Author | Version, Date | Copyright |
---|---|---|
Arne Mueller | RasMol 2.6x1 May 1998 | © Arne Mueller 1998 |
Gary Grossman and Marco Molinaro | RasMol 2.5-ucb November 1995 RasMol 2.6-ucb November 1996 | © UC Regents/ModularCHEM Consortium 1995, 1996 |
Philippe Valadon | RasTop 1.3 August 2000 | © Philippe Valadon 2000 |
Herbert J. Bernstein | RasMol 2.7.0 March 1999 RasMol 2.7.1 June 1999 RasMol 2.7.1.1 January 2001 RasMol 2.7.2 August 2000 RasMol 2.7.2.1 April 2001 RasMol 2.7.2.1.1 January 2004 RasMol 2.7.3 February 2005 RasMol 2.7.3.1 Apr 06 RasMol 2.7.4 November 2007 RasMol 2.7.4.1 January 2008 RasMol 2.7.4.2 March 2008 RasMol 2.7.5 June 2009 RasMol 2.7.5.1 July 2009 | © Herbert J. Bernstein 1998-2009 |
RasMol 2.7.5 incorporates changes by T. Ikonen, G. McQuillan, N. Darakev and L. Andrews (via the neartree package). Work on RasMol 2.7.5 supported in part by grant 1R15GM078077-01 from the National Institute of General Medical Sciences (NIGMS), U.S. National Institutes of Health and by grant ER63601-1021466-0009501 from the Office of Biological & Environmental Research (BER), Office of Science, U. S. Department of Energy. RasMol 2.7.4 incorporated changes by G. Todorov, Nan Jia, N. Darakev, P. Kamburov, G. McQuillan, and J. Jemilawon. Work on RasMol 2.7.4 supported in part by grant 1R15GM078077-01 from the NIGMS/NIH and grant ER63601-1021466-0009501 from BER/DOE. RasMol 2.7.3 incorporates changes by Clarice Chigbo, Ricky Chachra, and Mamoru Yamanishi. Work on RasMol 2.7.3 supported in part by grants DBI-0203064, DBI-0315281 and EF-0312612 from the U.S. National Science Foundation and grant DE-FG02-03ER63601 from BER/DOE. The content is solely the responsibility of the authors and does not necessarily represent the official views of the funding organizations.
The code for use of RasMol under GTK in RasMol 2.7.4.2 was written by Teemu Ikonen.
Author | Item | Language |
---|---|---|
Isabel Serván Martínez, José Miguel Fernández Fernández | 2.6 Manual | Spanish |
José Miguel Fernández Fernández | 2.7.1 Manual | Spanish |
Fernando Gabriel Ranea | 2.7.1 menus and messages | Spanish |
Jean-Pierre Demailly | 2.7.1 menus and messages | French |
Giuseppe Martini, Giovanni Paolella, A. Davassi, M. Masullo, C. Liotto | 2.7.1 menus and messages 2.7.1 help file | Italian |
G. Pozhvanov | 2.7.3 menus and messages | Russian |
G. Todorov | 2.7.3 menus and messages | Bulgarian |
Nan Jia, G. Todorov | 2.7.3 menus and messages | Chinese |
Mamoru Yamanishi, Katajima Hajime | 2.7.3 menus and messages | Japanese |
The original RasMol manual was created by Roger Sayle. In July 1996, Dr. Margaret Wong of the Chemistry Department, Swinburne University of Technology, Australia, made extensive revisions to the RasMol 2.5 manual to accurately reflect the operation of RasMol 2.6. Eric Martz of the University of Massachusetts made further revisions. In May 1997, William McClure of Carnegie Mellon University reorganized the HTML version of the manual into multiple sections which could be downloaded quickly and added use of frames. Portions of the 2.7.1 version of the RasMol manual were derived with permission from William McClure's version using Roger Sayle's rasmol.doc for version 2.6.4 as the primary source. Changes have been made in August 2000 for RasMol version 2.7.2, January 2001 for RasMol version 2.7.1.1, April 2001 for RasMol version 2.7.2.1 and February 2005 for RasMol version 2.7.3 and November 2007, January 2008 and March 2008 for RasMol version 2.7.4.
Thanks to the efforts of José Miguel Fernández Fernández (Departamento de Bioquímica y Biología Molecular. Universidad de Granada. España (jmfernan@ugr.es)) a translation of the Manual for Rasmol version 2.7.1 into Spanish is now available. La traducción española del manual de la versión de la Dra. Wong revisada por Eric Martz fue realizada por Isabel Serván Martínez y José Miguel Fernández Fernández. La actual traducción del Manual de RasMol 2.7.1 ha sido realizada usando como base la anterior de RasMol 2.6 por José Miguel Fernández Fernández.
Thanks to translations by Fernando Gabriel Ranea
This version is based directly on RasMol version 2.7.4.2, on RasMol version 2.7.4.1, on RasMol version 2.7.4, on RasMol version 2.7.3.1, on RasMol vesion 2.7.3, on RasMol version 2.7.2.1.1, on RasMol version 2.7.2, on RasMol version 2.7.1, on RasMol version 2.6_CIF.2, on RasMol version 2.6x1, on RasMol version 2.6.4, and RasMol 2.5-ucb and 2.6-ucb.
Please read the file NOTICE for important notices which apply to this package and for license terms (GPL or RASLIC).
RasMol Copyright © Roger Sayle 1992-1999
Version 2.6x1 Mods Copyright © Arne Mueller 1998
Versions 2.5-ucb and 2.6-ucb Mods Copyright ©
UC Regents/ModularCHEM Consortium 1995, 1996
RasTop 1.3 Copyright © Philippe Valadon 2000
Version 2.7.0, 2.7.1, 2.7.1.1, 2.7.2, 2.7.2.1, 2.7.2.1.1,
2.7.3, 2.7.3.1, 2.7.4, 2.7.4.1, 2.7.4.2, 2.7.5, 2.7.5.1 Mods
Copyright © Herbert J. Bernstein 1998-2009
All rights reserved. Use of copyright notice does not imply publication or disclosure. The information supplied in this document is believed to be true but no liability is assumed for its use or for the infringements of the rights of the others resulting from its use. Information in this document is subject to change without notice and does not represent a commitment on the part of the supplier.
This software has been created from several sources. Much of the code is from RasMol 2.6, as created by Roger Sayle.
See: http://www.dcs.ed.ac.uk/home/rasmol
The torsion angle code, new POVRAY3 code and other features are derived from the RasMol2.6x1 revisions by Arne Mueller.
See: ftp://nexus.roko.goe.net/pub/rasmol
The Ramachandran printer plot code was derived from fisipl created by Frances C. Bernstein. See the Protein Data Bank program tape.
The code to display multiple molecules and to allow bond rotation is derived in large part from the UCB mods by Gary Grossman and Marco Molinaro, included with permission of Eileen Lewis of the ModularCHEM Consortium.
See: http://mc2.CCHem.Berkeley.EDU/RasMol
The CIF modifications make use of a library based in part on CBFlib by Paul J. Ellis and Herbert J. Bernstein.
See: http://www.bernstein-plus-sons.com/software/CBF
Parts of CBFlib is loosely based on the CIFPARSE software package from the NDB at Rutgers university.
See http://www.iucr.org/iucr-top/cif/mmcif/ndb/software/CIFPARSE/
Please type the RasMol commands 'help copying', 'help general', 'help IUCR', 'help CBFlib', and 'help CIFPARSE' for applicable notices. Please type 'help copyright' for copyright notices. If you use RasMol V2.6 or an earlier version, type the RasMol command 'help oldnotice'.
This version is based directly on RasMol version 2.7.4.2, on RasMol verion 2.7.4.2, on RasMol version 2.7.4, on RasMol version 2.7.3.1, on RasMol version 2.7.3, on RasMol version 2.7.2.1.1, Rasmol version 2.7.2, RasMol version 2.7.1.1 and RasTop version 1.3 and indirectly on the RasMol 2.5-ucb and 2.6-ucb versions and version 2.6_CIF.2, RasMol 2.6x1 and RasMol_2.6.4.
RasMol 2.7.5 may be distributed under the terms of the GNU General Public License (the GPL), see
http://www.gnu.org/licenses/gpl.txt
or the file GPL or type the command 'help GPL'
or RasMol 2.7.5 may be distributed under the RASMOL license. See the file NOTICE or type the command 'help RASLIC'
GNU GENERAL PUBLIC LICENSE
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Copyright (C) 1989, 1991 Free Software Foundation, Inc.
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TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
0. This License applies to any program or other work which contains
a notice placed by the copyright holder saying it may be distributed
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refers to any such program or work, and a "work based on the Program"
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either verbatim or with modifications and/or translated into another
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the term "modification".) Each licensee is addressed as "you".
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Whether that is true depends on what the Program does.
1. You may copy and distribute verbatim copies of the Program's
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How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest
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To do so, attach the following notices to the program. It is safest
to attach them to the start of each source file to most effectively
convey the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.
<one line to give the program's name and a brief idea of what it does.>
Copyright (C) <year> <name of author>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
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Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Also add information on how to contact you by electronic and paper mail.
If the program is interactive, make it output a short notice like this
when it starts in an interactive mode:
Gnomovision version 69, Copyright (C) year name of author
Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate
parts of the General Public License. Of course, the commands you use may
be called something other than `show w' and `show c'; they could even be
mouse-clicks or menu items--whatever suits your program.
You should also get your employer (if you work as a programmer) or your
school, if any, to sign a "copyright disclaimer" for the program, if
necessary. Here is a sample; alter the names:
Yoyodyne, Inc., hereby disclaims all copyright interest in the program
`Gnomovision' (which makes passes at compilers) written by James Hacker.
<signature of Ty Coon>, 1 April 1989
Ty Coon, President of Vice
This General Public License does not permit incorporating your program into
proprietary programs. If your program is a subroutine library, you may
consider it more useful to permit linking proprietary applications with the
library. If this is what you want to do, use the GNU Library General
Public License instead of this License.
If you do not use the GPL, the following license terms apply:
RasMol License
Even though the authors of the various documents and software found here have made a good faith effort to ensure that the documents are correct and that the software performs according to its documentation, and we would greatly appreciate hearing of any problems you may encounter, the programs and documents any files created by the programs are provided **AS IS** without any warranty as to correctness, merchantability or fitness for any particular or general use.
THE RESPONSIBILITY FOR ANY ADVERSE CONSEQUENCES FROM THE USE OF PROGRAMS OR DOCUMENTS OR ANY FILE OR FILES CREATED BY USE OF THE PROGRAMS OR DOCUMENTS LIES SOLELY WITH THE USERS OF THE PROGRAMS OR DOCUMENTS OR FILE OR FILES AND NOT WITH AUTHORS OF THE PROGRAMS OR DOCUMENTS.
Subject to your acceptance of the conditions stated above, and your respect for the terms and conditions stated in the notices below, if you are not going to make any modifications or create derived works, you are given permission to freely copy and distribute this package, provided you do the following:
1. Either include the complete documentation, especially the file NOTICE, with what you distribute or provide a clear indication where people can get a copy of the documentation; and
2. Please give credit where credit is due citing the version and original authors properly; and
3. Please do not give anyone the impression that the original authors are providing a warranty of any kind.
If you would like to use major pieces of RasMol in some other program, make modifications to RasMol, or in some other way make what a lawyer would call a "derived work", you are not only permitted to do so, you are encouraged to do so. In addition to the things we discussed above, please do the following:
4. Please explain in your documentation how what you did differs from this version of RasMol; and
5. Please make your modified source code available.
This version of RasMol is _not_ in the public domain, but it is given freely to the community in the hopes of advancing science. If you make changes, please make them in a responsible manner, and please offer us the opportunity to include those changes in future versions of RasMol.
The following notice applies to this work as a whole and to the works included within it:
* Creative endeavors depend on the lively exchange of ideas. There are laws and customs which establish rights and responsibilities for authors and the users of what authors create. This notice is not intended to prevent you from using the software and documents in this package, but to ensure that there are no misunderstandings about terms and conditions of such use.
* Please read the following notice carefully. If you do not understand any portion of this notice, please seek appropriate professional legal advice before making use of the software and documents included in this software package. In addition to whatever other steps you may be obliged to take to respect the intellectual property rights of the various parties involved, if you do make use of the software and documents in this package, please give credit where credit is due by citing this package, its authors and the URL or other source from which you obtained it, or equivalent primary references in the literature with the same authors.
* Some of the software and documents included within this software package are the intellectual property of various parties, and placement in this package does not in any way imply that any such rights have in any way been waived or diminished.
* With respect to any software or documents for which a copyright exists, ALL RIGHTS ARE RESERVED TO THE OWNERS OF SUCH COPYRIGHT.
* Even though the authors of the various documents and software found here have made a good faith effort to ensure that the documents are correct and that the software performs according to its documentation, and we would greatly appreciate hearing of any problems you may encounter, the programs and documents and any files created by the programs are provided **AS IS** without any warranty as to correctness, merchantability or fitness for any particular or general use.
* THE RESPONSIBILITY FOR ANY ADVERSE CONSEQUENCES FROM THE USE OF PROGRAMS OR DOCUMENTS OR ANY FILE OR FILES CREATED BY USE OF THE PROGRAMS OR DOCUMENTS LIES SOLELY WITH THE USERS OF THE PROGRAMS OR DOCUMENTS OR FILE OR FILES AND NOT WITH AUTHORS OF THE PROGRAMS OR DOCUMENTS.
See the files GPL and RASLIC for two alternate ways to license this package.
The following notice applies to RasMol V 2.6 and older RasMol versions.
Information in this document is subject to change without notice and does not represent a commitment on the part of the supplier. This package is sold/distributed subject to the condition that it shall not, by way of trade or otherwise, be lent, re-sold, hired out or otherwise circulated without the supplier's prior consent, in any form of packaging or cover other than that in which it was produced. No part of this manual or accompanying software may be reproduced, stored in a retrieval system on optical or magnetic disk, tape or any other medium, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording or otherwise for any purpose other than the purchaser's personal use.
This product is not to be used in the planning, construction, maintenance, operation or use of any nuclear facility nor the flight, navigation or communication of aircraft or ground support equipment. The author shall not be liable, in whole or in part, for any claims or damages arising from such use, including death, bankruptcy or outbreak of war.
The IUCr Policy for the Protection and the Promotion of the STAR File and CIF Standards for Exchanging and Archiving Electronic Data.
Overview
The Crystallographic Information File (CIF)[1] is a standard for information interchange promulgated by the International Union of Crystallography (IUCr). CIF (Hall, Allen & Brown, 1991) is the recommended method for submitting publications to Acta Crystallographica Section C and reports of crystal structure determinations to other sections of Acta Crystallographica and many other journals. The syntax of a CIF is a subset of the more general STAR File[2] format. The CIF and STAR File approaches are used increasingly in the structural sciences for data exchange and archiving, and are having a significant influence on these activities in other fields.
Statement of intent
The IUCr's interest in the STAR File is as a general data interchange standard for science, and its interest in the CIF, a conformant derivative of the STAR File, is as a concise data exchange and archival standard for crystallography and structural science.
Protection of the standards
To protect the STAR File and the CIF as standards for interchanging and archiving electronic data, the IUCr, on behalf of the scientific community,
* holds the copyrights on the standards themselves,
* owns the associated trademarks and service marks, and
* holds a patent on the STAR File.
These intellectual property rights relate solely to the interchange formats, not to the data contained therein, nor to the software used in the generation, access or manipulation of the data.
Promotion of the standards
The sole requirement that the IUCr, in its protective role, imposes on software purporting to process STAR File or CIF data is that the following conditions be met prior to sale or distribution.
* Software claiming to read files written to either the STAR File or the CIF standard must be able to extract the pertinent data from a file conformant to the STAR File syntax, or the CIF syntax, respectively.
* Software claiming to write files in either the STAR File, or the CIF, standard must produce files that are conformant to the STAR File syntax, or the CIF syntax, respectively.
* Software claiming to read definitions from a specific data dictionary approved by the IUCr must be able to extract any pertinent definition which is conformant to the dictionary definition language (DDL)[3] associated with that dictionary.
The IUCr, through its Committee on CIF Standards, will assist any developer to verify that software meets these conformance conditions.
Glossary of terms
[1] CIF:
is a data file conformant to the file syntax defined at http://www.iucr.org/iucr-top/cif/spec/index.html
[2] STAR File:
is a data file conformant to the file syntax defined at http://www.iucr.org/iucr-top/cif/spec/star/index.html
[3] DDL:
is a language used in a data dictionary to define data items in terms of "attributes". Dictionaries currently approved by the IUCr, and the DDL versions used to construct these dictionaries, are listed at http://www.iucr.org/iucr-top/cif/spec/ddl/index.html
Last modified: 30 September 2000
IUCr Policy Copyright (C) 2000 International Union of Crystallography
The following Disclaimer Notice applies to CBFlib V0.1, from which this code in part is derived.
* The items furnished herewith were developed under the sponsorship of the U.S. Government. Neither the U.S., nor the U.S. D.O.E., nor the Leland Stanford Junior University, nor their employees, makes any warranty, express or implied, or assumes any liability or responsibility for accuracy, completeness or usefulness of any information, apparatus, product or process disclosed, or represents that its use will not infringe privately-owned rights. Mention of any product, its manufacturer, or suppliers shall not, nor is it intended to, imply approval, disapproval, or fitness for any particular use. The U.S. and the University at all times retain the right to use and disseminate the furnished items for any purpose whatsoever.
Notice 91 02 01
Portions of this software are loosely based on the CIFPARSE software package from the NDB at Rutgers University. See
http://ndbserver.rutgers.edu/NDB/mmcif/software
CIFPARSE is part of the NDBQUERY application, a program component of the Nucleic Acid Database Project [ H. M. Berman, W. K. Olson, D. L. Beveridge, J. K. Westbrook, A. Gelbin, T. Demeny, S. H. Shieh, A. R. Srinivasan, and B. Schneider. (1992). The Nucleic Acid Database: A Comprehensive Relational Database of Three-Dimensional Structures of Nucleic Acids. Biophys J., 63, 751-759.], whose cooperation is gratefully acknowledged, especially in the form of design concepts created by J. Westbrook.
Please be aware of the following notice in the CIFPARSE API:
This software is provided WITHOUT WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR ANY OTHER WARRANTY, EXPRESS OR IMPLIED. RUTGERS MAKE NO REPRESENTATION OR WARRANTY THAT THE SOFTWARE WILL NOT INFRINGE ANY PATENT, COPYRIGHT OR OTHER PROPRIETARY RIGHT.
The program reads in a molecule coordinate file and interactively displays the molecule on the screen in a variety of colour schemes and molecule representations. Currently available representations include depth-cued wireframes, 'Dreiding' sticks, spacefilling (CPK) spheres, ball and stick, solid and strand biomolecular ribbons, atom labels and dot surfaces.
Up to 5 molecules may be loaded and displayed at once. Any one or all of the molecules may be rotated and translated.
The X Windows version of RasMol provides optional support for a hardware dials box and accelerated shared memory communication (via the XInput and MIT-SHM extensions) if available on the current X Server.
The program reads in molecular coordinate files and interactively displays the molecule on the screen in a variety of representations and colour schemes. Supported input file formats include Protein Data Bank (PDB), Tripos Associates' Alchemy and Sybyl Mol2 formats, Molecular Design Limited's (MDL) Mol file format, Minnesota Supercomputer Center's (MSC) XYZ (XMol) format, CHARMm format, CIF format and mmCIF format files. If connectivity information is not contained in the file this is calculated automatically. The loaded molecule can be shown as wireframe bonds, cylinder 'Dreiding' stick bonds, alpha-carbon trace, space-filling (CPK) spheres, macromolecular ribbons (either smooth shaded solid ribbons or parallel strands), hydrogen bonding and dot surface representations. Atoms may also be labelled with arbitrary text strings. Alternate conformers and multiple NMR models may be specially coloured and identified in atom labels. Different parts of the molecule may be represented and coloured independently of the rest of the molecule or displayed in several representations simultaneously. The displayed molecule may be rotated, translated, zoomed and z-clipped (slabbed) interactively using either the mouse, the scroll bars, the command line or an attached dial box. RasMol can read a prepared list of commands from a 'script' file (or via inter-process communication) to allow a given image or viewpoint to be restored quickly. RasMol can also create a script file containing the commands required to regenerate the current image. Finally, the rendered image may be written out in a variety of formats including either raster or vector PostScript, GIF, PPM, BMP, PICT, Sun rasterfile or as a MolScript input script or Kinemage.
