambient
4302
command to ensure the maximum contrast in resulting images.
4303
4304
.TP
4305
.B Tcl/Tk IPC support
4306
Version 4 of Tk
4307
graphics library changed the protocol used to communicate between Tk
4308
applications. RasMol version 2.6 was modified such that it could
4309
communicate with both this new protocol and the previous version 3 protocol
4310
supported by RasMol v2.5. Although Tcl/Tk 3.x applications may only
4311
communicate with other 3.x applications and Tcl/Tk 4.x applications with other
4312
4.x applications, these changes allow RasMol to communicate between
4313
processes with both protocols (potentially concurrently).
4314
4315
.TP
4316
.B UNIX sockets based IPC
4317
The UNIX implementation of RasMol
4318
supports BSD-style socket communication. An identical socket mechanism is
4319
also being developed for VMS, Apple Macintosh and Microsoft Windows
4320
systems. This should allow RasMol to interactively display results of a
4321
computation on a remote host. The current protocol acts as a TCP/IP server on
4322
port 21069 that executes command lines until either the command
4323
.B exit
4324
or the
4325
command
4326
.B quit
4327
is typed. The command
4328
exit
4329
from the RasMol server, the command
4330
.B quit
4331
both disconnects the current
4332
session and terminates RasMol. This functionality may be tested using the
4333
UNIX command
4334
.B telnet <hostname> 21069.
4335
4336
.TP
4337
.B Compiling RasWin with Borland and MetroWerks
4338
A number of changes were made to the
4339
source code in the transition from version 2.5 to 2.6 to allow
4340
the Microsoft Windows version of RasMol to compile
4341
using the Borland C/C++ compiler. These fixes include name changes for the
4342
standard library and special code to avoid a bug in _fmemset.
4343
Additional changes were made in the transition from 2.6 to 2.7 to
4344
allow compilation with the MetroWerks compilers.
4345
4346
.SH BIBLIOGRAPHY
4347
4348
.B Molecular Graphics
4349
4350
[1] Nelson Max, "Computer Representation of Molecular Surfaces", IEEE
4351
Computer Graphics and Applications, pp.21-29, August 1983.
4352
4353
[2] Arthur M. Lesk, "Protein Architecture: A Practical Approach", IRL
4354
Press Publishers, 1991.
4355
4356
.B Molecular Graphics Programs
4357
4358
[3] Per J. Kraulis, "MOLSCRIPT: A Program to Produce both Detailed and
4359
Schematic Plots of Protein Structures", Journal of Applied
4360
Crystallography, Vol.24, pp.946-950, 1991.
4361
4362
[4] David Bacon and Wayne F. Anderson, "A Fast Algorithm for Rendering
4363
Space-Filling Molecule Pictures", Journal of Molecular Graphics, Vol.6,
4364
No.4, pp.219-220, December 1988.
4365
4366
[5] David C. Richardson and Jane S. Richardson, "The Kinemage: A tool
4367
for Scientific Communication", Protein Science, Vol.1, No.1,pp.3-9,
4368
January 1992.
4369
4370
[6] Mike Carson, "RIBBONS 2.0", Journal of Applied Crystallography,
4371
Vol.24, pp.958-961, 1991.
4372
4373
[7] Conrad C. Huang, Eric F. Pettersen, Teri E. Klein, Thomas E.
4374
Ferrin and Robert Langridge, "Conic: A Fast Renderer for
4375
Space-Filling Molecules with Shadows", Journal of Molecular Graphics,
4376
Vol.9, No.4, pp.230-236, December 1991.
4377
4378
.B Molecular Biology Algorithms
4379
4380
[8] Wolfgang Kabsch and Christian Sander, "Dictionary of Protein
4381
Secondary Structure: Pattern Recognition of Hydrogen-Bonded and
4382
Geometrical Features", Biopolymers, Vol.22, pp.2577-2637, 1983.
4383
4384
[9] Michael L. Connolly, "Solvent-Accessible Surfaces of Proteins and Nucleic
4385
Acids", Science, Vol.221, No.4612, pp.709-713, August 1983.