The RasMol help facility can be accessed by typing "help <topic>" or "help <topic> <subtopic>" from the command line. A complete list of RasMol commands may be displayed by typing "help commands". A single question mark may also be used to abbreviate the keyword "help". Please type "help notices" for important notices.
RasMol Molecular Renderer Roger Sayle, August 1995 Copyright (C) Roger Sayle 1992-1999 Version 2.7.3 February 2005 Copyright (C) Herbert J. Bernstein 1998-2005 *** See "help notice" for further notices *** [32-bit version]Immediately underneath this banner message appears the program's command line prompt 'RasMol>'. If the program is being executed under the X Window System, the program determines the type of the display being used. If the screen has either an 8 bit or 24 bit colour frame buffer, RasMol creates another window, which is used to display menu options and the rendered images. If a suitable screen is not available, RasMol may only be used from the command line. Commands may be typed to manipulate the model, and to output the generated image to a raster file.
If the program is run under the X Window System environment with
a suitable colour screen, RasMol creates an additional window to
display the rendered molecule interactively, as it is manipulated.
If RasMol is not run under the X Window System, the program displays
the message 'No suitable display detected!'. RasMol may be instructed
not to display a graphics window by using the command line option
'-nodisplay'. This is particularly useful for running RasMol as a
background or batch process.
It is possible to specify either a coordinate filename or a script
filename or both on the UNIX/VMS command line. A script file
may be specified by adding the option
'-script <filename>' to the command line.
A molecule coordinate file may be specified by placing
its name on the command line, optionally preceded by a file
format option. If no format option is given, the specified
coordinate file is assumed to be in PDB, CIF or mmCIF format.
Valid format options include '-pdb', '-mdl', '-mol2', '-xyz',
'- alchemy', '-charmm', '-mopac' and '-cif' which
correspond to Protein Data Bank format, Molecular Design Limited's
Mol file format, Tripos's Sybyl Mol2 file format, MSC's XMOL XYZ
file format, Tripos's Alchemy file format, CHARMm file format,
J. P. Stewart's MOPAC file format and IUCr CIF or mmCIF file format,
respectively. If both a coordinate file and a script file are
specified on the command line, the molecule is loaded first, then
the script commands are applied to it. If either file is not found,
the program displays the error message 'Error: File not found!' and
the user is presented the RasMol prompt.
It is also possible to specify the initial graphics window
size or position or both the size and the position with the
options '-height
In order to leave RasMol, the user can type the command quit or
exit at the RasMol prompt, and the program will return the user
to the familiar unix prompt. Alternatively, if a prompt other
than the main RasMol prompt is being displayed, the user may
hit control-C (^C) to leave the program. The message '***Quit***'
will be output to the terminal, before the usual unix prompt is
redisplayed. The program may also be terminated by selecting
the Quit menu option, on the bottom of the main menu.
It is possible to specify either a coordinate filename or a script
filename or both on the windows command line. A script file
may be specified by adding the option '-script <filename>'
to the command line. A molecule coordinate file may be specified
by placing its name on the command line, optionally preceded by
a file format option. If no format option is given, the specified
coordinate file is assumed to be in PDB, CIF or mmCIF format.
Valid format options include '-pdb', '-mdl', '-mol2', '-xyz',
'- alchemy', '-charmm', '-mopac' and '-cif' which
correspond to Protein Data Bank format, Molecular Design Limited's
Mol file format, Tripos's Sybyl Mol2 file format, MSC's XMOL XYZ
file format, Tripos's Alchemy file format, CHARMm file format,
J. P. Stewart's MOPAC file format and IUCr CIF or mmCIF file format,
respectively. If both a coordinate file and a script file are
specified on the command line, the molecule is loaded first, then
the script commands are applied to it. If either file is not found,
the program displays the error message 'Error: File not found!' and
the user is presented the RasMol prompt.
It is also possible to specify the initial graphics window
size or position or both the size and the position with the
options '-height
Dragging and dropping multi-file 'movie' scripts onto aliases or
copies of the RasMol application file may fail due to confusion
about which is the correct script folder. Double-clicking on a
script may lead to similar problems if copies are present.
Note that because on a Macintosh only one 'instance' of an
application may be running at any one time, if you were
double click on another file owned by 'RSML', the running
copy of RasMol would
zap
its molecule and load the newly specified file.
While the mouse pointer is located within the graphics area
of the main display window, the mouse pointer is drawn as a
cross-hair cursor, to enable the
'picking'
of objects being displayed; otherwise the mouse pointer is drawn as an
arrowhead. Any characters that are typed at the keyboard while the
display window is in 'focus' (meaning active or foreground) are
redirected to the command line in the terminal window. Hence you
do not need continually to switch focus between the command line
and graphics windows.
The normal behavior of the scroll bars can be changed by the
'rotate bond'
and
'rotate all'
commands and restored to normal operation by the
'rotate molecule'
command. Alternatively the equivalent items in the "Settings" menu
may be used. When
'rotate bond'
is selected, the bottom scroll bar controls. rotation around a bond
selected by the
'bond <src> <dst> pick'
command (or by use of the "Pick Bond" item in the "Settings" menu).
When
'rotate all'
is selected, the scroll bars control rotation of all the loaded
molecules instead of just rotating the currently selected molecule.
The program will display, in the terminal window, the atom's type,
serial number, residue name and residue number. If the atom is a
member of a named chain, the chain identifier is also displayed.
Two examples of the output generated by selecting an atom are
displayed below:
Clicking the mouse on an atom can be used not only to
identify it, but also to find the coordinates, the
distances between
two atoms (or to display a distance monitor), the
bond angle defined by three atoms, the torsion angle
defined by four atoms, to toggle labels on or off,
to specify the centre of rotation, or to specify
a bond as the axis of rotation. See
the 'set picking'
command for details.
The rotation about the X and Y axes automatically updates the
indicators on the appropriate scroll bars. All the rotation
dials rotate the molecule 180 degrees for a complete revolution
of the dial. All the remaining dials clamp their values to
permissible ranges; turning these dials past their limits
has no effect. The centre of rotation of the molecule may be
changed using the 'centre'
command on the command line, or the command
'set
picking centre' followed by a
mouse click.
The 'ZOOM' dial allows the interactive zooming of the
molecule between 10% and 200% of the original default
magnification. Rotating the dial clockwise magnifies the
molecule and anticlockwise shrinks it. A complete
revolution of the dial corresponds to a 100% change in scale.
The 'SLAB' dial, which is only effective when slabbing is
enabled, allows the user to move the front z-clipping plane
from the nearest point on the molecule to the furthest. A
complete rotation of the SLAB dial corresponds to moving
the clipping plane half the distance between the front and
back of the molecule. Turning the SLAB knob clockwise moves
the clipping plane closer to the viewer (increasing the
number of objects displayed), and turning it anticlockwise
moves it further away (preventing more objects from being displayed).
Slabbing mode is enabled by typing the command 'slab on'
on the command line or toggling the slab option on the options menu.
Translation along the X and Y axis allows the centre of the molecule
to be moved within the canvas area of the screen. Rotation and zooming
are still performed relative to the centre of rotation and the molecule,
respectively, which may often not be at the centre of the canvas. The
TRANS Z dial currently has no effect.
If a syntax error is detected on entering an interactive
command, RasMol indicates the location of the error on the
command line by placing the '^' character under the offending
word or character, and writing an error message on the following
line. If a command is not recognised by RasMol, the program will
generate an 'Unrecognised command!' error and redisplay the main
prompt. If surplus information is given at the end of a command
line, RasMol will execute the recognised command, but issue the
warning message 'Warning: Ignoring rest of command!'. Some
commands may prompt the user for more information. These
commands display a different prompt and are discussed in the
command reference.
Whenever RasMol outputs diagnostic or error messages to the
screen owing to selecting options from the menu or picking
objects on the screen, the current command line is cleared. The
prompt is redisplayed after any text has been displayed.
RasMol maintains a history of recently used commands, so that the
user never needs to type the same commands repeatedly.
Typing ^P (Control-P) on the command line will display the
previous command in the history and ^N will display the following
command. These commands may be edited using the features described
below. Moving forward or backward through the command history
undoes the modifications made to the current line. The number
of commands retained in the history depends upon their length.
RasMol can retain more short command lines and fewer long ones.
Users with the Microsoft Windows version or the X windows version
and with 'vt100' or compatible terminals (such as an 'xterm') can
use the cursor control characters on the keyboard to abbreviate the
control keys. The right and left cursor keys have the same affect
as ^F and ^B, moving the cursor forward and back a single character,
respectively. Similarly, the up and down cursor keys have the same
function as ^P and ^N, producing the previous and next entries in
the command history, respectively.
Users with the Macintosh version can use the four 'arrow keys'
to move up and down through previous command line entries; and
back and forth within a single command line statement. Hitting
'return' or 'enter' at any time will result in the execution of
the current, e.g. selected or edited, command line contents.
RasMol first looks for the initialisation file in the current
directory and if it is not found will look for it in the user's
home directory. On all systems the environment variable
HOME may be used to name the user's home
directory. If no personal initialisation file is found the
program looks for the file rasmolrc (or RASMOLRC)
in the RasMol system directory pointed to by the environment
variable RASMOLPATH. This directory should also contain
the on-line help file rasmol.hlp. On UNIX systems
RASMOLPATH is typically set to be '/usr/local/lib/rasmol'.
Unlike the command
'script ".rasmolrc"',
the program
will not generate an error message if the file is not found.
The system rasmolrc file is commonly used by system managers to
display information about the local installation and who to
contact for help. Such system rasmolrc files will contain RasMol
'echo'
commands detailing a
telephone number or e-mail address to be used for contacting
somebody for local assistance.
When RasMol starts up on an X window system it
registers itself with the X window Server as a Tcl
interpreter. From within a Tcl application such as
'wish', you can use the Tcl command 'winfo interps' to
determine the currently register interpreters on that display.
The first instance of RasMol registers itself as 'rasmol', the
second as 'rasmol #2', the third as 'rasmol #3' and so on. The
Tcl interpreter can easily send a command to rasmol using the
built-in 'send' command. RasMol interprets the string parameter
to the send command not as a Tcl function to execute but as a
RasMol command. Hence, typing 'send {rasmol} {background red}'
into the wish interpreter will cause RasMol's display window to
change colour. Using the same encoding as Microsoft's DDE Execute
protocol, multiple commands may be sent in a single 'send' by
placing the consecutive commands in square brackets. RasMol will
execute all of the commands in a 'send' before refreshing the screen.
Under Microsoft Windows, RasMol supports a complete DDE protocol.
The simplest layers of the protocol may be accessed by sending a DDE
Execute command to application 'RasWin' and any topic. This will start a
DDE conversation
with the most recently launched instance of RasMol.
Although any topic name can be used, the use of
'System' and/or 'RemoteControl' are recommended.
Once again the contents of the execute package consists of a
string for RasMol to execute. If the first non-whitespace
character is an open bracket, the string is interpreted to be a
sequence of consecutive commands enclosed in square brackets;
otherwise the string consists of just a single command. Commands in
square brackets may optionally be separated by whitespace and/or
semi- colons. RasMol can also act as a 'data server' supporting
hot, cold and warm links. Currently supported DDE items include
'Name', 'Image', 'Pick', 'Count' which denotes the Molecule name,
the currently displayed image (in Microsoft DIB format), the atom
expression of the last picked atom (or an empty string) and the
number of selected atoms, respectively. Using a hot or warm link
on the 'Pick' item, for example, allows an application such as
Microsoft Word, Excel or Visual Basic to respond each time the
user clicks on an atom in RasMol.
RasMol on the Apple Macintosh supports AppleEvents.
Currently the only supported AppleEvents are the four 'core' events,
Open Application, Open Document, Print Document and Quit. However,
because OpenDocument determines its actions by the file's type
signature this can be used to implement generic IPC. Because RasMol
for the Macintosh treats all files of type 'RSML' as scripts, the
sending application need only place all the commands to be executed
in a temporary file, set the type of the file to 'RSML' and then
send RasMol an OpenDocument AppleEvent with the file as parameter.
All commands may be prefixed by a parenthesized
'atom expression'
to temporarily select certain atoms just for the execution
of that one command. After execution of the command, the
previous selection is restored except for the commands
'select'
,
'restrict'
and
'script'.
The commands/keywords currently recognised by RasMol are given below.
The RasMol
'backbone'
command permits the representation of a polypeptide
backbone as a series of bonds connecting the adjacent alpha carbons of
each amino acid in a chain. The display of these backbone 'bonds' is
turned on and off by the command parameter in the same way as with the
'wireframe'
command. The command
'backbone off'
turns off the selected 'bonds', and
'backbone on'
or with a number turns them on. The number can be used
to specify the cylinder radius of the representation in either Ångstrom
or RasMol units. A parameter value of 500 (2.0 Ångstroms) or above
results in a "Parameter value too large" error. Backbone objects may be
coloured using the RasMol
'colour backbone'
command.
The reserved word backbone is also used as a predefined set ("help sets")
and as a parameter to the
'set hbond'
and
'set ssbond'
commands. The
RasMol command
'trace'
renders a smoothed backbone, in contrast to
'backbone'
which connects alpha carbons with straight lines.
The backbone may be displayed with dashed lines by use of the
'backbone dash'
command.
The RasMol
'background'
command is used to set the colour of the "canvas" background. The
colour may be given as either a colour name or a comma separated
triple of Red, Green and Blue (RGB) components enclosed in square
brackets. Typing the command
'help colours'
will give a list of the predefined colour names recognised by RasMol.
When running under X Windows, RasMol also recognises colours in the
X server's colour name database.
The
'background'
command is synonymous with the RasMol
'set background'
command.
The RasMol command
'bond <number> <number> +'
adds the designated bond to the drawing, increasing the bond order
if the bond already exists. The command
'bond <number> <number> pick'
selects the two atoms specified by the atom serial numbers
as the two ends of a bond around which the
'rotate bond <angle>'
command will be applied. If no bond exists, it is created.
Rotation around a previously picked bond may be specified by the
'rotate bond <angle>'
command, or may also be controlled with the mouse, using the
'bond rotate on/off'
or the equivalent
'rotate bond on/off'
commands.
The RasMol
'Bulgarian'
command sets the menus and messages to the Bulgarian versions.
This command may not work correctly unless appropriate fonts
have been installed. The commands
'Bulgarian',
'Chinese',
'English',
'French',
'Italian',
'Russian'
and
'Spanish'
may be used to select Bulgarian, Chinese, English, French,
Italian, Japanese, Russian and Spanish menus and messages if the
appropriate fonts have been installed.
The RasMol
'cartoon'
command does a display of a molecule
'ribbons'
as Richardson (MolScript) style protein
'cartoons',
implemented as thick (deep) ribbons. The
easiest way to obtain a cartoon representation of a protein is
to use the
'Cartoons'
option on the
'Display'
menu. The
'cartoon'
command represents the currently selected residues
as a deep ribbon with width specified by the command's argument.
Using the command without a parameter results in the ribbon's
width being taken from the protein's secondary structure,
as described in the
'ribbons'
command. By default, the C-termini of beta-sheets are displayed
as arrow heads. This may be enabled and disabled using the
'set cartoons'
command.
The depth of the cartoon may be adjusted using the
'set cartoons <number>'
command. The
'set cartoons'
command without any parameters returns these two options
to their default values.
The RasMol
'centre'
command defines the point about which the
'rotate'
command and the scroll bars rotate the current molecule. Without a
parameter the centre command resets the centre of rotation to be the
centre of gravity of the molecule. If an atom expression is specified,
RasMol rotates the molecule about the centre of gravity of the set of
atoms specified by the expression. Hence, if a single atom is specified
by the expression, that atom will remain 'stationary' during rotations.
Type
'help expression'
for more information on RasMol atom expressions.
Alternatively the centring may be given as a comma separated triple of
[CenX, CenY, CenZ] offsets in RasMol units (1/250 of an Ångstrom) from
the centre of gravity. The triple must be enclosed in square brackets.
The optional forms
'centre ... translate'
and
'centre ... center'
may be used to specify use of a translated centre of rotation (not
necessarily in the centre of the canvas) or a centre of rotation
which is placed at the centre of the canvas. Starting with
RasMol 2.7.2, the default is
to center the new axis on the canvas.
The RasMol
'Chinese'
command sets the menus and messages to the Chinese versions.
This command may not work correctly unless appropriate fonts
have been installed. The commands
'Bulgarian',
'Chinese',
'English',
'French',
'Italian',
'Russian'
and
'Spanish'
may be used to select Bulgarian, Chinese, English, French,
Italian, Japanese, Russian and Spanish menus and messages if the
appropriate fonts have been installed.
The RasMol
'clipboard'
command places a copy of the currently displayed image on the local
graphics 'clipboard'. Note: this command is not yet supported on
UNIX or VMS machines. It is intended to make transfering images
between applications easier under Microsoft Windows or on an Apple
Macintosh.
When using RasMol on a UNIX or VMS system this functionality may be
achieved by generating a raster image in a format that can be read
by the receiving program using the RasMol
'write'
command.
Colour the atoms (or other objects) of the selected region. The colour may
be given as either a colour name or a comma separated triple of Red, Green
and Blue (RGB) components enclosed in square brackets. Typing the command
'help colours'
will give a list of all the predefined colour names recognised
by RasMol.
Allowed objects are
'atoms',
'bonds',
'backbone',
'ribbons',
'labels',
'dots',
'hbonds',
'map',
and
'ssbonds'.
If no object is specified, the default keyword
'atom'
is assumed.
Some colour schemes are defined for certain object types. The colour scheme
'none'
can be applied to all objects except atoms and dots, stating that the selected
objects have no colour of their own, but use the colour of their associated
atoms (i.e. the atoms they connect).
'Atom'
objects can also be coloured by
'alt',
'amino',
'chain',
'charge',
'cpk',
'group',
'model',
'shapely',
'structure',
'temperature'
or
'user'.
Hydrogen bonds can also be coloured by
'type'
and dot surfaces can also be coloured by
'electrostatic potential'.
For more information type
'help colour <colour>'.
Map objects may be coloured by specific color of by nearest atom.
ColourMode allows the user to switch between using the new
'colour'
method. At present, the new coloring technique is the same as
the old one, but to preserve compatibility for older scripts
it may be wise to add a "colormode on" near the top of your
script somewhere, if the script was designed for version 2.7.3
of RasMol or earlier. The new color method, when completed,
aims to fix a few bugs in the coloring routines.
The RasMol
'connect'
command is used to force RasMol to (re)calculate the connectivity
of the current molecule.
If the original input file contained connectivity information, this
is discarded. The command
'connect false'
uses a fast heuristic
algorithm that is suitable for determining bonding in large
bio-molecules such as proteins and nucleic acids. The command
"connect true"
uses a slower more accurate algorithm based upon
covalent radii that is more suitable to small molecules containing
inorganic elements or strained rings. If no parameters are given,
RasMol determines which algorithm to use based on the number of atoms
in the input file. Greater than 255 atoms causes RasMol to use the
faster implementation. This is the method used to determine bonding,
if necessary, when a molecule is first read in using the
'load'
command.
The RasMol
'defer'
command adds the command given to the macro with given name,
if no name is given, the command is added to the macro with a
blank name. The command
'zap'
is a special case. In that case the macro is erased. If no name is
given the command must begin with a selection, e.g.
"defer (selection).spacefill"
The defered command accumulated under the given name can be executed
using the
'execute'
command
The RasMol
'define'
command allows the user to associate an arbitrary set of atoms with a
unique identifier. This allows the definition of user-defined sets. These
sets are declared statically, i.e. once defined the contents of the set
do not change, even if the expression defining them depends on the
current transformation and representation of the molecule.
The RasMol
'depth'
command enables, disables or positions the back-clipping plane of the
molecule. The program only draws those portions of the
molecule that are closer to the viewer than the clipping plane.
Integer values range from zero at the very back of the molecule to
100 which is completely in front of the molecule. Intermediate values
determine the percentage of the molecule to be drawn.
This command interacts with the
'slab <value>'
command, which clips to the front of a given z-clipping plane.
The RasMol
'dots'
command is used to generate a van der Waals' dot surface around the
currently selected atoms. Dot surfaces display regularly spaced points
on a sphere of van der Waals' radius about each selected atom. Dots that
would are 'buried' within the van der Waals' radius of any other atom
(selected or not) are not displayed.
The command
'dots on'
deletes any existing dot surface and generates a dots surface around
the currently selected atom set with a default dot density of 100. The
command
'dots off'
deletes any existing dot surface. The dot density may be
specified by providing a numeric parameter between 1 and 1000. This
value approximately corresponds to the number of dots on the surface
of a medium sized atom.
By default, the colour of each point on a dot surface is the colour
of its closest atom at the time the surface is generated. The colour
of the whole dot surface may be changed using the
'colour dots'
command.
The RasMol
'echo'
command is used to display a message in the RasMol command/terminal
window. The string parameter may optionally be delimited in double
quote characters. If no parameter is specified, the
'echo'
command displays a blank line. This command is particularly useful
for displaying text from within a RasMol
'script'
file.
The RasMol
'English'
command sets the menus and messages to the English versions.
This command may not work correctly unless appropriate fonts
have been installed. The commands
'Bulgarian',
'Chinese',
'English',
'French',
'Italian',
'Russian'
and
'Spanish'
may be used to select Bulgarian, Chinese, English, French,
Italian, Japanese, Russian and Spanish menus and messages if the
appropriate fonts have been installed.
The RasMol
'execute'
command:
1. saves the old poise of the molecule (translation,
rotation and zoom)
2. executes the specified macro suppressing both screen
updates and recording
3. animates motion of the newly rendered molecule linearly
'defer'
command.
The animation of the motion depends on the prior settings of the
'record'
command.
The RasMol
'French'
command sets the menus and messages to the French versions.
This command may not work correctly unless appropriate fonts
have been installed. The commands
'Bulgarian',
'Chinese',
'English',
'French',
'Italian',
'Russian'
and
'Spanish'
may be used to select Bulgarian, Chinese, English, French,
Italian, Japanese, Russian and Spanish menus and messages if the
appropriate fonts have been installed.
The RasMol
'hbond'
command is used to represent the hydrogen bonding of the protein
molecule's backbone. This information is useful in assessing the
protein's secondary structure. Hydrogen bonds are represented as
either dotted lines or cylinders between the donor and acceptor
residues. The first time the
'hbond'
command is used, the program searches the structure of the
molecule to find hydrogen bonded residues and reports the number of bonds
to the user. The command
'hbonds on'
displays the selected 'bonds' as dotted lines, and the
'hbonds off'
turns off their display. The colour of hbond objects may be changed
by the
'colour hbond'
command. Initially, each hydrogen bond has the colours of its connected
atoms.
By default the dotted lines are drawn between the accepting oxygen and
the donating nitrogen. By using the
'set hbonds'
command the alpha carbon positions of the appropriate residues may be
used instead. This is especially useful when examining proteins in
backbone representation.
The RasMol
'help'
command provides on-line help on the given topic.
The RasMol
'Italian'
command sets the menus and messages to the Italian versions.
This command may not work correctly unless appropriate fonts
have been installed. The commands
'Bulgarian',
'Chinese',
'English',
'French',
'Italian',
'Russian'
and
'Spanish'
may be used to select Bulgarian, Chinese, English, French,
Italian, Japanese, Russian and Spanish menus and messages if the
appropriate fonts have been installed.
The RasMol
'Japanese'
command sets the menus and messages to the Japanese versions.
This command may not work correctly unless appropriate fonts
have been installed. The commands
'Bulgarian',
'Chinese',
'English',
'French',
'Italian',
'Russian'
and
'Spanish'
may be used to select Bulgarian, Chinese, English, French,
Italian, Japanese, Russian and Spanish menus and messages if the
appropriate fonts have been installed.
The RasMol
'label'
command allows an arbitrary formatted text string to be
associated with each currently selected atom. This string may contain
embedded 'expansion specifiers' which display properties of the atom
being labelled. An expansion specifier consists of a '%' character
followed by a single alphabetic character specifying the property to be
displayed (similar to C's printf syntax).
An actual '%' character may be displayed by using the expansion
specifier '%%'.
Atom labelling for the currently selected atoms may be turned off with
the command
'label off'.
By default, if no string is given as a parameter, RasMol uses labels
appropriate for the current molecule.
RasMol uses the label '%n%r:%c.%a' if the molecule contains more than
one chain, '%e%i' if the molecule has only a single residue (a small
molecule) and '%n%r.%a' otherwise.
The colour of each label may be changed using the
'colour label'
command. By default, each label is drawn in the same colour as the atom
to which it is attached. The size and spacing of the displayed text
may be changed using the
'set fontsize'
command. The width of the strokes in the displayed text may be changed
using the
'set fontstroke'
command.
The following table lists the current expansion specifiers:
Load a molecule coordinate file into RasMol. Valid molecule file
formats are
'pdb'
(Protein Data Bank format),
'mdl'
(Molecular Design Limited's MOL file format),
'alchemy'
(Tripos' Alchemy file format),
'mol2'
(Tripos' Sybyl Mol2 file format),
'charmm'
(CHARMm file format),
'xyz'
(MSC's XMol XYZ file format),
'mopac'
(J. P. Stewart's MOPAC file format) or
'cif'
(IUCr CIF or mmCIF file format). If no file format is specified,
'PDB',
'CIF',
or
'mmCIF'
is assumed by default. Up to 20 molecules may be loaded at a time.
If CHEM_COMP ligand models are included in an mmCIF file, they will be loaded
as NMR models, first giving the all the NMR models for model
coordinates if specified and then giving all the NMR models for
ideal model coordinates.
To delete a molecule prior to loading another use the RasMol
'zap'
command. To select a molecule for manipulation use the RasMol
'molecule <n>'
command.
The
'load'
command selects all the atoms in the molecule, centres it on the
screen and renders it as a CPK coloured wireframe model. If the molecule
contains no bonds (i.e. contains only alpha carbons), it is drawn as
an alpha carbon backbone. If the file specifies fewer bonds than atoms,
RasMol determines connectivity using the
'connect'
command.
The
'load inline'
command also allows the storing of atom coordinates in scripts
to allow better integration with WWW browsers. A load command
executed inside a script file may specify the keyword
'inline'
instead of a conventional filename. This option specifies that
the coordinates of the molecule to load are stored in the same
file as the currently executing commands.
Typically this is used in the command
'load pdb inline',
which is followed by a number of RasMol commands terminated by
the command
'exit'.
The
'exit'
command terminates execution of the current script and returns
control to the command line (or the calling script). This means
any lines following
'exit'
are never interpreted by RasMol. These may be used to store
atomic coordinates in PDB, CIF or mmCIF file format.
One possible use is a standard RasMol script prefix that may be
concatenated with an appropriate PDB file on-the-fly.
The RasMol
'map'
commands manipulate electron density maps in coordination
with the display of molecules. These commands are very
memory intensive and may not work on machines with
limited memory. Each molecule may have as many maps
as available memory permits. Maps may be read from
files or generated from Gaussian density distributions
around atoms.
'map colour',
to colour a map according to a given colour scheme,
'map generate',
to generate a map from selected atoms based on pseudo-Gaussians,
'map level',
to set the contouring level for selected maps,
'map load',
to load a map from a file,
'map mask'
to designate a mask for the selected maps,
'map resolution',
to set the resolution for contouring selected maps,
'map restrict',
to select one or more maps and to disable all others,
'map save',
to save map information to a file,
'map scale',
'control the scaling of pseudo-Gaussians when generating maps',
'map select',
to select one or more maps,
'map show',
to display information about one or more maps or about the
parameters to be used in generating or loading the next map,
'map spacing',
to set the spacing betwen contour lines of selected maps,
'map spread',
to set the variance of the Gaussians for map generation as a fraction
of the atomic radius, and
'map zap'
to delete previously generated or loaded maps.
The effect of
'map generate'
and
'map load'
commands is modified by the
'map mask'
command which limits the portion of the display space
that can be considered for display of maps.
The RasMol
'map colour'
command colours the selected maps according to the specified
colour scheme. The colour scheme may be a colour name or
and RBG triple in brackets, or the keyword
'atom'
to cause the map points to be coloured by the color of the
nearest atom.
The RasMol
'map generate'
command generates a map from whatever atoms are currently selected,
by summing electron densities approximated by Gaussian distributions.
The height of each Gaussian is determined by the setting of the
' map scale'
command.
In the default of map scale true, each Gaussian has a height proportional
element type of the atom.
If the optional 'LRSurf' parameter is given or if map scale false
has been executed, each Gaussian is scaled so that
the Gaussian contour level 1 is at the van der Waals radius.
In either case a standard deviation determined by the
most recently specified spread or resolution is used. If a non-zero spread has been
given the radius of the atom is multiplied by the spread to find the
standard deviation. The default is 2/3rds. If a resolution
has been given, the spread is inferred as 2/3rds of the resolution.
For example, if the resolution is given as 1., and the atom in question
is a Carbon with a van der Waals radius of 468 RasMol units (1.87 Ångstroms),
the inferred spead is .6667, and the standard deviation of the Gaussian
is taken as 1.25 Ångstroms.
If the spread has been set to zero, the spread for each atom is determined
from the van der Waals radius and the probe atom radius to simulate the
effect of a Lee-Richards surface.
If no specific map was given by the map selector, the new map is
given the next available map number.
If a specific map was given by the map selector, the new map replaces
that map. If more than one map was given by the map selector, the
new map replaces the lowest numbered of the selected maps. In any
case the new map becomes the currently selected map.
The map is displayed as dots, mesh or a surface, depending on the last
map rendering mode selected or the mode selected on the command itself.
The RasMol
'map level'
command sets the contour level to be used in creating subsequent
representations of generated or loaded maps. If the keyword MEAN
in used the level is relative to the mean of the map data. Otherwise
the level is absolute.
In general, a lower level results in a map containing more of the
displayed volume, while a higher level results in a map containing
less of the displayed volume.
The RasMol
'map load'
command loads a map file into RasMol. The valid formats are
CCP4 map format and imgCIF format.
If no specific map was given by the map selector, the new map is
given the next available map number.
If a specific map was given by the map selector, the new map replaces
that map. If more than one map was given by the map selector, the
new map replaces the lowest numbered of the selected maps. In any
case the new map becomes the currently selected map.
The map is displayed as dots, mesh or a surface depending on the
last map rendering mode selected.
The RasMol
'map mask'
command specifies a mask to be used to limit the display space
to be used for making representations of other maps or removes
an earlier mask specification.
The 'selected' option indicates that the mask is to be created
from the currently selected atoms. The '<number>' option indicates
that the mask is to be copied from the map of the number specified.
The 'none' option removes the previously specified mask, if any.
The map selector specifies the map or maps to which the specified mask
will the applied. For example, 'map next mask selected' specifies
that the currently selected atoms are to be used to generate a
mask to be applied to any maps created by subsequent 'map load'
or 'map generate' commands.
Any map may be used as a mask. The portions of the mask map greater than
than or equal to the average value of the mask map allow the values of the
map being masked to be used as given. The portions of the mask
map lower than the average value of the mask map cause the values of
the map being masked to be treated as if they were equal to the
lowest data value of the map being masked.
The RasMol
'map resolution'
command specifies the resolution in RasMol units or,
if a number containing a decimal point is given, the
resolution in Ångstroms to be used in generating and
in representing maps.
The resolution is used at the map spacing for
representations of maps, indicating the separation
between contour levels (see the
'map spacing'
command) and to infer the map spread to be used in
generated maps from selected atoms (see the
'map spread'
command). The map spread is set to two thirds of
the specified resolution.
The RasMol
'map restrict'
command selects particular maps to make them active for
subsequent map commands. This is similar to the
'map select'
command, but does disables the display of the
maps that were not selected.
The RasMol
'map save'
command saves an imgCIF map file.
If no specific map was given by the map selector, the currently
selected maps and their masks are written to the file, one
map and mask pair per data block.
The RasMol
'map scale'
command selects the scaling of pseudo-Gaussians in the
'map generate'
commands.
In the default of map scale true, each Gaussian has a height proportional
element type of the atom.
If map scale false has been executed, each Gaussian is scaled so that
the Gaussian contour level 1 is at the van der Waals radius.
In either case a standard deviation determined by the
most recently specified spread or resolution is used.
The RasMol
'map select'
command selects particular maps to make them active for
subsequent map commands. This is similar to the
'map restrict'
command, but does not disable the display of the
maps that were not selected.
If the optional
'atom'
parameter is given, the command selects the atoms with centres closest to the
map points. The radius of the search may be specified by the parameter
'search_radius'.
The default is to look for atoms within 4 Ångstroms plus the probe radius.
If the optional
'within'
parameter is given, the new selection is taken from within the currently
selected atoms. If the options
'add'
parameter is given, the new selection is added to the currently selected atoms.
The default is to search within all atoms.
The RasMol
'map show'
command causes information about the maps specified by
the map selector to be written to the command window.
The RasMol
'map spacing'
command specifies the spacing to be used between contour lines
in creating representations of maps. The spacing is typically
given in Ångstroms with a decimal point, but may also be
specified in RasMol units (250ths of an Angstom) as an
integer. For maps loaded in grid coordinates that spacing
is parallel to the cell edges. The default spacing is
one half Ångstrom.
The RasMol
'map spread'
command specifies the reciprocal of the number of
standard deviations per radius to be used in
generating maps as sums of Gaussians centered
on atomic positions. The default spread is one
two thirds (i.e. each radius covers 1.5 standard deviations).
If the spread has been set to zero, the spread for each atom is determined
from the van der Waals radius and the probe atom radius to simulate the
effect of a Lee-Richards surface.
The RasMol
'map zap'
command removes the data and representations of the
maps specified by the map selector. The map numbers
of maps that have not been removed are not changed.
The RasMol
'molecule'
command selects one of up to 5 previously loaded molecules
for active manipulation. While all the molcules are displayed
and may be rotated collectively (see the
'rotate all'
command), only one molecule at a time
time is active for manipulation by the commands which
control the details of rendering.
The RasMol
'monitor'
command allows the display of distance monitors. A distance
monitor is a dashed (dotted) line between an arbitrary pair
of atoms, optionally labelled by the distance between them.
The RasMol command
'monitor <number> <number>'
adds such a distance monitor between the two atoms specified by the atom
serial numbers given as parameters
Distance monitors are turned off with the command
'monitors off'.
By default, monitors display the
distance between its two end points as a label at the centre of
the monitor. These distance labels may be turned off with the
command
'set monitors off',
and re-enabled with the command
'set monitors on'.
Like most other representations,
the colour of a monitor is taken from the colour of its end points unless
specified by the
'colour monitors'
command.
Distance monitors may also be added to a molecule interactively with
the mouse, using the
'set picking monitor'
command. Clicking on an atom results
in its being identified on the rasmol command line. In addition
every atom picked increments a modulo counter such that, in monitor
mode, every second atom displays the distance between this atom and
the previous one. The shift key may be used to form distance monitors
between a fixed atom and several consecutive positions. A distance
monitor may also be removed (toggled) by selecting the appropriate
pair of atom end points a second time.
The RasMol
'NoToggle'
command enables or disables the use of the toggle ability
that is used by some of the other RasMol commands.
When no boolean value is specified, NoToggle mode is ENABLED.
When NoToggle mode is ENABLED, all toggle functionality is
DISABLED. To turn it off, one must explicitly set
'notoggle off'.
Some commands which use the toggle feature are:
'ColourMode'.
More functions that utilize this capability may be added
at a later date.
The RasMol
'pause'
command is used in script files to stop the script file for local
manipulation by a mouse, until any key is pushed to restart the
script file.
'Wait'
is synonymous with
'pause'.
This command may be executed in RasMol script files to suspend
the sequential execution of commands and allow the user to examine
the current image. When RasMol executes a
'pause'
command in a script file, it suspends execution of the rest
of the file, refreshes the image on the screen and allows the
manipulation of the image using the mouse and scroll bars, or
resizing of the graphics window. Once a key is pressed, control
returns to the script file at the line following the
'pause'
command. While a script is suspended the molecule may be rotated,
translated, scaled, slabbed and picked as usual, but all menu
commands are disabled.
The
'pause'
can probably
be used most effectively with
'echo'
commands in education pre-scripted demonstrations,
where a description of the current image is presented to
the user/student. Typically the command before a
'pause'
should be
'echo Press any key to continue'.
Execution of a script can be cancelled by pressing Control-D or
Control-Z (on VAX/VMS, Control-C) while standing at a pause.
The command
'set picking none'
disables picking, which avoids the display of spurious messages
whilst a script is suspended at a pause.
The RasMol
'play'
command specifies the recording medium from which to play back a movie.
The playback frame start time is given in seconds to millisecond precision.
Since we are working on computers, the medium is specified as a set of files,
each marked with the playback frame start time in milliseconds as part of the
name. The place in the name at which to look for the playback frame start
time in milliseconds is marked by the characters "ssssss" with an
appropriate number of digits. RasMol accepts either upper or lower case
s's or decimal digits to mark the place for the time. The play off and play
eject commands effectively remove the specified medium from use. If no medium
is specified, play off suspends playing and play on resumes playing.
Normally play starts immediately and runs to the end of the medium. However,
if play off and/or or some combination of play from and play until is entered
before
"play type medium",
those settings will be used.
As of release 2.7.5, RasMol support play from scripts and data files.
The RasMol
'print'
command sends the currently displayed image to the local default printer
using the operating system's native printer driver. Note: this command
is not yet supported under UNIX or VMS. It is intended to take advantage
of Microsoft Windows and Apple Macintosh printer drivers. For example,
this allows images to be printed directly on a dot matrix printer.
When using RasMol on a UNIX or VMS system this functionality may be
achieved by either generating a PostScript file using the RasMol
'write ps'
or
'write vectps'
commands and printing that or generating a raster image file and using a
utility to dump that to the local printer.
Exit from the RasMol program. The RasMol commands
'exit'
and
'quit'
are synonymous, except within nested scripts. In that case,
'exit'
terminates only the current level, while
'quit'
terminates all nested levels of scripts.
The RasMol
'record'
command specifies the recording medium to hold the movie. Since we are
working on computers, the medium is specified as a template for a set of
files, each marked with the playback frame start time in milliseconds
(rather than as seconds to avoid embedding a decimal point) as part of
the name. The place in the name to be replaced with the playback frame
start time in milliseconds is marked by the characters "ssssss" with
an appropriate number of digits. RasMol accepts either upper or lower case
s's or decimal digits to mark the place for the time. The record off
commands remove the specified medium from use. If no medium is specified,
record off suspends recording and record on resumes recording with the
next available time on the same medium. The screen is the default medium
and is, by default, on. Writing to disk must be explicitly specified so
that the disk does not get filled up unintentionally. The type of a
recording medium may be an image type such as gif, pict or png to record
the actual screen images or script to record the RasMol commands used to
generate the frames.
Normally recording starts at playback frame start time 0 seconds.
A non-zero starting time in seconds can be specified with the
"record from"
command as in
"record from 25"
or
"record from 37.25"
to help in organizing scenes of movies to be assembled later in an
appropriate order.
The
"record until"
command allows an upper limit to be set on recording time in seconds.
The default is to have no limit. Issuing the commands
'record from 600'
'record until 1800'
would result in a 20 minute movie segment intended to start 10
The RasMol
'refresh'
command redraws the current image. This is useful in scripts
to ensure application of a complex list of parameter changes.
The RasMol
'renumber'
command sequentially numbers the residues in a macromolecular chain.
The optional parameter specifies the value of the first residue in the
sequence. By default, this value is one. For proteins,
each amino acid is numbered consecutively from the N terminus to the C
terminus. For nucleic acids, each base is numbered from the 5' terminus
to the 3' terminus. All chains in the current database are renumbered and gaps
in the original sequence are ignored. The starting value for numbering may
be negative.
The RasMol
'reset'
command restores the original viewing transformation
and centre of rotation. The scale is set to its default value,
'zoom 100',
the centre of rotation is set to the geometric centre of the currently
loaded molecule,
'centre all',
this centre is translated to the middle of the screen and
the viewpoint set to the default orientation.
This command should not be mistaken for the RasMol
'zap'
command which deletes the currently stored molecule, returning the
program to its initial state.
The RasMol
'restrict'
command both defines the currently selected region of the
molecule and disables the representation of (most of) those parts of the
molecule no longer selected. All subsequent RasMol commands that modify
a molecule's colour or representation affect only the currently selected
region. The parameter of a
'restrict'
command is a RasMol atom expression that is evaluated for every atom
of the current molecule. This command is very similar to the RasMol
'select'
command, except
'restrict'
disables the
'wireframe',
'spacefill'
and
'backbone'
representations in the non-selected region.
Type "help expression" for more information on RasMol atom expressions or
see section
'Atom Expressions'.