4386
4387
[10] Khaled Belhadj-Mostefa, Ron Poet and E. James Milner-White,
4388
"Displaying Inter-Main Chain Hydrogen Bond Patterns in Proteins",
4389
Journal of Molecular Graphics, Vol.9, No.3, pp.194-197, September 1991.
4390
4391
[11] Mike Carson, "Ribbon Models of Macromolecules", Journal of
4392
Molecular Graphics, Vol.5, No.2, pp.103-106, June 1987.
4393
4394
[12] Mike Carson and Charles E. Bugg, "Algorithm for Ribbon Models of
4395
Proteins", Journal of Molecular Graphics, Vol.4, No.2, pp.121-122, June
4396
1986.
4397
4398
[13] H. Iijima, J. B. Dunbar Jr. and G. Marshall, "Calibration of
4399
Effective van der Waals Atomic Contact Radii for Proteins and
4400
Peptides", Proteins: Structure, Functions and Genetics, Vol.2,
4401
pp.330-339,1987.
4402
4403
.B Graphics Algorithms
4404
4405
[14] J. Foley, A. van Dam, S. Feiner and J. Hughes, "Computer Graphics:
4406
Principles and Practice", 2nd Edition, Addison Wesley Publishers, 1990.
4407
4408
[15] J. Cleary and G. Wyvill, "Analysis of an Algorithm for Fast Ray
4409
Tracing using Uniform Space Subdivision", The Visual Computer, Vol.4,
4410
pp.65-83, 1988.
4411
4412
[16] Thomas Porter,"Spherical Shading", Computer Graphics Vol.12, ACM
4413
SIGGRAPH, pp.282-285, 1978.
4414
4415
[17] Jean-Michel Cense, "Exact Visibility Calculation for Space-Filling
4416
Molecular Models", Journal of Molecular Graphics, Vol.9, No.3,
4417
pp.191-193, September 1991.
4418
4419
[18] Chris Schafmeister, "Fast Algorithm for Generating CPK Images on
4420
Graphics Workstations", Journal of Molecular Graphics, Vol.8, No.4,
4421
pp.201-206, December 1990.
4422
4423
[19] Bruce A. Johnson, "MSURF: A Rapid and General Program for the
4424
Representation of Molecular Surfaces", Journal of Molecular Graphics,
4425
Vol.5, No.3, pp.167-169, September 1987.
4426
4427
.B File Formats
4428
4429
[20] Frances C. Bernstein et al., "The Protein Data Bank: A
4430
Computer-Based Archival File for Macromolecular Structures", Journal of
4431
Molecular Biology, Vol.112, pp.535-542, 1977.
4432
4433
[21] Arthur Dalby, James G. Nourse, W. Douglas Hounshell, Ann K. I.
4434
Gushurst, David L. Grier, Burton A. Leland and John Laufer, "Description
4435
of Several Chemical File Formats Used by Computer Programs Developed at
4436
Molecular Design Limited", Journal of Chemical Information and Computer
4437
Sciences, Vol.32, No.3, pp.244-255, 1992.
4438
4439
[22] Adobe Systems Inc., "PostScript Language Reference Manual",
4440
Addison-Wesley Publishers, Reading, Mass., 1985.
4441
4442
[23] Philip E. Bourne et al., "The Macromolecular Crystallographic
4443
Information File (mmCIF)", Meth. Enzymol. (1997) 277, 571-590.
4444
4445
[24] Sydney R. Hall, "The STAR File: a New Format for Electronic Data
4446
Transfer and Archiving", Journal of Chemical Information and Computer
4447
Sciences, Vol. 31, 326-333, 1991.
4448
4449
.SH SEE ALSO
4450
The RasMol User Manual!
4451
4452
.SH AUTHOR
4453
1992-1998 by Roger Sayle (rasmol@ggr.co.uk)
Loggerhead is a web-based interface for Breezy
Version: 2.0.1