The RasMol
'ribbons'
command displays the currently loaded protein or nucleic acid as a
smooth solid "ribbon" surface passing along the backbone of the protein.
The ribbon is drawn between each amino acid whose alpha carbon is
currently selected. The colour of the ribbon is changed by the RasMol
'colour ribbon'
command. If the current ribbon colour is
'none'
(the default), the colour is taken from the alpha carbon at each
position along its length.
The width of the ribbon at each position is determined by the optional
parameter in the usual RasMol units. By default the width of the ribbon
is taken from the secondary structure of the protein or a constant value
of 720 (2.88 Ångstroms) for nucleic acids.
The default width of protein alpha helices and beta sheets is 380 (1.52
Ångstroms) and 100 (0.4 Ångstroms) for turns and random coil. The
secondary structure assignment is either from the PDB file or calculated
using the DSSP algorithm as used by the
'structure'
command. This command is similar to the RasMol command
'strands'
which renders the biomolecular ribbon as parallel depth-cued curves.
Rotate the molecule about the specified axis.
Permitted values for the axis parameter are
"x", "y" and "z".
The integer parameter states the angle in degrees for the structure to
be rotated. For the X and Y axes, positive values move the closest point
up and right, and negative values move it down and left, respectively. For
the Z axis, a positive rotation acts clockwise and a negative angle
anti-clockwise.
Alternatively, this command may be used to specify which rotations
the mouse or dials will control. If
'rotate bond true'
is selected, the horizontal scroll bar will control rotation around
the axis selected by the
'bond src dst pick'
command. If
'rotate all true'
is selected, and multiple molecules have been loaded, then all molecules
will rotate together. In all other cases, the mouseand dials control the
the rotation of the molecule selected by the
'molecule n'
command.
The RasMol
'Russian'
command sets the menus and messages to the Russian versions.
This command may not work correctly unless appropriate fonts
have been installed. The commands
'Bulgarian',
'Chinese',
'English',
'French',
'Italian',
'Russian'
and
'Spanish'
may be used to select Bulgarian, Chinese, English, French,
Italian, Japanese, Russian and Spanish menus and messages if the
appropriate fonts have been installed.
Save the currently selected set of atoms in a Protein
Data Bank (PDB), MDL, Alchemy(tm) or XYZ format file.
The distinction between this command and the RasMol
'write'
command has been dropped. The only difference is that without a format
specifier the
'save'
command generates a
'PDB'
file and the
'write'
command generates a
'GIF'
image.
The RasMol
'script'
command reads a set of RasMol commands sequentially from a
text file and executes them. This allows sequences of commonly used
commands to be stored and performed by single command. A RasMol script
file may contain a further script command up to a maximum "depth" of 10,
allowing complicated sequences of actions to be executed. RasMol
ignores all characters after the first '#' character on each line
allowing the scripts to be annotated. Script files are often also
annotated using the RasMol
'echo'
command.
The most common way to generate a RasMol script file is to use the
'write script'
or
'write rasmol'
commands to output the sequence of commands that are needed to
regenerate the current view, representation and colouring of the
currently displayed molecule.
The RasMol command
'source'
is synonymous with the
'script'
command.
Scripts may also be created with a text editor.
Define the currently selected region of the molecule. All subsequent RasMol
commands that manipulate a molecule or modify its colour or representation
only affect the currently selected region. The parameter of a
'select'
command is a RasMol expression that is evaluated for every atom of the
current molecule. The currently selected (active) region of the molecule
are those atoms that cause the expression to evaluate true. To select
the whole molecule use the RasMol command
'select all'.
The behaviour of the
'select'
command without any parameters is determined by the RasMol
'hetero'
and
'hydrogen'
parameters.
Type "help expression" for more information on RasMol atom expressions or
see section
'Atom Expressions'.
The RasMol
'set'
command allows the user to alter various internal program parameters
such as those controlling rendering options. Each parameter has its
own set or permissible parameter options. Typically, omitting the
paramter option resets that parameter to its default value. A list of
valid parameter names is given below.
The RasMol
'show'
command display details of the status of the currently
loaded molecule. The command
'show information'
lists the molecule's name,
classification, PDB code and the number of atoms, chains, groups it contains.
If hydrogen bonding, disulphide bridges or secondary structure have been
determined, the number of hbonds, ssbonds, helices, ladders and turns
are also displayed, respectively. The command
'show centre'
shows any non-zero centering values selected by the
'centre [CenX, CenY, CenZ]'
command. The command
'show phipsi'
shows the phi and psi angles of the currently selected residues and
the omega angles of cis peptide bonds. The command
'show RamPrint'
(or 'show RPP' or 'show RamachandranPrinterPlot') shows a simple
Ramachandran printer plot in the style of Frances Bernstein's fisipl
program. The command
'show rotation'
(or 'show rot' or 'show 'rotate') shows the currently selected values
of z, y, x and bond rotations, if any.
The command
'show selected'
(or 'show selected group' or 'show selected chain' or 'show selected atom' )
shows the groups (default), chains or atoms of the current selection.
The command
'show sequence'
lists the residues that comprise each chain of the molecule. The command
'show symmetry'
shows the space group and unit cell of the molecule. The command
'show translation'
shows any non-zero translation values selected by the
'translate <axis> <value>'
command. The command
'show zoom'
shows any non-zero zoom value selected by the
'zoom <value>'
command.
The RasMol
'slab'
command enables, disables or positions the z-clipping plane of the
molecule. The program only draws those portions of the
molecule that are further from the viewer than the slabbing plane.
Integer values range from zero at the very back of the molecule to
100 which is completely in front of the molecule. Intermediate values
determine the percentage of the molecule to be drawn.
This command interacts with the
'depth <value>'
command, which clips to the rear of a given z-clipping plane.
The RasMol
'spacefill'
command is used to represent all of the currently selected atoms as solid
spheres. This command is used to produce both union-of-spheres and
ball-and-stick models of a molecule. The command,
'spacefill true',
the default, represents each atom as a sphere of van der Waals radius.
The command
'spacefill off'
turns off the representation of the selected atom as spheres. A sphere
radius may be specified as an integer in RasMol units (1/250th Ångstrom)
or a value containing a decimal point. A value of 500 (2.0
Ångstroms) or greater results in a "Parameter value too large" error.
The
'temperature'
option sets the radius of each sphere to the value stored in its temperature
field. Zero or negative values have no effect and values greater than
2.0 are truncated to 2.0. The
'user'
option allows the radius of each sphere to be specified by additional lines
in the molecule's PDB file using Raster 3D's COLOUR record extension.
The RasMol command
'cpk'
is synonymous with the
'spacefill'
command.
The RasMol command
'cpknew'
is synonymous with the
'spacefill'
command, except that a slightly different set of colours is used.
The RasMol
'Spanish'
command sets the menus and messages to the Spanish versions.
This command may not work correctly unless appropriate fonts
have been installed. The commands
'Bulgarian',
'Chinese',
'English',
'French',
'Italian',
'Russian'
and
'Spanish'
may be used to select Bulgarian, Chinese, English, French,
Italian, Japanese, Russian and Spanish menus and messages if the
appropriate fonts have been installed.
The RasMol
'ssbonds'
command is used to represent the disulphide bridges of the protein
molecule as either dotted lines or cylinders between the connected
cysteines. The first time that the
'ssbonds'
command is used, the program searches the structure of the protein to
find half-cysteine pairs (cysteines whose sulphurs are within 3 Ångstroms
of each other) and reports the number of bridges to the user. The command
'ssbonds on'
displays the selected "bonds" as dotted lines, and the command
'ssbonds off'
disables the display of ssbonds in the currently selected area. Selection
of disulphide bridges is identical to normal bonds, and may be adjusted
using the RasMol
'set bondmode'
command. The colour of disulphide bonds may be changed using the
'colour ssbonds'
command. By default, each disulphide bond has the colours of its connected
atoms.
By default disulphide bonds are drawn between the sulphur atoms within
the cysteine groups. By using the
'set ssbonds'
command the position of the cysteine's alpha carbons may be used instead.
The RasMol
'star'
command is used to represent all of the currently selected atoms as
stars (six strokes, one each in the x, -x, y, -y, z and -z directions).
The commands
'select not bonded'
followed by
'star 75'
are useful to mark unbonded atoms in a
'wireframe'
display with less overhead than provided by
'spacefill 75'.
This can be done automatically for all subsequent wireframe
displays with the command
'set bondmode not bonded'.
The command
'star true',
the default, represents each atom as a star with strokes
length equal to van der Waals radius.
The command
'star off'
turns off the representation of the selected atom as stars. A star
stroke length may be specified as an integer in RasMol units
(1/250th Ångstrom)
or a value containing a decimal point. A value of 500 (2.0
Ångstroms) or greater results in a "Parameter value too large" error.
The
'temperature'
option sets the stroke length of each star to the value stored
in its temperature
field. Zero or negative values have no effect and values greater than
2.0 are truncated to 2.0. The
'user'
option allows the stroke length of each star to be specified by
additional lines
in the molecule's PDB file using Raster 3D's COLOUR record extension.
The RasMol
'spacefill'
command can be used for more artistic rendering of atoms as spheres.
The RasMol
'stereo'
command provides side-by-side stereo display of images. Stereo
viewing of a molecule may be turned on (and off) either by
selecting
'Stereo'
from the
'Options'
menu, or by
typing the commands
'stereo on'
or
'stereo off'.
Starting with RasMol version 2.7.2.1, the
'Stereo'
menu selection and the command
'stereo'
without arguments cycle from the initial state of
'stereo off'
to
'stereo on'
in cross-eyed mode to
'stereo on'
in wall-eyed mode and then back to
'stereo off'.
The separation angle between
the two views may be adjusted with the
'set stereo [-] <number>'
command, where positive values result in crossed eye
viewing and negative values in relaxed (wall-eyed) viewing.
The inclusion of
'[-] <number>'
in the
'stereo'
command, as for example in
'stereo 3'
or
'stereo -5',
also controls angle and direction.
The stereo command is only partially
implemented. When stereo is turned on, the image is not properly
recentred. (This can be done with a
'translate x -<number>'
command.)
It is not supported in vector PostScript output files, is not
saved by the
'write script'
command, and in
general is not yet properly interfaced with several other
features of the program.
The RasMol
'strands'
command displays the currently loaded protein or nucleic acid as a
smooth "ribbon" of depth-cued curves passing along the backbone of the
protein. The ribbon is composed of a number of strands that run parallel
to one another along the peptide plane of each residue. The ribbon is
drawn between each amino acid whose alpha carbon is currently selected.
The colour of the ribbon is changed by the RasMol
'colour ribbon'
command. If the current ribbon colour is
'none'
(the default), the colour is taken from the alpha carbon at each
position along its length. The central and outermost
strands may be coloured independently using the
'colour ribbon1'
and
'colour ribbon2'
commands, respectively. The number of strands in the ribbon may be
altered using the RasMol
'set strands'
command.
The width of the ribbon at each position is determined by the optional
parameter in the usual RasMol units. By default the width of the ribbon
is taken from the secondary structure of the protein or a constant value
of 720 for nucleic acids (which produces a ribbon 2.88 Ångstroms wide).
The default width of protein alpha helices and beta sheets is 380 (1.52
Ångstroms) and 100 (0.4 Ångstroms) for turns and random coil. The
secondary structure assignment is either from the PDB file or calculated
using the DSSP algorithm as used by the
'structure'
command. This command is similar to the RasMol command
'ribbons'
which renders the biomolecular ribbon as a smooth shaded surface.
The RasMol
'structure'
command calculates secondary structure assignments
for the currently loaded protein. If the original PDB file contained
structural assignment records (HELIX, SHEET and TURN) these are discarded.
Initially, the hydrogen bonds of the current molecule are found, if this
hasn't been done already. The secondary structure is then determined using
Kabsch and Sander's DSSP algorithm. Once finished the program reports the
number of helices, strands and turns found.
The RasMol
'surface'
command renders a Lee-Richards molecular surface resulting
from rolling a probe atom on the selected atoms.
The value given specifies the radius of the probe.
If given in the first form, the evolute of the surface
of the probe is shown (the solvent excluded surface).
If given in the second form, the envelope of the
positions of the center of the probe is shown
(the solvent accessible surface).
The RasMol
'trace'
command displays a smooth spline between consecutive alpha
carbon positions. This spline does not pass exactly through
the alpha carbon position of each residue, but follows the
same path as
'ribbons',
'strands'
and
'cartoons'.
Note that residues may be displayed as
'ribbons',
'strands',
'cartoons'
or as a
'trace'.
Enabling one of these
representations disables the others. However, a residue
may be displayed simultaneously as backbone and as one of
the above representations. This may change in future
versions of RasMol. Prior to version 2.6,
'trace'
was synonymous with
'backbone'.
'Trace temperature'
displays the backbone as a wider cylinder
at high temperature factors and thinner at lower. This
representation is useful to X-ray crystallographers and NMR spectroscopists.
The RasMol
'translate'
command moves the position of the centre of the molecule on the
screen. The axis parameter specifies along which axis the molecule
is to be moved and the integer parameter specifies the absolute
position of the molecule centre from the middle of the screen.
Permitted values for the axis parameter are
"x", "y" and "z".
Displacement values must be between -100 and 100 which correspond to
moving the current molecule just off the screen. A positive
"x"
displacement moves the molecule to the right, and a positive
"y"
displacement moves the molecule down the screen. The pair of commands
'translate x 0'
and
'translate y 0'
centres the molecule on the screen.
The RasMol command
'unbond <number> <number>'
removes the designated bond from the drawing.
The command
'unbond'
without arguments removes a bond previously picked by the
'bond <number> <number> pick'
command.
The RasMol
'wireframe'
command represents each bond within the selected region of the molecule
as a cylinder, a line or a depth-cued vector. The display of bonds
as depth-cued vectors (drawn darker the further away from the viewer)
is turned on by the command
'wireframe'
or
'wireframe on'.
The selected bonds are displayed as cylinders by specifying a radius
either as an integer in RasMol units or containing a decimal point as
a value in Ångstroms. A parameter value of 500 (2.0 Ångstroms) or
above results in an "Parameter value too large" error. Bonds may be
coloured using the
'colour bonds'
command.
If the selected bonds involved atoms of alternate conformers then
the bonds are narrowed in the middle to a radius of .8 of the specified
radius (or to the radius specifed as the optional second parameter).
Non-bonded atoms, which could become invisible in an
ordinary
'wireframe'
display can be marked by a preceding
'set bondmode not bonded'
command. If nearly co-linear bonds to atoms cause them to be
difficult to see in a wireframe display, the
'set bondmode all'
command will add markers for
'all'
atoms in subsequent
'wireframe'
command executions.
Write the current image to a file in a standard format. Currently
supported image file formats include
'bmp'
(Microsoft bitmap) and
'gif'
(Compuserve GIF),
'iris'
(IRIS RGB),
'ppm'
(Portable Pixmap),
'ras'
(Sun rasterfile),
'ps'
and
'epsf'
(Encapsulated PostScript),
'monops'
(Monochrome Encapsulated PostScript),
'pict'
(Apple PICT),
'vectps'
(Vector Postscript). The
'write'
command may also be used to generate command scripts for other graphics
programs. The format
'script'
writes out a file containing the RasMol
'script'
commands to reproduce the current image. The format
'molscript'
writes out the commands required to render the current view of the
molecule as ribbons in Per Kraulis' Molscript program and the format
'kinemage'
the commands for David Richardson's program Mage. The following
formats are useful for further processing:
'povray'
(POVRay 2),
'povray3'
(POVRay 3 -- under development),
'vrml'
(VRML file).
Finally, several
formats are provided to provide phi-psi data for listing or for
'phipsi'
(phi-psi data as an annotated list with cis omegas),
'ramachan'
and
'RDF'
and
'RamachandranDataFile'
(phi-psi data as columns of numbers for gnuplot),
'RPP'
and
'RamachandranPrinterPlot'
(phi-psi data as a printer plot).
The distinction between this command and the RasMol
'save'
command has been dropped. The only difference is that without a format
specifier the
'save'
command generates a
'PDB'
file and the
'write'
command generates a
'GIF'
image.
Deletes the contents of the current database and resets parameter
variables to their initial default state.
Change the magnification of the currently displayed image. Boolean
parameters either magnify or reset the scale of current molecule. An
integer parameter specifies the desired magnification as a percentage
of the default scale. The minimum parameter value is 10; the maximum
parameter value is dependent upon the size of the molecule being
displayed. For medium sized proteins this is about 500.
A complete list of internal parameter names is given below.
The RasMol
'ambient'
parameter is used to control the amount of ambient (or surrounding)
light in the scene. The
'ambient'
value must be between 0 and 100. It controls the percentage intensity
of the darkest shade of an object. For a solid object, this is the
intensity of surfaces facing away from the light source or in shadow.
For depth-cued objects this is the intensity of objects furthest from
the viewer.
This parameter is commonly used to correct for monitors with different
"gamma values" (brightness), to change how light or dark a hardcopy
image appears when printed or to alter the feeling of depth for
wireframe or ribbon representations.
The RasMol
'axes'
parameter controls the display of orthogonal coordinate axes on
the current display. The coordinate axes are those used in the
molecule data file, and the origin is the centre of the molecule's
bounding box. The
'set axes'
command is similar to the commands
'set boundbox'
and
'set unitcell'
that display the bounding box and the crystallographic unit cell,
respectively.
The RasMol
'backfade'
parameter is used to control backfade to the specified background
colour, rather than black. This is controlled by the commands
'set backfade on'
and
'set backfade off'.
For example, this may be used to generate depth-cued images that
fade to white, rather than black.
The RasMol
'background'
parameter is used to set the colour of the "canvas" background. The
colour may be given as either a colour name or a comma separated
triple of Red, Green, Blue (RGB) components enclosed in square
brackets. Typing the command
'help colours'
will give a list of the predefined colour names recognised by RasMol.
When running under X Windows, RasMol also recognises colours in the
X server's colour name database.
The command
'set background'
is synonymous with the RasMol command
'background'.
The RasMol
'set bondmode'
command controls the mechanism used to select individual bonds
and modifies the display of bonded and non-bonded atoms by subsequent
'wireframe'
commands.
When using the
'select'
and
'restrict'
commands, a given bond will be selected if i) the bondmode is
'or'
and either of the connected atoms is selected, or ii) the bondmode is
'and'
and both atoms connected by the bond are selected. Hence an individual
bond may be uniquely identified by using the command
'set bondmode and'
and then uniquely selecting the atoms at both ends.
The
'bondmode [all | none | not bonded]'
commands add
'star 75'
or
'spacefill 75'
markers for the designated atoms to
'wireframe'
displays. Stars are used when the specified wireframe radius is zero.
The RasMol
'bonds'
parameter is used to control display of double and triple bonds as
multiple lines or cylinders. Currently bond orders are only read
from MDL Mol files, Sybyl Mol2 format files, Tripos Alchemy format
files, CIF and mmCIF, and suitable PDB files. Double (and triple) bonds
are specified in some PDB files by specifying a given bond twice (and
three times) in CONECT records. The command
'set bonds on'
enables the display of bond orders, and the command
'set bonds off'
disables them.
The RasMol
'boundbox'
parameter controls the display of the current molecule's bounding box
on the display. The bounding box is orthogonal to the data file's
original coordinate axes. The
'set boundbox'
command is similar to the commands
'set axes'
and
'set unitcell'
that display orthogonal coordinate axes and the bounding box,
respectively.
The RasMol
'cartoon'
parameter is used to control display of the cartoon version of the
'ribbons'
display. By default, the C-termini of beta-sheets are displayed as
arrow heads. This may be enabled and disabled using the
'set cartoons <boolean>'
command. The depth of the cartoon may be adjusted using the
'cartoons <number>'
command. The
'set cartoons'
command without any parameters returns these two options to
their default values.
The RasMol
'cisangle'
parameter controls the cutoff angle for identifying cis peptide
bonds. If no value is given, the cutoff is set to 90 degrees.
This command controls the display mode within RasMol. By default,
'set display normal',
RasMol displays the molecule in the representation specified by the
user. The command
'set display selected'
changes the display mode such that the molecule is temporarily drawn
so as to indicate currently selected portion of the molecule. The
user specified colour scheme and representation remains unchanged.
In this representation all selected atoms are shown in yellow and
all non selected atoms are shown in blue. The colour of the background
is also changed to a dark grey to indicate the change of display mode.
This command is typically only used by external Graphical User
Interfaces (GUIs).
The RasMol
'set fontsize'
command is used to control the size of the characters that
form atom labels. This value corresponds to the height of
the displayed character in pixels. The maximum value of
'fontsize'
is 48 pixels, and the default value is 8 pixels high.
Fixed or proportional spacing may be selected by appending the
"FS" or "PS" modifiers, respectively. The default is "FS".
To display atom labels on the screen use the RasMol
'label'
command and to change the colour of displayed labels, use
the
'colour labels'
command.
The RasMol
'set fontstroke'
command is used to control the size of the stroke width of the
characters that form atom labels. This value is the radius in
pixels of cylinders used to form the strokes. The special value
of "0" is the default used for the normal single pixel stroke width,
which allows for rapid drawing and rotation of the image.
Non-zero values are provided to allow for more artistic atom
labels for publication at the expense of extra time in rendering
the image.
When wider strokes are used, a larger font size is recommend, e.g.
by using the RasMol
'set fontsize 24 PS'
command, followed by
'set fontstroke 2'
The character sets used by RasMol rendered with fixed spacing with
single-pixel-width strokes and with proportional spacing with
2-pixel-radius cylinder strokes are shown in the following sample:
To display atom labels on the screen use the RasMol
'label'
command, and to change the colour of displayed labels use
the
'colour labels'
command.
The RasMol
'hbonds'
parameter determines whether hydrogen bonds are drawn between
the donor and acceptor atoms of the hydrogen bond,
'set hbonds sidechain'
or between the alpha carbon atoms of the protein backbone and between
the phosphorous atoms of the nucleic acid backbone,
'set hbonds backbone'.
The actual display of hydrogen bonds is controlled by the
'hbonds'
command. Drawing hydrogen bonds between protein alpha carbons or
nucleic acid phosphorous atoms is useful when the rest of the molecule
is shown in only a schematic representation such as
'backbone',
'ribbons'
or
'strands'.
This parameter is similar to the RasMol
'ssbonds'
parameter.
The RasMol
'hetero'
parameter is used to modify the 'default' behaviour of the RasMol
'select'
command, i.e. the behaviour of
'select'
without any parameters. When this value is
'false',
the default
'select'
region does not include any heterogeneous atoms (refer to the
predefined set
'hetero'
). When this value is
'true',
the default
'select'
region may contain hetero atoms. This parameter is similar to
the RasMol
'hydrogen'
parameter which determines whether hydrogen atoms should be
included in the default set. If both
'hetero'
and
'hydrogen'
are
'true',
'select'
without any parameters is equivalent to
'select all'.
The RasMol
'hourglass'
parameter allows the user to enable and disable the use of the 'hour
glass' cursor used by RasMol to indicate that the program is currently
busy drawing the next frame. The command
'set hourglass on'
enables the indicator, whilst
'set hourglass off'
prevents RasMol from changing the cursor. This is useful when spinning
the molecule, running a sequence of commands from a script file or
using interprocess communication to execute complex sequences of
commands. In these cases a 'flashing' cursor may be distracting.
The RasMol
'hydrogen'
parameter is used to modify the "default" behaviour of the RasMol
'select'
command, i.e. the behaviour of
'select'
without any parameters. When this value is
'false',
the default
'select'
region does not include any hydrogen, deuterium or tritium atoms (refer
to the predefined set
'hydrogen'
). When this value is
'true',
the default
'select'
region may contain hydrogen atoms. This parameter is similar to
the RasMol
'hetero'
parameter which determines whether heterogeneous atoms should be
included in the default set. If both
'hydrogen'
and
'hetero'
are
'true',
'select'
without any parameters is equivalent to
'select all'.
The RasMol
'set kinemage'
command controls the amount of detail stored in a Kinemage output
file generated by the RasMol
'write kinemage'
command. The output kinemage files are intended to be displayed by
David Richardson's Mage program.
'set kinemage false',
the default, only stores the currently displayed representation in
the generated output file. The command
'set kinemage true',
generates a more complex Kinemage that contains both the wireframe
and backbone representations as well as the coordinate axes,
bounding box and crystal unit cell.
The RasMol
'set menus'
command enables the canvas window's menu buttons or menu bar. This
command is typically only used by graphical user interfaces or to
create as large an image as possible when using Microsoft Windows.
The RasMol
'set monitor'
command enables
'monitors'.
The distance monitor labels may be turned off with the command
'set monitor off',
and re-enabled with the command
'set monitor on'.
The RasMol
'set mouse'
command sets the rotation, translation, scaling and zooming mouse
bindings. The default value is
'rasmol'
which is suitable for two button mice (for three button mice the
second and third buttons are synonymous); X-Y rotation is controlled
by the first button, and X-Y translation by the second. Additional
functions are controlled by holding a modifier key on the keyboard.
[Shift] and the first button performs scaling, [shift] and the second
button performs Z-rotation, and [control] and the first mouse button
controls the clipping plane. The
'insight'
and
'quanta'
options provide the same mouse bindings as other packages for experienced
users.
The RasMol
'set picking'
series of commands affects how a user may interact with a
molecule displayed on the screen in RasMol.
Enabling/Disabling Atom Identification Picking:
Clicking on an atom with the mouse results in identification and
the display of its residue name, residue number, atom name, atom serial
number and chain in the command window. This behavior may be disabled
with the command
'set picking none'
and restored with the command
'set picking ident'.
The command
'set picking coord'
adds the atomic coordinates of the atom to the display.
Disabling picking, by using
'set picking off'
is useful when executing the
'pause'
command in RasMol scripts as it prevents the display of
spurious message on the command line while the script is suspended.
Measuring Distances, Angles and Torsions:
Interactive measurement of distances, angles and torsions
is achieved using the commands:
'set picking distance',
'set picking monitor',
'set picking angle'
and
'set picking torsion',
respectively. In these modes, clicking on an atom results in it
being identified on the rasmol command line. In addition every
atom picked increments a modulo counter such that in distance
mode, every second atom displays the distance (or distance monitor)
between this atom and the previous one. In angle mode, every
third atom displays the angle between the previous three atoms
and in torsion mode every fourth atom displays the torsion between
the last four atoms. By holding down the shift key while picking an
atom, this modulo counter is not incremented and allows, for
example, the distances of consecutive atoms from a fixed atom to
be displayed. See the
'monitor'
command for how to control the display of distance monitor lines and labels.
Labelling Atoms with the Mouse:
The mouse may also be used to toggle the display of an atom label
on a given atom. The RasMol command
'set picking label'
removes a label from a picked atom if it already has one or
displays a concise label at that atom position otherwise.
Centring Rotation with the Mouse:
A molecule may be centred on a specified atom position using the
RasMol commands
'set picking centre'
or
'set picking center'.
In this mode, picking an atom causes all futher rotations to be
about that point.
Picking a Bond as a Rotation Axis:
Any bond may be picked as an axis of rotation for the portion of
the molecule beyond the second atom selected. This feature should
be used with caution, since, naturally, it changes the conformation
of the molecule. After executing
'set picking bond'
or using the equivalent "Pick Bond" in the "Settings" menu,
a bond to be rotated is picked with the same sort of mouse clicks
as are used for picking atoms for a distance measurement. Normally
this should be done where a bond exists, but if no bond exists, it
will be added. The bond cannot be used for rotation if it is part
of a ring of any size. All bonds selected for rotation are remembered
so that they can be properly reported when writing a script, but
only the most recently selected bond may be actively rotated.
Enabling Atom/Group/Chain Selection Picking:
Atoms, groups and chains may be selected (as if with the
'select'
command), with the
'set picking atom',
'set picking group',
'set picking chain'
commands. For each of these commands, the shift key may be used to
have a new selection added to the old, and the control key may be
used to have a new selection deleted from the old. When the
'set picking atom'
command is given, the mouse can be used to pick or to drag a box around
the atoms for which selection is desired. When the
'set picking group'
command is given, picking any an atom will cause selection
of all atoms which agree in residue number with the picked atom,
even if in different chains.
When the
'set picking chain'
command is given, picking any atom will cause selection
of all atoms which agree in chain identifier with the picked atom.
The RasMol
'set play.fps'
command gives the number of frames per second for playback by the
'play'
command (default 24 frames per second).
In the current release of RasMol, the play timing is not controlled
by this parameter.
The RasMol
'set radius'
command is used to alter the behaviour of the RasMol
'dots'
command depending upon the value of the
'solvent'
parameter.
When
'solvent'
is
'true',
the
'radius'
parameter controls whether a true van der Waals' surface
is generated by the
'dots'
command. If the value of
'radius'
is anything other than zero, that value is used as the
radius of each atom instead of its true vdW value. When
the value of
'solvent'
is
'true',
this parameter determines the 'probe sphere' (solvent) radius.
The parameter may be given as an integer in rasmol units or
containing a decimal point in Ångstroms. The default value of
this parameter is determined by the value of
'solvent'
and changing
'solvent'
resets
'radius'
to its new default value.
The RasMol
'set record.aps'
gives the maximum on-screen velocity in Ångstroms per second in animating
translations, rotations and zooms (default 10 A/second).
The RasMol
'set record.aps'
command gives number of frames per second for recording by the
'record'
command (default 24 frames per second).
The RasMol
'set record.dwell'
command sets the time in seconds to dwell on a change in appearance
(default .5 sec).
The
'shadepower'
parameter (adopted from RasTop) determines the shade repartition (the contrast)
used in rendering solid objects. This value between 0 and 100 adjusts
shading on an object surface oriented along the direction to the
light source. Changing the shadepower parameter does not change the
maximum or the minimum values of this shading, as does changing the
'ambient'
parameter. A value of 100 concentrates the light on the top of spheres,
giving a highly specular, glassy rendering (see the
'specpower'
parameter).
A value of 0 distributes the light on the entire object.
This implementation of shadepower differs from the one in RasTop
only in the choice of range (0 to 100 versus -20 to 20 in RasTop).
The RasMol
'set shadow'
command enables and disables ray-tracing of the currently rendered image.
Currently only the spacefilling representation is shadowed or can cast
shadows. Enabling shadowing will automatically disable the Z-clipping
(slabbing) plane using the command
'slab off'.
Ray-tracing typically takes about several seconds for a moderately sized protein.
It is recommended that shadowing be normally disabled whilst the
molecule is being transformed or manipulated, and only enabled once
an appropiate viewpoint is selected, to provide a greater impression
of depth.
The RasMol
'slabmode'
parameter controls the rendering method of objects cut by the
slabbing (z-clipping) plane. Valid slabmode parameters are
"reject", "half",
"hollow", "solid" and
"section".
The RasMol
'set solvent'
command is used to control the behaviour of the RasMol
'dots'
command. Depending upon the value of the
'solvent'
parameter, the
'dots'
command either generates a van der Waals' or a solvent
accessible surface around the currently selected set of
atoms. Changing this parameter automatically resets the
value of the RasMol
'radius'
parameter.
The command
'set solvent false',
the default value, indicates that a van der Waals' surface
should be generated and resets the value of
'radius'
to zero. The command
'set solvent true'
indicates that a 'Connolly' or 'Richards' solvent
accessible surface should be drawn and sets the
'radius'
parameter, the solvent radius, to 1.2 Ångstroms (or 300
RasMol units).
The RasMol
'set specular'
command enables and disables the display of specular highlights on
solid objects drawn by RasMol. Specular highlights appear as white
reflections of the light source on the surface of the object. The
current RasMol implementation uses an approximation function to
generate this highlight.
The specular highlights on the surfaces of solid objects may be
altered by using the specular reflection coefficient, which is
altered using the RasMol
'set specpower'
command.
The
'specpower'
parameter determines the shininess of solid objects rendered by
RasMol. This value between 0 and 100 adjusts the reflection
coefficient used in specular highlight calculations. The specular
highlights are enabled and disabled by the RasMol
'set specular'
command. Values around 20 or 30 produce plastic looking surfaces.
High values represent more shiny surfaces such as metals, while
lower values produce more diffuse/dull surfaces.
The RasMol
'ssbonds'
parameter determines whether disulphide bridges are drawn between
the sulphur atoms in the sidechain (the default) or between the alpha
carbon atoms in the backbone of the cysteines residues. The actual
display of disulphide bridges is controlled by the
'ssbonds'
command. Drawing disulphide bridges between alpha carbons is useful
when the rest of the protein is shown in only a schematic
representation such as
'backbone',
'ribbons'
or
'strands'.
This parameter is similar to the RasMol
'hbonds'
parameter.
The RasMol
'set stereo'
parameter controls the separation between the left and
right images. Turning stereo on and off doesn't reposition
the centre of the molecule.
Stereo viewing of a molecule may be turned on (and off) either
by selecting
'Stereo'
from the
'Options'
menu, or by typing the commands
'stereo on'
or
'stereo off'.
The separation angle between the two views may be adjusted with the
'set stereo [-] <number>'
command, where positive values result in crossed eye viewing and
negative values in relaxed (wall-eyed) viewing. Currently, stereo viewing
is not supported in
'vector PostScript'
output files.
The RasMol
'strands'
parameter controls the number of parallel strands that are displayed
in the ribbon representations of proteins. The permissible values for
this parameter are 1, 2, 3, 4, 5 and 9. The default value is 5. The
number of strands is constant for all ribbons being displayed.
However, the ribbon width (the separation between strands) may be
controlled on a residue by residue basis using the RasMol
'ribbons'
command.
The RasMol
'transparent'
parameter controls the writing of transparent GIFs by the
'write gif <filename>'
command. This may be controlled by the
'set transparent on'
and
'set transparent off'
commands.
The RasMol
'unitcell'
parameter controls the display of the crystallographic unit cell on
the current display. The crystal cell is only enabled if the appropriate
crystal symmetry information is contained in the PDB, CIF or mmCIF data
file. The
RasMol command
'show symmetry'
display details of the crystal's space group and unit cell axes. The
'set unitcell'
command is similar to the commands
'set axes'
and
'set boundbox'
that display orthogonal coordinate axes and the bounding box,
respectively.
The RasMol
'vectps'
parameter is use to control the way in which the RasMol
'write'
command generates vector PostScript output files. The command
'set vectps on'
enables the use of black outlines around spheres and cylinder bonds
producing "cartoon-like" high resolution output. However, the current
implementation of RasMol incorrectly cartoons spheres that are intersected
by more than one other sphere. Hence "ball and stick" models are rendered
correctly but not large spacefilling spheres models. Cartoon outlines
can be disabled, the default, by the command
'set vectps off'.
The RasMol
'write'
parameter controls the use of the
'save'
and
'write'
commands within scripts, but it may only be executed from the
command line. By default, this value is
'false',
prohibiting the generation of files in any scripts executed at
start-up (such as those launched from a WWW browser). However,
animators may start up RasMol interactively: type
'set write on'
and then execute a script to generate each frame using the
source command.
The logical operators allow complex queries to be constructed out of
simpler ones using the standard boolean connectives
'and',
'or'
and
'not'.
These may be abbreviated by the symbols
"&", "|" and "!",
respectively. Parentheses (brackets) may be used to alter the
precedence of the operators. For convenience, a comma may also
be used for boolean disjunction.
The atom expression is evaluated for each atom, hence
'protein and backbone'
selects protein backbone atoms, not the protein and [nucleic] acid
backbone atoms!
The following table gives some useful examples of RasMol
atom expressions.
RasMol primitive expressions are the fundamental building blocks
of atom expressions. There are two types of primitive expression.
The first type is used to identify a given residue number or range
of residue numbers. A single residue is identified by its number
(position in the sequence), and a range is specified by lower and
upper bounds separated by a hyphen character. For example
'select 5,6,7,8'
is also
'select 5-8'.
Note that this selects the given residue numbers in all macromolecule
chains.
The second type of primitive expression specifies a sequence of fields
that must match for a given atom. The first part specifies a residue
(or group of residues) and an optional second part specifies the atoms
within those residues. The first part consists of a residue name,
optionally followed by a residue number and/or chain identifier.
A residue name typically consists of up to three alphabetic characters,
which are case insensitive. Hence the primitive expressions
'SER'
and
'ser'
are equivalent, identifying all serine residues.
Residue names that contain non-alphabetic characters, such as
sulphate groups, may be delimited using square brackets, i.e.
'[SO4]'.
The residue number is intended to be the residue's position in
the macromolecule sequence, but negative sequence numbers, gaps
in numbering, or even reverse numbering are permitted in the PDB format.
Care must be taken when specifying both residue name and number.
If the group at the specified position isn't the specified residue
then no atoms are selected.
The chain identifier is typically a single case-insensitive
alphabetic or numeric character. Numeric chain identifiers must
be distinguished or separated from residue numbers by a colon
character. For example,
"SER70A"
for the alphabetic chain identifier, "A", or
"SER70:1"
for the numeric chain identifier, "1".
The second part consists of a period character followed by an atom
name. An atom name may be up to four alphabetic or numeric characters.
An optional semicolon followed by an alternate conformation
identifier may be appended. An optional slash followed by a
model number may also be appended.
An atom name may be up to four alphabetic or numeric characters.
An asterisk may be used as a wild card for a whole field and a
question mark as a single character wildcard.
Parts of a molecule may also be distinguished using equality,
inequality and ordering operators on their properties. The format
of such comparison expression is a property name, followed by a
comparison operator and then an integer value.
The atom properties that may be used in RasMol are
'atomno'
for the atom serial number,
'elemno'
for the atom's atomic number (element),
'resno'
for the residue number,
'radius'
for the spacefill radius in RasMol units (or zero if not represented
as a sphere) and
'temperature'
for the PDB isotropic temperature value.
The equality operator is denoted either
"=" or "==".
The inequality operator as either
"<>", "!=" or
"/=".
The ordering operators are
"<"
for less than,
"<="
for less than or equal to,
">"
for greater than, and
">="
for greater than or equal to.
A RasMol
'within'
expression allows atoms to be selected on their proximity to
another set of atoms. A
'within'
expression takes two parameters separated by a comma and surrounded
by parentheses. The first argument is an integer value called the
"cut-off" distance of the within expression and the second argument
is any valid atom expression. The cut-off distance is expressed in
either integer RasMol units or Ångstroms containing a decimal point.
An atom is selected if it is within the cut-off distance of any of
the atoms defined by the second argument. This allows complex
expressions to be constructed containing nested
'within'
expressions.
For example, the command
'select within(3.2,backbone)'
selects any atom within a 3.2 Ångstrom radius of any atom in a
protein or nucleic acid backbone.
'Within'
expressions are particularly useful for selecting the atoms
around an active site.
RasMol atom expressions may contain predefined sets. These sets
are single keywords that represent portions of a molecule of interest.
Predefined sets are often abbreviations of primitive atom expressions.
In some cases the use of predefined sets allows selection of areas of
a molecule that could not otherwise be distinguished.
A list of the currently predefined sets
is given below.
In addition to the sets listed here, RasMol also treats element names
(and their plurals) as predefined sets containing all atoms of that
element type, i.e. the command
'select oxygen'
is equivalent to the command
'select elemno=8'.
This set contains the atoms in the complementary nucleotides
adenosine and thymidine (A and T, respectively). All nucleotides
are classified as either the set
'at'
or the set
'cg'
This set is equivalent to the RasMol atom expressions
"a,t",
and
"nucleic and not cg".
The set of acidic amino acids.
These are the residue types Asp and Glu.
All amino acids are classified as either
'acidic',
'basic'
'or'
'neutral'.
This set is equivalent to the RasMol atom expressions
"asp, glu"
and
"amino and not (basic or neutral)".
The set of atoms in amino acids not containing a cycle or
ring. All amino acids are classified as either
'cyclic'
or
'acyclic'.
This set is equivalent to the RasMol atom expression
"amino and not cyclic".
This set contains the aliphatic amino acids.
These are the amino acids Ala, Gly, Ile, Leu and Val.
This set is equivalent to the RasMol atom expression
"ala, gly, ile, leu, val".
The set of alpha carbons in the protein molecule. This set is
approximately equivalent to the RasMol atom expression
"*.CA".
This command should not be confused with the predefined set
'helix'
which contains the atoms in the amino acids of the protein's
alpha helices.
This set contains all the atoms contained in amino acid residues.
This is useful for distinguishing the protein from the nucleic
acid and heterogeneous atoms in the current molecule database.
The set of atoms in amino acids containing aromatic rings.
These are the amino acids His, Phe, Trp and Tyr.
Because they contain aromatic rings all members of this
set are member of the predefined set
'cyclic'.
This set is equivalent to the RasMol atom expressions
"his, phe, trp, tyr"
and
"cyclic and not pro".
This set contains the four atoms of each amino acid that form the
polypeptide N-C-C-O backbone of proteins, and the atoms of the sugar
phosphate backbone of nucleic acids.
Use the RasMol predefined sets
'protein'
and
'nucleic'
to distinguish between the two forms of backbone.
Atoms in nucleic acids and proteins are either
'backbone'
or
'sidechain'.
This set is equivalent to the RasMol expression
"(protein or nucleic) and not sidechain".
The predefined set
'mainchain'
is synonymous with the set
'backbone'.
The set of basic amino acids.
These are the residue types Arg, His and Lys.
All amino acids are classified as either
'acidic',
'basic'
or
'neutral'.
This set is equivalent to the RasMol atom expressions
"arg, his, lys"
and
"amino and not (acidic or neutral)".
This set contain all the atoms in the current molecule database that
are bonded to at least one other atom.
This set contains the atoms in those amino acids that tend
(prefer) to be buried inside protein, away from contact with
solvent molecules. This set refers to the amino acids
preference and not the actual solvent accessibility for
the current protein.
All amino acids are classified as either
'surface'
or
'buried'.
This set is equivalent to the RasMol atom expression
"amino and not surface".
This set contains the atoms in the complementary nucleotides
cytidine and guanosine (C and G, respectively). All nucleotides
are classified as either the set
'at'
or the set
'cg'
This set is equivalent to the RasMol atom expressions
"c,g"
and
"nucleic and not at".
This set contains the charged amino acids. These are the amino
acids that are either
'acidic'
or
'basic'.
Amino acids are classified as being either
'charged'
or
'neutral'.
This set is equivalent to the RasMol atom expressions
"acidic or basic"
and
"amino and not neutral".
The set of atoms in amino acids containing a cycle or rings.
All amino acids are classified as either
'cyclic'
or
'acyclic'.
This set consists of the amino acids His, Phe, Pro, Trp and Tyr.
The members of the predefined set
'aromatic'
are members of this set.
The only cyclic but non-aromatic amino acid is proline.
This set is equivalent to the RasMol atom expressions
"his, phe, pro, trp, tyr"
and
"aromatic or pro"
and
"amino and not acyclic".
This set contains the atoms of cysteine residues that form part
of a disulphide bridge, i.e. half cystines. RasMol automatically
determines disulphide bridges, if neither the predefined set
'cystine'
nor the RasMol
'ssbonds'
command have been used since the molecule was loaded. The set of
free cysteines may be determined using the RasMol atom expression
"cys and not cystine".
This set contains all atoms that form part of a protein alpha
helix as determined by either the PDB file author or Kabsch and
Sander's DSSP algorithm. By default, RasMol uses the secondary
structure determination given in the PDB file if it exists.
Otherwise, it uses the DSSP algorithm as used by the RasMol
'structure'
command.
This predefined set should not be confused with the predefined set
'alpha'
which contains the alpha carbon atoms of a protein.
This set contains all the heterogeneous atoms in the molecule. These
are the atoms described by HETATM entries in the PDB file. These
typically contain water, cofactors and other solvents and ligands. All
'hetero'
atoms are classified as either
'ligand'
or
'solvent'
atoms. These heterogeneous
'solvent'
atoms are further classified as either
'water'
or
'ions'.
This predefined set contains all the hydrogen, deuterium and tritium atoms
of the current molecule. This predefined set is equivalent to the
RasMol atom expression
"elemno=1".
This set contains all the hydrophobic amino acids.
These are the amino acids Ala, Leu, Val, Ile, Pro, Phe, Met and Trp.
All amino acids are classified as either
'hydrophobic'
or
'polar'.
This set is equivalent to the RasMol atom expressions
"ala, leu, val, ile, pro, phe, met, trp"
and
"amino and not polar".
This set contains all the heterogeneous phosphate and sulphate ions in
the current molecule data file. A large number of these ions are
sometimes associated with protein and nucleic acid structures determined
by X-ray crystallography. These atoms tend to clutter an image. All
'hetero'
atoms are classified as either
'ligand'
or
'solvent'
atoms. All
'solvent'
atoms are classified as either
'water'
or
'ions'.
All amino acids are classified as either
'small',
'medium'
or
'large'.
This set is equivalent to the RasMol atom expression
"amino and not (small or medium)".
This set contains all the heterogeneous cofactor and ligand moieties that
are contained in the current molecule data file. This set is defined
to be all
'hetero'
atoms that are not
'solvent'
atoms. Hence this set is equivalent to the RasMol atom expression
"hetero and not solvent".
All amino acids are classified as either
'small',
'medium'
or
'large'.
This set is equivalent to the RasMol atom expression
"amino and not (large or small)".
The set of neutral amino acids.
All amino acids are classified as either
'acidic',
'basic'
or
'neutral'.
This set is equivalent to the RasMol atom expression
"amino and not (acidic or basic)".
The set of all atoms in nucleic acids, which consists of the four
nucleotide bases adenosine, cytidine, guanosine and thymidine (A,
C, G and T, respectively). All neucleotides are classified as either
'purine'
or
'pyrimidine'.
This set is equivalent to the RasMol atom expressions
"a,c,g,t"
and
"purine or pyrimidine".
The symbols for RNA nucleotides (U, +U, I, 1MA, 5MC, OMC,
1MG, 2MG, M2G, 7MG, OMG, YG, H2U, 5MU, and PSU) are also
recognized as members of this set.
This set contains the polar amino acids.
All amino acids are classified as either
'hydrophobic'
or
'polar'.
This set is equivalent to the RasMol atom expression
"amino and not hydrophobic".
The set of all atoms in proteins. This consists of the RasMol
predefined set
'amino'
and common post-translation modifications.
The set of purine nucleotides.
These are the bases adenosine and guanosine (A and G, respectively).
All nucleotides are either
'purines'
or
'pyrimidines'.
This set is equivalent to the RasMol atom expressions
"a,g"
and
"nucleic and not pyrimidine".
The set of pyrimidine nucleotides.
These are the bases cytidine and thymidine (C and T, respectively).
All nucleotides are either
'purines'
or
'pyrimidines'.
This set is equivalent to the RasMol atom expressions
"c,t"
and
"nucleic and not purine".
This set contains the set of atoms in the currently selected
region. The currently selected region is defined by the preceding
'select'
or
'restrict'
command and not the atom expression containing the
'selected'
keyword.
This set contains all atoms that form part of a protein beta
sheet as determined by either the PDB file author or Kabsch and
Sander's DSSP algorithm. By default, RasMol uses the secondary
structure determination given in the PDB file if it exists.
Otherwise, it uses the DSSP algorithm as used by the RasMol
'structure'
command.
This set contains the functional sidechains of any amino acids
and the base of each nucleotide. These are the atoms not part of
the polypeptide N-C-C-O backbone of proteins or the sugar
phosphate backbone of nucleic acids.
Use the RasMol predefined sets
'protein'
and
'nucleic'
to distinguish between the two forms of sidechain.
Atoms in nucleic acids and proteins are either
'backbone'
or
'sidechain'.
This set is equivalent to the RasMol expression
"(protein or nucleic) and not backbone".
All amino acids are classified as either
'small',
'medium'
or
'large'.
This set is equivalent to the RasMol atom expression
"amino and not (medium or large)".
This set contains the solvent atoms in the molecule coordinate file.
These are the heterogeneous water molecules, phosphate and sulphate
ions. All
'hetero'
atoms are classified as either
'ligand'
or
'solvent'
atoms. All
'solvent'
atoms are classified as either
'water'
or
'ions'.
This set is equivalent to the RasMol atom expressions
"hetero and not ligand"
and
"water or ions".
This set contains the atoms in those amino acids that tend
(prefer) to be on the surface of proteins, in contact with
solvent molecules. This set refers to the amino acids
preference and not the actual solvent accessibility for
the current protein.
All amino acids are classified as either
'surface'
or
'buried'.
This set is equivalent to the RasMol atom expression
"amino and not buried".
This set contains all atoms that form part of a protein turns
as determined by either the PDB file author or Kabsch and
Sander's DSSP algorithm. By default, RasMol uses the secondary
structure determination given in the PDB file if it exists.
Otherwise, it uses the DSSP algorithm as used by the RasMol
'structure'
command.
This set contains all the heterogeneous water molecules in the current
database. A large number of water molecules are sometimes associated
with protein and nucleic acid structures determined by X-ray
crystallography. These atoms tend to clutter an image.
All
'hetero'
atoms are classified as either
'ligand'
or
'solvent'
atoms. The
'solvent'
atoms are further classified as either
'water'
or
'ions'.
The table below summarises RasMol's classification of the common amino acids.
Note that the rendering of the hexadecimal-equivalent colours shown
here will depend on many factors.
Thus, they only approximate how RasMol will render the RGB colours on
your computer.
If you frequently wish to use a colour not predefined, you can write
a one-line script. For example, if you make the file
'grey.col'
containing the line,
'colour [180,180,180] #grey',
then the command
'script grey.col'
colours the currently selected atom set grey.
The RasMol
'alt'
(Alternate Conformer)
colour scheme codes the base
structure with one colour and applies a limited number of colours to each
alternate conformer. In a RasMol built for 8-bit colour systems, 4 colours
are allowed for alternate conformers. Otherwise, 8 colours are available.
The RasMol
'amino'
colour scheme colours amino acids according to traditional amino acid
properties. The purpose of colouring is to identify amino acids in an
unusual or surprising environment. The outer parts of a protein that are
polar are visible (bright) colours and non-polar residues darker. Most
colours are hallowed by tradition. This colour scheme is similar to the
'shapely'
scheme.
The RasMol
'chain'
colour scheme assigns each macromolecular chain a unique colour. This
colour scheme is particularly useful for distinguishing the parts of
multimeric structure or the individual 'strands' of a DNA chain.
'Chain'
can be selected from the RasMol
'Colours'
menu.
The RasMol
'charge'
colour scheme colour codes each atom according to the charge value
stored in the input file (or beta factor field of PDB files). High
values are coloured in blue (positive) and lower values coloured in
red (negative). Rather than use a fixed scale this scheme determines
the maximum and minimum values of the charge/temperature field and
interpolates from red to blue appropriately. Hence, green cannot be
assumed to be 'no net charge' charge.
The difference between the
'charge'
and
'temperature'
colour schemes is that increasing temperature values proceed from blue
to red, whereas increasing charge values go from red to blue.
If the charge/temperature field stores reasonable values it is possible
to use the RasMol
'colour dots potential'
command to colour code a dot surface (generated by the
'dots'
command) by electrostatic potential.
The RasMol
'cpk'
colour scheme is based upon the colours of the popular plastic
spacefilling models which were developed by Corey, Pauling and later
improved by Kultun. This colour scheme colours 'atom' objects by the
atom (element) type. This is the scheme conventionally used by chemists.
The assignment of the most commonly used element types to colours is
given below.
Note that except for green, white, blue,
and orange, these colour names are not the ones specified as
"Predefined colours" in RasMol; thus, they can only be specified
on the command line as RGB triplets.
In the CPK colouring scheme, RasMol will attempt to assign a colour to
each element from the periodic table from a list of 16 colours (the
colour codes listed are to help in understanding the mapping and are
not used by RasMol):
In the CPKnew colouring scheme, RasMol uses brighter colours:
For X-ray crystallographic models of proteins and nucleic acids
(i.e. without hydrogens) the display can be 'brightened' by converting
the O, C, and N atoms from the RasMol default cpk colors to
"true red, white and blue" using RasMol's predefined colour scheme.
Use the following sequence of
commands to try it:
The RasMol
'group'
colour scheme colour codes residues by their position in a macromolecular
chain. Each chain is drawn as a smooth spectrum from blue through green,
yellow and orange to red. Hence the N terminus of proteins and 5' terminus
of nucleic acids are coloured red and the C terminus of proteins and 3'
terminus of nucleic acids are drawn in blue. If a chain has a large number
of heterogeneous molecules associated with it, the macromolecule may not be
drawn in the full 'range' of the spectrum.
'Group'
can be selected from the RasMol
'Colours'
menu.
If a chain has a large number of heterogeneous molecules associated with it,
the macromolecule may not be drawn in the full range of the spectrum. When
RasMol performs group colouring it decides the range of colours it uses from
the residue numbering given in the PDB file. Hence the lowest residue
number is displayed in blue and the highest residue number is displayed as
red. Unfortunately, if a PDB file contains a large number of heteroatoms,
such as water molecules, that occupy the high residue numbers, the protein
is displayed in the blue-green end of the spectrum and the waters in the
yellow-red end of the spectrum. This is aggravated by there typically being
many more water molecules than amino acid residues. The solution to this
problem is to use the command
'set hetero off'
before applying the group
colour scheme. This can also be achieved by toggling
'Hetero Atoms'
on the
'Options'
menu before selecting
'Group'
on the
'Colour'
menu. This command
instructs RasMol to only use non-hetero residues in the group colour scaling.
The RasMol
'model'
colour scheme codes each NMR model with a distinct
colour. The NMR model number is taken as a numeric value. High values
are coloured in blue and lower values coloured in red. Rather than use a
fixed scale this scheme determines the maximum value of the
NMR model number and interpolates from red to blue appropriately.
The RasMol
'shapely'
colour scheme colour codes residues by amino acid property. This scheme
is based upon Bob Fletterick's "Shapely Models". Each amino acid and
nucleic acid residue is given a unique colour. The
'shapely'
colour scheme is used by David Bacon's Raster3D program. This colour
scheme is similar to the
'amino'
colour scheme.
The RasMol
'structure'
colour scheme colours the molecule by protein secondary structure.
Alpha helices are coloured magenta, [240,0,128], beta sheets are
coloured yellow, [255,255,0], turns are coloured pale blue, [96,128,255]
and all other residues are coloured white. The secondary structure
is either read from the PDB file (HELIX, SHEET and TURN records), if available,
or determined using Kabsch and Sander's DSSP algorithm. The RasMol
'structure'
command may be used to force DSSP's structure assignment to be used.
The RasMol
'temperature'
colour scheme colour codes each atom according to the anisotropic
temperature (beta) value stored in the PDB file. Typically this gives
a measure of the mobility/uncertainty of a given atom's position. High
values are coloured in warmer (red) colours and lower values in colder
(blue) colours. This feature is often used to associate a "scale" value
[such as amino acid variability in viral mutants] with each atom in a
PDB file, and colour the molecule appropriately.
The difference between the
'temperature'
and
'charge'
colour schemes is that increasing temperature values proceed from blue
to red, whereas increasing charge values go from red to blue.
The RasMol
'user'
colour scheme allows RasMol to use the colour scheme stored in the
PDB file. The colours for each atom are stored in COLO records placed
in the PDB data file. This convention was introduced by David Bacon's
Raster3D program.
The RasMol
'type'
colour scheme applies only to hydrogen bonds, hence is used in the command
'colour hbonds type'.
This scheme colour codes each hydrogen bond according to the
distance along a protein chain between hydrogen bond donor and acceptor.
This schematic representation was introduced by Belhadj-Mostefa and
Milner-White. This representation gives a good insight into protein
secondary structure (hbonds forming alpha helices appear red, those
forming sheets appear yellow and those forming turns appear magenta).
The RasMol
'potential'
colour scheme applies only to dot surfaces, hence is used in the command
'colour dots potential'.
This scheme colours each currently displayed dot by the electrostatic
potential at that point in space. This potential is calculated using
Coulomb's law taking the temperature/charge field of the input file to
be the charge assocated with that atom. This is the same interpretation
used by the
'colour charge'
command. Like the
'charge'
colour scheme low values are blue/white and high values are red.
The table below shows the static assignment of colours using a
dielectric constant value of 10.
The following table lists the names, single letter and three letter
codes of each of the amino acids.
A boolean parameter is a truth value. Valid boolean values are 'true' and
'false', and their synonyms 'on' and 'off'. Boolean parameters are commonly
used by RasMol to either enable or disable a representation or option.
Protein Data Bank Files
If you do not have the PDB documentation, you may find the
following summary of the PDB file format useful. The Protein Data Bank
is a computer-based archival database for macromolecular structures.
The database was established in 1971 by Brookhaven National
Laboratory, Upton, New York, as a public domain repository for resolved
crystallographic structures. The Bank uses a uniform format to store
atomic coordinates and partial bond connectivities as derived from
crystallographic studies. In 1999 the Protein Data Bank moved
to the Research Collaboratory for Structural Biology.
PDB file entries consist of records of 80 characters each. Using the
punched card analogy, columns 1 to 6 contain a record-type identifier,
the columns 7 to 70 contain data. In older entries, columns 71 to 80
are normally blank,
but may contain sequence information added by library management
programs. In new entries conforming to the 1996 PDB format, there
is other information in those columns. The first four characters of
the record identifier are
sufficient to identify the type of record uniquely, and the syntax of
each record is independent of the order of records within any entry for
a particular macromolecule.
The only record types that are of major interest to the RasMol program
are the ATOM and HETATM records which describe the position of each
atom. ATOM/HETATM records contain standard atom names and residue
abbreviations, along with sequence identifiers, coordinates in
Ångstrom units, occupancies and thermal motion factors. The exact
details are given below as a FORTRAN format statement. The "fmt"
column indicates use of the field in all PDB formats,
in the 1992 and earlier formats or in the 1996 and later formats.
Residues occur in order starting from the N-terminal residue
for proteins and
5'-terminus for nucleic acids. If the residue sequence is known,
certain atom serial numbers may be omitted to allow for future insertion
of any missing atoms. Within each residue, atoms are ordered in a
standard manner, starting with the backbone (N-C-C-O for proteins) and
proceeding in increasing remoteness from the alpha carbon, along the
side chain.
HETATM records are used to define post-translational modifications and
cofactors associated with the main molecule. TER records are
interpreted as breaks in the main molecule's backbone.
If present, RasMol also inspects HEADER, COMPND, HELIX, SHEET, TURN,
CONECT, CRYST1, SCALE, MODEL, ENDMDL, EXPDTA and END records. Information such as the
name, database code, revision date and classification of the molecule
are extracted from HEADER and COMPND records, initial secondary
structure assignments are taken from HELIX, SHEET and TURN records, and
the end of the file may be indicated by an END record.
Atoms located at 9999.000, 9999.000, 9999.000 are assumed to be Insight
pseudo atoms and are ignored by RasMol. Atom names beginning ' Q' are
also assumed to be pseudo atoms or position markers.
When a data file contains an NMR structure, multiple conformations may
be placed in a single PDB file delimited by pairs of MODEL and ENDMDL
records. RasMol displays all the NMR models contained in the file.
Residue names "CSH", "CYH" and "CSM" are considered pseudonyms for
cysteine "CYS". Residue names "WAT", "H20", "SOL" and "TIP" are
considered pseudonyms for water "HOH". The residue name "D20" is
consider heavy water "DOD". The residue name "SUL" is considered a
sulphate ion "SO4". The residue name "CPR" is considered to be
cis-proline and is translated as "PRO". The residue name "TRY" is
considered a pseudonym for tryptophan "TRP".
RasMol uses the HETATM fields to define the sets hetero, water, solvent
and ligand. Any group with the name "HOH", "DOD", "SO4" or "PO4" (or
aliased to one of these names by the preceding rules) is considered a
solvent and is considered to be defined by a HETATM field.
RasMol only respects CONECT connectivity records in PDB files containing
fewer than 256 atoms. This is explained in more detail in the section on
determining molecule connectivity. CONECT records that define a bond
more than once are interpreted as specifying the bond order of that
bond, i.e. a bond specified twice is a double bond and a bond specified
three (or more) times is a triple bond. This is not a standard PDB feature.
RasMol also accepts the supplementary COLO record type in the PDB
files. This record format was introduced by David Bacon's Raster3D
program for specifying the colour scheme to be used when rendering the
molecule. This extension is not currently supported by the PDB. The
COLO record has the same basic record type as the ATOM and HETATM
records described above.
Colours are assigned to atoms using a matching process. The Mask field
is used in the matching process as follows. First RasMol reads in and
remembers all the ATOM, HETATM and COLO records in input order. When the
user-defined ('User') colour scheme is selected, RasMol goes through
each remembered ATOM/HETATM record in turn, and searches for a COLO
record that matches in all of columns 7 through 30. The first such COLO
record to be found determines the colour and radius of the atom.
Note that the Red, Green and Blue components are in the same positions
as the X, Y, and Z components of an ATOM or HETA record, and the van
der Waals radius goes in the place of the Occupancy. The Red, Green and
Blue components must all be in the range 0 to 1.
In order that one COLO record can provide colour and radius
specifications for more than one atom (e.g. based on residue, atom
type, or any other criterion for which labels can be given somewhere in
columns 7 through 30), a 'don't-care' character, the hash mark "#"
(number or sharp sign) is used. This character, when found in a COLO
record, matches any character in the corresponding column in a
ATOM/HETATM record. All other characters must match identically to count
as a match. As an extension to the specification, any atom that fails
to match a COLO record is displayed in white.
RasMol loads all of the NMR models from a PDB file no matter which
command is used:
'load pdb <filename>'
or
'load nmrpdb <filename>'
Once multiple NMR conformations have been loaded they may be
manipulated with the atom expression extensions described in
'Primitive Expressions'.
In particular, the command
'restrict */1'
will restrict the display to the first model only.
CIF is the IUCr standard for presentation of small molecules and mmCIF
is intended as the replacement for the fixed-field PDB format for
presentation of macromolecular structures. RasMol can accept data sets
in either format.
There are many useful sites on the World Wide Web where information
tools and software related to CIF, mmCIF and the PDB can be found. The
following are good starting points for exploration:
The International Union of Crystallography (IUCr) provides access to
software, dictionaries, policy statements and documentation relating to
CIF and mmCIF at: IUCr, Chester, England (www.iucr.org/iucr-top/cif/)
with many mirror sites.
The Nucleic Acid Database Project provides access to its entries,
software and documentation, with an mmCIF page giving access to the
dictionary and mmCIF software tools at Rutgers University, New Jersey,
USA (http://ndbserver.rutgers.edu/NDB/mmcif) with many mirror sites.
This version of RasMol restricts CIF or mmCIF tag values to essentially
the same conventions as are used for the fixed-field PDB format. Thus
chain identifiers and alternate conformation identifiers are limited to
a single character, atom names are limited to 4 characters, etc. RasMol
interprets the following CIF and mmCIF tags:
In the following sections, support for
'Monochrome X-Windows',
'Tcl/Tk IPC',
'UNIX sockets based IPC',
'Compiling RasWin with Borland and MetroWerks'
are described.
RasMol supports the many
monochrome UNIX workstations typically found in academia, such as low-end
SUN workstations and NCD X-terminals. The X11 version of RasMol (when
compiled in 8 bit mode) now detects black and white X-Windows displays and
enables dithering automatically. The use of run-time error diffusion dithering
means that all display modes of RasMol are available when in monochrome
mode. For best results, users should experiment with the set ambient
command to ensure the maximum contrast in resulting images.
Version 4 of Tk
graphics library changed the protocol used to communicate between Tk
applications. RasMol version 2.6 was modified such that it could
communicate with both this new protocol and the previous version 3 protocol
supported by RasMol v2.5. Although Tcl/Tk 3.x applications may only
communicate with other 3.x applications and Tcl/Tk 4.x applications with other
4.x applications, these changes allow RasMol to communicate between
processes with both protocols (potentially concurrently).
The UNIX implementation of RasMol
supports BSD-style socket communication. An identical socket mechanism is
also being developed for VMS, Apple Macintosh and Microsoft Windows
systems. This should allow RasMol to interactively display results of a
computation on a remote host. The current protocol acts as a TCP/IP server on
port 21069 that executes command lines until either the command
'exit'
or the
command
'quit'
is typed. The command
exit
from the RasMol server, the command
'quit'
both disconnects the current
session and terminates RasMol. This functionality may be tested using the
UNIX command
'telnet <hostname> 21069'.
A number of changes were made to the
source code in the transition from version 2.5 to 2.6 to allow
the Microsoft Windows version of RasMol to compile
using the Borland C/C++ compiler. These fixes include name changes for the
standard library and special code to avoid a bug in _fmemset.
Additional changes were made in the transition from 2.6 to 2.7 to
allow compilation with the MetroWerks compilers.
Molecular Graphics
[1] Nelson Max, "Computer Representation of Molecular Surfaces", IEEE
Computer Graphics and Applications, pp.21-29, August 1983.
[2] Arthur M. Lesk, "Protein Architecture: A Practical Approach", IRL
Press Publishers, 1991.
Molecular Graphics Programs
[3] Per J. Kraulis, "MOLSCRIPT: A Program to Produce both Detailed and
Schematic Plots of Protein Structures", Journal of Applied
Crystallography, Vol.24, pp.946-950, 1991.
[4] David Bacon and Wayne F. Anderson, "A Fast Algorithm for Rendering
Space-Filling Molecule Pictures", Journal of Molecular Graphics, Vol.6,
No.4, pp.219-220, December 1988.
[5] David C. Richardson and Jane S. Richardson, "The Kinemage: A tool
for Scientific Communication", Protein Science, Vol.1, No.1,pp.3-9,
January 1992.
[6] Mike Carson, "RIBBONS 2.0", Journal of Applied Crystallography,
Vol.24, pp.958-961, 1991.
[7] Conrad C. Huang, Eric F. Pettersen, Teri E. Klein, Thomas E.
Ferrin and Robert Langridge, "Conic: A Fast Renderer for
Space-Filling Molecules with Shadows", Journal of Molecular Graphics,
Vol.9, No.4, pp.230-236, December 1991.
Molecular Biology Algorithms
[8] Wolfgang Kabsch and Christian Sander, "Dictionary of Protein
Secondary Structure: Pattern Recognition of Hydrogen-Bonded and
Geometrical Features", Biopolymers, Vol.22, pp.2577-2637, 1983.
[9] Michael L. Connolly, "Solvent-Accessible Surfaces of Proteins and Nucleic
Acids", Science, Vol.221, No.4612, pp.709-713, August 1983.
[10] Khaled Belhadj-Mostefa, Ron Poet and E. James Milner-White,
"Displaying Inter-Main Chain Hydrogen Bond Patterns in Proteins",
Journal of Molecular Graphics, Vol.9, No.3, pp.194-197, September 1991.
[11] Mike Carson, "Ribbon Models of Macromolecules", Journal of
Molecular Graphics, Vol.5, No.2, pp.103-106, June 1987.
[12] Mike Carson and Charles E. Bugg, "Algorithm for Ribbon Models of
Proteins", Journal of Molecular Graphics, Vol.4, No.2, pp.121-122, June
1986.
[13] H. Iijima, J. B. Dunbar Jr. and G. Marshall, "Calibration of
Effective van der Waals Atomic Contact Radii for Proteins and
Peptides", Proteins: Structure, Functions and Genetics, Vol.2,
pp.330-339,1987.
Graphics Algorithms
[14] J. Foley, A. van Dam, S. Feiner and J. Hughes, "Computer Graphics:
Principles and Practice", 2nd Edition, Addison Wesley Publishers, 1990.
[15] J. Cleary and G. Wyvill, "Analysis of an Algorithm for Fast Ray
Tracing using Uniform Space Subdivision", The Visual Computer, Vol.4,
pp.65-83, 1988.
[16] Thomas Porter,"Spherical Shading", Computer Graphics Vol.12, ACM
SIGGRAPH, pp.282-285, 1978.
[17] Jean-Michel Cense, "Exact Visibility Calculation for Space-Filling
Molecular Models", Journal of Molecular Graphics, Vol.9, No.3,
pp.191-193, September 1991.
[18] Chris Schafmeister, "Fast Algorithm for Generating CPK Images on
Graphics Workstations", Journal of Molecular Graphics, Vol.8, No.4,
pp.201-206, December 1990.
[19] Bruce A. Johnson, "MSURF: A Rapid and General Program for the
Representation of Molecular Surfaces", Journal of Molecular Graphics,
Vol.5, No.3, pp.167-169, September 1987.
File Formats
[20] Frances C. Bernstein et al., "The Protein Data Bank: A
Computer-Based Archival File for Macromolecular Structures", Journal of
Molecular Biology, Vol.112, pp.535-542, 1977.
[21] Arthur Dalby, James G. Nourse, W. Douglas Hounshell, Ann K. I.
Gushurst, David L. Grier, Burton A. Leland and John Laufer, "Description
of Several Chemical File Formats Used by Computer Programs Developed at
Molecular Design Limited", Journal of Chemical Information and Computer
Sciences, Vol.32, No.3, pp.244-255, 1992.
[22] Adobe Systems Inc., "PostScript Language Reference Manual",
Addison-Wesley Publishers, Reading, Mass., 1985.
[23] Philip E. Bourne et al., "The Macromolecular Crystallographic
Information File (mmCIF)", Meth. Enzymol. (1997) 277, 571-590.
[24] Sydney R. Hall, "The STAR File: a New Format for Electronic Data
Transfer and Archiving", Journal of Chemical Information and Computer
Sciences, Vol. 31, 326-333, 1991.
Running RasMol Under Microsoft Windows
To start RasMol under Microsoft Windows, double click on the
RasMol icon in the program manager. When RasMol first starts,
the program displays a single main window (the display window)
with a black background on the screen and provides the command
line window minimized as a small icon at the bottom of the screen.
The command line or terminal window may be opened by double clicking
on this RasMol icon.
Running RasMol on the Apple Macintosh/PPC
To start RasMol on the Macintosh, double click on the RasMol
icon using Finder. When RasMol first starts, the program displays
two windows, the top window (with the black background) is the
graphics or canvas window and the window underneath it (with the
white background) is the RasMol command line window.
RasMol on the Macintosh may also be started by double clicking
on a file owned/created by the application with the signature
'RSML'. This will start up RasMol and pass the selected file to be
loaded. There is no way of specifying the file format on the command
line with a Macintosh so RasMol attempts to determine the file format
by inspecting the file's type signature. Files with type signature
'RSML' are assumed to be RasMol scripts, files of type 'mMOL' are
assumed to be MDL Mol files and all other types (principally 'TEXT')
are assumed to be in PDB format. Unlike other versions of RasMol
it is impossible to specify both a script and a coordinate file
simultaneously.
RasMol's Window
On all platforms RasMol displays two windows, the main graphics
or canvas window with a black background and a command line
or terminal window. At the top of the graphics window (or at the
top of the screen for the Macintosh) is the RasMol menu bar. The contents
of the menu bar change from platform to platform to support the local
user interface guidelines; however, all platforms support the 'File',
'Display', 'Colours', 'Export', 'Options' and 'Settings' pull-down menus.
The Main graphics window also has two scroll bars, one on the
right and one at the bottom, that may be used to rotate the
molecule interactively.
The display window may be resized at any point during the session.
This has the effect of simply rescaling the image displayed on
the canvas. RasMol imposes limits on the size of the display window
such that the window must be large enough to display the menu and
scroll bars and yet small enough to fit on a single screen. Attempts
to enlarge the screen may fail owing to insufficient memory on the
host machine, in which case RasMol reports the error message
'Renderer Error: Unable to allocate frame buffer!' or some
similar error.
On eight bit displays, when the number of colours required by
the program exceeds the number of free colours on the screen,
the program uses its own colourmap. This has the effect of
temporarily displaying all windows other than the display
window in false colours while the mouse pointer is within the
display windows. If the mouse pointer is moved outside the
display windows, the original colours of the other windows
return, and the image on the canvas is shown in 'false colour'.
Once the number of colours required by the program drops again,
the presentation of colours returns to normal.
Mouse Controls
Here is a summary of RasMol's mouse click-and-drag controls.
The 'set mouse'
command mode defaults to 'set mouse rasmol', which gives the controls
summarized below. However, there are also 'set mouse
insight' and 'set mouse quanta' modes (not shown below).
Action Windows Macintosh Rotate X, Y Left Unmodified
Translate X, Y Right Command*
Rotate Z Shift-Right Shift-Command*
Zoom Shift-Left Shift
Slab Plane Ctrl-Left Ctrl
Scroll Bars
The scroll bar across the bottom of the canvas area is used to rotate
the molecule about the y-axis, i.e. to spin the nearest point
on the molecule left or right; and the scroll bar to the right of
the canvas rotates the molecule about the x-axis, i.e. the
nearest point up or down. Each scroll bar has an 'indicator' to
denote the relative orientation of the molecule, which is initially
positioned in the centre of the scroll bar. These scroll bars may be
operated in either of two ways. The first is by clicking any mouse
button on the dotted scroll bar background to indicate a direct
rotation relative to the current indicator position; the second
is by clicking one of the arrows at either end of the scroll bar
to rotate the molecule in fixed sized increments. Rotating the
molecule by the second method may cause the indicators on the scroll
bars to wrap around from one end of the bar to the other. A complete
revolution is indicated by the indicator travelling the length of
the scroll bar. The angle rotated by using the arrows depends upon
the current size of the display window.
Picking
In order to identify a particular atom or bond being displayed,
RasMol allows the users to 'pick' objects on the screen. The mouse
is used to position the cross-hair cursor over the appropriate
item, and then any of the mouse buttons is depressed. Provided that
the pointer is located close enough to a visible object, the program
determines the identity of the nearest atom to the point identified.
Atom: CA 349 Group: SER 70
Atom: O 526 Hetero: HOH 205 Chain: P
The first line describes the alpha carbon of the serine-70 amino
acid in a protein. The unique Protein Data Bank serial number for this
atom is 349. The following line describes the oxygen atom in a
water molecule attached to the P chain of the main molecule. The
word 'Hetero' distinguishes heterogeneous molecules (such as cofactors)
from the residues in the main molecule, noted by 'Group'. [These two
atoms are referred to by the two atom expressions 'SER70.CA'
and 'HOH205:P.O', respectively, when using the RasMol commands
'select' and 'restrict'.]
Dials Box
If RasMol detects a 'dials box' attached to the user's
workstation, it also allows the molecule to be manipulated
interactively by the dials. Once RasMol starts up, it labels
the LED displays above each dial, 'ROTATE X', 'ROTATE Y', 'ROTATE Z'
and 'ZOOM' across the top row from left to right, and
'TRANS X', 'TRANS Y', 'TRANS Z' and 'SLAB' from left to right
across the bottom row. Rotating any of the knobs will
automatically transform and redisplay the molecule interactively.
The dials only have effect while the mouse pointer is within the
display window. If more than one application is using the dials
box at a time, care must be taken to remember the dial labels
assigned by each program, as each application may overwrite the
dial-label LEDS.
Command Line Interface
RasMol allows the execution of interactive commands typed at the
RasMol prompt in the terminal window. Characters typed into
either the terminal or the display window are processed on the
command line. Each command must be given on a separate line
terminated by a newline or carriage return character. Keywords
are case insensitive and may be entered in both lower and upper
case letters. All whitespace (space, tab and formfeed)
characters are ignored, except to separate the keyword and the
arguments of a command. Blank lines (those containing only
whitespace) are ignored. There is an internal restriction that
command lines are limited to a maximum of 256 characters.
Strings may be delimited by matching single or double quotation
marks. Placing a hash '#' character anywhere outside quotes
terminates the line. RasMol will ignore the rest of the line,
which may be used to comment on the command.
Command Line Editing
RasMol allows basic editing of the command line. Pressing
either backspace, delete or ^H (Control-H) will delete the
previous character, and the key ^D may be used to delete the
character under the cursor. Several characters may be used to
move the cursor along the command line. The
characters ^B, ^F, ^A and ^E move the cursor back a
single character, forward a single character, to the
beginning of the line and to the end of the line, respectively.
When the cursor is not at the end of the command line, typed
characters are inserted into the line and do not overwrite
existing characters. After a command line has been edited, a
newline or carriage return will enter the entire line, regardless
of where the cursor is positioned. Because RasMol is unable to
move the cursor up to the previous line, care must be taken
when editing commands that wrap over several lines. In the event
that another process overwrites or corrupts the command line,
the character ^L may be used to redisplay the line on the screen.
Dimensions within RasMol
All dimensions in RasMol, such as radii and distances, may be
specified in either 'RasMol units' or Ångstroms (Å). The
RasMol units were first introduced to allow reasonably sized
values to be specified for most of the operations performed in
RasMol. A single RasMol unit corresponds to 1/250th of an
Ångstrom; therefore the most frequently used values are in
the hundreds. For this reason, if RasMol is given a distance
parameter that does not contain a decimal point, it is assumed
to be in RasMol units. For example, the command 'spacefill 300'
specifies a sphere radius of 300 RasMol units, or 1.2 Å.
However, dimensions within RasMol can also be specified in
Ångstroms by placing a decimal point in the number. For
example, 'spacefill 1.2' specifies a sphere radius of 1.2 Å.
This is particularly useful for the cut-off distance parameter in
within expressions.
Start-up Initialisation Files
Each time RasMol is started, it searches for an initialisation
file of commands to run before the command prompt is presented
to the user. The file is called .rasmolrc on UNIX systems,
and RASMOL.INI on VMS and Microsoft Windows Systems. The
format and execution of this file is identical to that of the
RasMol script command.
Inter-Process Communication
RasMol supports Inter Process Communication (IPC) in one form or
another on all platforms. Under Microsoft Windows, IPC is
implemented using Dynamic Data Exchange (DDE), on the
MacIntosh IPC is implemented using Apple Events and on X Windows
systems IPC is implemented using John Ousterhaut's Tcl/Tk
communication protocol.
Command Reference
RasMol allows the execution of interactive commands typed at the
'RasMol>'
prompt in the terminal window. Each command must be given on
a separate line. Keywords are case insensitive and may be entered in
either upper or lower case letters. All whitespace characters are
ignored except to separate keywords and their arguments.
Backbone
Syntax: backbone {<boolean>}
backbone <value>
backbone dash
Background
Syntax: background <colour>
Bond
Syntax: bond <number> <number> +
bond <number> <number> pick
bond rotate {<boolean>}
Bulgarian
Syntax: Bulgarian
Cartoon
Syntax: cartoon {<number>}
Centre
Syntax: centre {<expression>} {translate|center}
center {<expression>} {translate|center}
Chinese
Syntax: Chinese
Clipboard
Syntax: clipboard
Colour
Syntax: colour {<object>} <colour>
color {<object>} <colour>
ColourMode
Syntax: colourmode {<boolean>}
colormode {<boolean>}
Syntax: connect {<boolean>}
Defer
Syntax: defer <name> <command to defer>
Define
Syntax: define <identifier> <expression>
Depth
Syntax: depth {<boolean>}
depth <value>
Dots
Syntax: dots {<boolean>}
dots <value>
Echo
Syntax: echo {<string>}
English
Syntax: English
Execute
Syntax: execute <name>
French
Syntax: French
HBonds
Syntax: hbonds {<boolean>}
hbonds <value>
Help
Syntax: help {<topic> {<subtopic>}}
? {<topic> {<subtopic>}}
Italian
Syntax: Italian
Japanese
Syntax: Japanese
Label
Syntax: label {<string>}
label <boolean>
%a Atom Name
%b %t B-factor/Temperature
%c %s Chain Identifier
%e Element Atomic Symbol
%i Atom Serial Number
%n Residue Name
%r Residue Number
%M NMR Model Number (with leading "/")
%A Alternate Conformation Identifier (with leading ";")
Load
Syntax: load {<format>} <filename>
Map
Syntax: map {<map_selector>} {<map_subcommand> <parameters>}
Map colour
Syntax: map {<map_selector>} colour <colour_scheme>
Map generate
Syntax: map {<map_selector>} generate {LRsurf} dots
map {<map_selector>} generate {LRsurf} mesh
map {<map_selector>} generate {LRsurf} surface
Map level
Syntax: map {<map_selector>} level {MEAN} <number>
Map load
Syntax: map {<map_selector>} load <filename>
Map mask
Syntax: map {<map_selector>} mask selected
map {<map_selector>} mask <number>
map {<map_selector>} mask none
Map resolution
Syntax: map {<map_selector>} resolution <number>
Map restrict
Syntax: map {<map_selector>} restrict
Map save
Syntax: map {<map_selector>} save <filename>
Map scale
Syntax: map {<map_selector>} scale <boolean>
Map select
Syntax: map {<map_selector>} select {atom {within} {add} {search_radius}}
Map show
Syntax: map {<map_selector>} show
Map spacing
Syntax: map {<map_selector>} spacing <number>
Map spread
Syntax: map {<map_selector>} spread <number>
Map zap
Syntax: map {<map_selector>} zap
Molecule
Syntax: molecule <number>
Monitor
Syntax: monitor <number> <number>
monitor {<boolean>}
Notoggle
Syntax: notoggle {<boolean>}
Pause
Syntax: pause
wait
Play
Syntax: play {from
Print
Syntax: print
Quit
Syntax: quit
exit
Record
Syntax: record {from
Refresh
Syntax: refresh
Renumber
Syntax: renumber {{-} <value>}
Reset
Syntax: reset
Restrict
Syntax: restrict {<expression>}
Ribbons
Syntax: ribbons {<boolean>}
ribbons <value>
Rotate
Syntax: rotate <axis> {-} <value>
rotate bond {<boolean>}
rotate molecule {<boolean>}
rotate all {<boolean>}
Russian
Syntax: Russian
Save
Syntax: save {pdb} <filename>
save mdl <filename>
save alchemy <filename>
save xyz <filename>
Script
Syntax: script <filename>
Select
Syntax: select {<expression>}
Set
Syntax: set <parameter> {<option>}
Show
Syntax: show information
show centre
show phipsi
show RamPrint
show rotation
show selected { group | chain | atom }
show sequence
show symmetry
show translation
show zoom
Slab
Syntax: slab {<boolean>}
slab <value>
Spacefill
Syntax: spacefill {<boolean>}
spacefill temperature
spacefill user
spacefill <value>
Spanish
Syntax: Spanish
SSBonds
Syntax: ssbonds {<boolean>}
ssbonds <value>
Star
Syntax: star {<boolean>}
star temperature
star user
star <value>
Stereo
Syntax: stereo on
stereo <number>
stereo off
Strands
Syntax: strands {<boolean>}
strands <value>
Structure
Syntax: structure
Surface
Syntax: surface molecule <value>
surface solvent <value>
Trace
Syntax: trace {<boolean>}
trace <value>
trace temperature
Translate
Syntax: translate <axis> {-} <value>
UnBond
Syntax: unbond <number> <number>
unbond
Wireframe
Syntax: wireframe {<boolean>}
wireframe <value> {
Write
Syntax: write {<format>} <filename>
Zap
Syntax: zap
Zoom
Syntax: zoom {<boolean>}
zoom <value>
Internal Parameters
RasMol has a number of internal parameters that may be modified using the
'set'
command. These parameters control a number of program options such as
rendering options and mouse button mappings.
Set Ambient
Syntax: set ambient {<value>}
Set Axes
Syntax: set axes <boolean>
Set Backfade
Syntax: set backfade <boolean>
Set Background
Syntax: set background {<colour>}
Set BondMode
Syntax: set bondmode and
set bondmode or
set bondmode all
set bondmode none
set bondmode not bonded
Set Bonds
Syntax: set bonds <boolean>
Set BoundBox
Syntax: set boundbox <boolean>
Set Cartoon
Syntax: set cartoon {<boolean>}
set cartoon {<number>}
Set CisAngle
Syntax: set cisangle {<value>}
Set Display
Syntax: set display selected
set display normal
Set FontSize
Syntax: set fontsize {<value>} { FS | PS }
Set FontStroke
Syntax: set fontstroke {<value>}
Set HBonds
Syntax: set hbonds backbone
set hbonds sidechain
Set Hetero
Syntax: set hetero <boolean>
Set HourGlass
Syntax: set hourglass <boolean>
Set Hydrogen
Syntax: set hydrogen <boolean>
Set Kinemage
Syntax: set kinemage <boolean>
Set Menus
Syntax: set menus <boolean>
Set Monitor
Syntax: set monitor <boolean>
Set Mouse
Syntax: set mouse rasmol
set mouse insight
set mouse quanta
Set Picking
Syntax: set picking <boolean>
set picking off
set picking none
set picking ident
set picking distance
set picking monitor
set picking angle
set picking torsion
set picking label
set picking centre
set picking center
set picking coord
set picking bond
set picking atom
set picking group
set picking chain
Set Play
Syntax: set play.fps {<value>}
Set Radius
Syntax: set radius {<value>}
Set Record
Syntax: set record.aps {<value>}
set record.fps {<value>}
Syntax: set record.dwell {<value>}
Set ShadePower
Syntax: set shadepower {<value>}
Set Shadow
Syntax: set shadow <boolean>
Set SlabMode
Syntax: set slabmode <slabmode>
Set Solvent
Syntax: set solvent <boolean>
Set Specular
Syntax: set specular <boolean>
Set SpecPower
Syntax: set specpower {<value>}
Set SSBonds
Syntax: set ssbonds backbone
set ssbonds sidechain
Set Stereo
Syntax: set stereo <boolean>
set stereo [-] <number>
Set Strands
Syntax: set strands {<value>}
Set Transparent
Syntax: set transparent <boolean>
Set UnitCell
Syntax: set unitcell <boolean>
Set VectPS
Syntax: set vectps <boolean>
Set Write
Syntax: set write <boolean>
Atom Expressions
RasMol atom expressions uniquely identify an arbitrary group of atoms
within a molecule. Atom expressions are composed of either primitive
expressions,
predefined sets,
comparison operators,
'within'
expressions,
or logical (boolean) combinations of the above expression types.
Examples: backbone and not helix
within( 8.0, ser70 )
not (hydrogen or hetero)
not *.FE and hetero
8, 12, 16, 20-28
arg, his, lys
Example Expressions
Expression Interpretation
* All atoms
cys Atoms in cysteines
hoh Atoms in heterogeneous water molecules
as? Atoms in either asparagine or aspartic acid
*120 Atoms at residue 120 of all chains
*p Atoms in chain P
*.n? Nitrogen atoms
cys.sg Sulphur atoms in cysteine residues
ser70.c? Carbon atoms in serine-70
hem*p.fe Iron atoms in the Heme groups of chain P
*.*;A All atoms in alternate conformation A
*/4 All atoms in model 4
Primitive Expressions
Comparison Operators
Examples: resno < 23
temperature >= 900
atomno == 487
Within Expressions
Predefined Sets
AT Acidic Acyclic
Aliphatic Alpha Amino
Aromatic Backbone Basic
Bonded Buried CG
Charged Cyclic Cystine
Helix Hetero Hydrogen
Hydrophobic Ions Large
Ligand Medium Neutral
Nucleic Polar Protein
Purine Pyrimidine Selected
Sheet Sidechain Small
Solvent Surface Turn
Water
AT Set
Acidic Set
Acyclic Set
Aliphatic Set
Alpha Set
Amino Set
Aromatic Set
Backbone Set
Basic Set
Bonded Set
Buried Set
CG Set
Charged Set
Cyclic Set
Cystine Set
Helix Set
Hetero Set
Hydrogen Set
Hydrophobic Set
Ions Set
Large Set
Ligand Set
Medium Set
Neutral Set
Nucleic Set
Polar Set
Protein Set
Purine Set
Pyrimidine Set
Selected Set
Sheet Set
Sidechain Set
Small Set
Solvent Set
Surface Set
Turn Set
Water Set
Set Summary
Residues: ala arg asn asp cys glu gln gly his ile leu lys met phe pro ser thr trp tyr val
A R N D C E Q G H I L K M F P S T W Y V
Predefined Set
A R N D C E Q G H I L K M F P S T W Y V
acidic
* *
acyclic * * *
* * * *
* * *
* *
* *
*
aliphatic *
* * *
*
aromatic
*
*
* *
basic *
*
*
buried *
*
* *
* *
*
*
charged *
* *
*
*
cyclic
*
* *
* *
hydrophobic *
* * *
* * *
* *
*
large *
* *
* * *
* * *
* *
medium *
* *
*
*
*
negative
* *
neutral * *
* *
* * * *
* * *
* * * *
*
polar * *
* * * *
*
*
* *
positive *
*
*
small *
*
*
surface * *
* * *
* *
* *
* * *
Colour Schemes
The RasMol
'colour'
command allows different objects (such as atoms, bonds and ribbon segments)
to be given a specified colour. Typically this colour is either a RasMol
predefined colour name or an RGB triple. Additionally RasMol also supports
'alt',
'amino',
'chain',
'charge',
'cpk',
'group',
'model',
'shapely',
'structure',
'temperature'
or
'user'
colour schemes for atoms, and
'hbond type'
colour scheme for hydrogen bonds and
'electrostatic potential'
colour scheme for dot surfaces.
The 24 currently predefined colour
names are
listed below with their corresponding RGB triplet and hexadecimal value.
Predefined colour
Sample
RGB Values
Hexadecimal
Black
[ 0, 0, 0]
000000
Blue
[ 0, 0,255]
0000FF
BlueTint
[175,214,255]
AFD7FF
Brown
[175,117,89]
AF7559
Cyan
[ 0,255,255]
00FFFF
Gold
[255,156, 0]
FC9C00
Grey
[125,125,125]
7D7D7D
Green
[ 0,255, 0]
00FF00
GreenBlue
[ 46,139,87]
2E8B57
GreenTint
[152,255,179]
98FFB3
HotPink
[255, 0,101]
FF0065
Magenta
[0,255,0]
FF00FF
Orange
[255,165, 0]
FFA500
Pink
[255,101,117]
FF6575
PinkTint
[255,171,187]
FFABBB
Purple
[160, 32,240]
A020F0
Red
[255, 0, 0]
FF0000
RedOrange
[255, 69, 0]
FF4500
SeaGreen
[ 0,250,109]
00FA6D
SkyBlue
[ 58,144,255]
3A90FF
Violet
[238,130,238]
EE82EE
White
[255,255,255]
FFFFFF
Yellow
[255,255, 0]
FFFF00
YellowTint
[246,246,117]
F6F675
Alt Colours
Amino Colours
Amino Acids
colour Name
Sample
RGB Values
Hexadecimal
ASP, GLU
Bright Red
[230,230, 10]
E60A0A
CYS, MET
Yellow
[230,230, 0]
E6E600
LYS, ARG
Blue
[ 20, 90,255]
145AFF
SER, THR
Orange
[250,150, 0]
FA9600
PHE, TYR
Mid Blue
[ 50, 50,170]
3232AA
ASN, GLN
Cyan
[ 0,220,220]
00DCDC
GLY
Light Grey
[235,235,235]
EBEBEB
LEU, VAL, ILE
Green
[ 15,130, 15]
0F820F
ALA
Dark Grey
[200,200,200]
C8C8C8
TRP
Purple
[180, 90,180]
B45AB4
HIS
Pale Blue
[130,130,210]
8282D2
PRO
Flesh
[220,150,130]
DC9682
Others
Tan
[190,160,110]
BEA06E
Chain Colours
Charge Colours
CPK Colours
Element
Colour Name
Sample
RGB Values
Hexadecimal
Carbon
light grey
[200,200,200]
C8C8C8
Oxygen
red
[240,0,0]
F00000
Hydrogen
white
[255,255,255]
FFFFFF
Nitrogen
sky blue
[143,143,255]
8F8FFF
Sulfur
yellow
[255,200,50]
FFC832
Phosphorus
orange
[255,165,0]
FFA500
Chlorine
green
[0,255,0]
00FF00
Bromine, Zinc
brown
[165,42,42]
A52A2A
Sodium
blue
[0,0,255]
0000FF
Iron
orange
[255,165,0]
FFA500
Magnesium
forest green
[34,139,34]
228B22
Calcium
dark grey
[128,128,144]
808090
Unknown
deep pink
[255,20,147]
FF1493
Code
colour Name
Sample
RGB Values
Hexadecimal
LG
Light Grey
[200,200,200]
C8C8C8
SB
Sky Blue
[143,143,255]
8F8FFF
R
Red
[240, 0, 0]
F00000
Y
Yellow
[255,200, 50]
FFC832
W
White
[255,255,255]
FFFFFF
Pk
Pink
[255,192,203]
FFC0CB
Go
Golden Rod
[218,165, 32]
DAA520
Bl
Blue
[ 0, 0,255]
0000FF
Or
Orange
[255,165, 0]
FFA500
DG
Dark Grey
[128,128,144]
808090
Br
Brown
[165, 42, 42]
A52A2A
P
Purple
[160, 32,240]
A020F0
DP
Deep Pink
[255, 20,147]
FF1493
G
Green
[ 0,255, 0]
00FF00
FB
Fire Brick
[178, 34, 34]
B22222
FG
Forest Green
[ 34,139, 34]
228B22
Code
colour Name
Sample
RGB Values
Hexadecimal
LG
Light Grey
[211,211,211]
D3D3D3
SB
Sky Blue
[135,206,235]
87CEE6
R
Red
[255, 0, 0]
FF0000
Y
Yellow
[255,255, 0]
FFFF00
W
White
[255,255,255]
FFFFFF
Pk
Pink
[255,192,203]
FFC0CB
Go
Golden Rod
[218,165, 32]
DAA520
Bl
Blue
[ 0, 0,255]
0000FF
Or
Orange
[255,170, 0]
FFAA00
DG
Dark Grey
[105,105,105]
696969
Br
Brown
[128, 40, 40]
802828
P
Purple
[160, 32,240]
A020F0
DP
Deep Pink
[250, 22,145]
FA1691
G
Green
[ 0,255, 0]
00FF00
FB
Fire Brick
[178, 33, 33]
B22121
FG
Forest Green
[ 34,139, 34]
228B22
1a 2a 3b 4b 5b 6b 7b
8
1b 2b 3a 4a 5a 6a 7a
0
H
1 W
He
2 Pk
Li
3 FBBe
4 DP
B
5 GC
6 LGN
7 SBO
8 RF
9 GoNe
10 DP
Na
11 BlMg
12 FG
Al
13 DGSi
14 GoP
15 OrS
16 YCl
17 GAr
18 DP
K
19 DPCa
20 DGSc
21 DPTi
22 DGV
23 DPCr
24 DGMn
25 DGFe
26 OrCo
27 DPNi
28 BrCu
29 BrZn
30 BrGa
31 DPGe
32 DPAs
33 DPSe
34 DPBr
35 BrKr
36 DP
Rb
37 DPSr
38 DPY
39 DPZr
40 DPNb
41 DPMo
42 DPTc
43 DPRu
44 DPRh
45 DPPd
46 DPAg
47 DGCd
48 DPIn
49 DPSn
50 DPSb
51 DPTe
52 DPI
53 PXe
54 DP
Cs
55 DPBa
56 OrLa
57 DPHf
72 DPTa
73 DPW
74 DPRe
75 DPOs
76 DPIr
77 DPPt
78 DPAu
79 GoHg
80 DPTl
81 DPPb
82 DPBi
83 DPPo
84 DPAt
85 DPRn
86 DP
Fr
87 DPRa
88 DPAc
89 DP
Lanthinide
SeriesCe
58 DPPr
59 DPNd
60 DPPm
61 DPSm
62 DPEu
63 DPGd
64 DPTb
65 DPDy
66 DPHo
67 DPEr
68 DPTm
69 DPYb
70 DPLu
71 DP
Actinide
SeriesTh
90 DPPa
91 DPU
92 DPNp
93 DPPu
94 DPAm
95 DPCm
96 DPBk
97 DPCf
98 DPEs
99 DPFm
100 DPMd
101 DPNo
102 DPLr
103 DP
select all
select oxygen
colour red
select carbon
colour white
select nitrogen
colour blue
select all
Extension of this idea to other atoms and colour schemes is straightforward.
Group Colours
NMR Model Colours
Shapely Colours
Residues
Colour Name
Sample
RGB Values
Hexadecimal
ALA
Medium Green
[140,255,140]
8CFF8C
GLY
White
[255,255,255]
FFFFFF
LEU
Olive Green
[ 69, 94, 69]
455E45
SER
Medium Orange
[255,112, 66]
FF7042
VAL
Light Purple
[255,140,255]
FF8CFF
THR
Dark Orange
[184, 76, 0]
B84C00
LYS
Royal Blue
[ 71, 71,184]
4747B8
ASP
Dark Rose
[160,0,66]
A00042
ILE
Dark Green
[ 0, 76, 0]
004C00
ASN
Light Salmon
[255,124,112]
FF7C70
GLU
Dark Brown
[102, 0, 0]
660000
PRO
Dark Grey
[ 82, 82, 82]
525252
ARG
Dark Blue
[ 0, 0,124]
00007C
PHE
Olive Grey
[ 83, 76, 66]
534C42
GLN
Dark Salmon
[255, 76, 76]
FF4C4C
TYR
Medium Brown
[140,112,76]
8C704C
HIS
Medium Blue
[112,112,255]
7070FF
CYS
Medium Yellow
[255,255,112]
FFFF70
MET
Light Brown
[184,160, 66]
B8A042
TRP
Olive Brown
[ 79, 70, 0]
4F4600
ASX,GLX,PCA,HYP
Medium Purple
[255, 0,255]
FF00FF
A
Light Blue
[160,160,255]
A0A0FF
C
Light Orange
[255,140,75]
FF8C4B
G
Medium Salmon
[255,112,112]
FF7070
T
Light Green
[160,255,160]
A0FFA0
Backbone
Light Grey
[184,184,184]
B8B8B8
Special
Dark Purple
[ 94, 0, 94]
5E005E
Default
Medium Purple
[255, 0,255]
FF00FF
Structure Colours
Temperature Colours
User Colours
HBond Type Colours
Offset Colour Triple
+2 white [255,255,255]
+3 magenta [255,0,255]
+4 red [255,0,0]
+5 orange [255,165,0]
-3 cyan [0,255,255]
-4 green [0,255,0]
default yellow [255,255,0]
Potential Colours
25 < V red [255,0,0]
10 < V < 25 orange [255,165,0]
3 < V < 10 yellow [255,255,0]
0 < V < 3 green [0,255,0]
-3 < V < 0 cyan [0,255,255]
-10 < V < 3 blue [0,0,255]
-25 < V < -10 purple [160,32,240]
V < -25 white [255,255,255]
Amino Acid Codes
Alanine A ALA Arginine R ARG
Asparagine N ASN Aspartic acid D ASP
Cysteine C CYS Glutamic acid E GLU
Glutamine Q GLN Glycine G GLY
Histidine H HIS Isoleucine I ILE
Leucine L LEU Lysine K LYS
Methionine M MET Phenylalanine F PHE
Proline P PRO Serine S SER
Threonine T THR Tryptophan W TRP
Tyrosine Y TYR Valine V VAL
Booleans
File Formats
FORMAT(6A1,I5,1X,A4,A1,A3,1X,A1,I4,A1,3X,3F8.3,2F6.2,1X,I3,2X,A4,2A2)
Column Content fmt
1-6 'ATOM' or 'HETATM' all
7-11 Atom serial number (may have gaps) all
13-16 Atom name, in IUPAC standard format all
17 Alternate location indicator indicated by A, B or C all
18-20 Residue name, in IUPAC standard format all
23-26 Residue sequence number all
27 Code for insertions of residues (i.e. 66A & 66B) all
31-38 X coordinate all
39-46 Y coordinate all
47-54 Z coordinate all
55-60 Occupancy all
61-66 Temperature factor all
68-70 Footnote number 92
73-76 Segment Identifier (left-justified) 96
77-78 Element Symbol (right-justified) 96
79-80 Charge on the Atom 96
RasMol Interpretation of PDB fields
PDB Colour Scheme Specification
Column Content
1-6 'COLOR' or 'COLOUR'
7-30 Mask (described below)
31-38 Red component
39-46 Green component
47-54 Blue component
55-60 Sphere radius in Ångstroms
61-70 Comments
Multiple NMR Models
CIF and mmCIF Format Files
mmCIF tag CIF tag Used for
_struct_biol.details Info.classification
_database_2.database_code Info.identcode
_entry.id
_struct_biol.id
_struct.title Info.moleculename
_chemical_name_common
_chemical_name_systematic
_chemical_name_mineral
_symmetry.space_group_name_H-M _symmetry_space_group_name_H-M Info.spacegroup
_cell.length_a _cell_length_a Info.cell
_cell.length_b _cell_length_b
_cell.length_c _cell_length_c
_cell.angle_alpha _cell_angle_alpha
_cell.angle_alpha _cell_angle_alpha
_cell.angle_beta _cell_angle_beta
_cell.angle_gamma _cell_angle_gamma
_atom_sites.fract_transf_matrix[1][1] _atom_sites_fract_tran_matrix_11 Used to compute orthogonal coords
... ...
_atom_sites.fract_transf_vector[1] _atom_sites_fract_tran_vector_1
... ...
_atom_sites.cartn_transf_matrix[1][1] _atom_sites_cartn_tran_matrix_11 Alternative to compute orth. coords
... ...
_atom_sites.cartn_transf_vector[1] _atom_sites_cartn_tran_vector_1
... ...
_atom_site.cartn_x _atom_site_cartn_x atomic coordinates
... ...
or
_atom_site.fract_x _atom_site_fract_x
... ...
_struct_conn.id bonds
...  
_geom_bond.atom_site_id_1 _geom_bond_atom_site_label_1
... ...
_struct_conf.id helices, sheets, turns
_struct_sheet_range.id
...
Machine-Specific Support
Monochrome X-Windows Support
Tcl/Tk IPC support
UNIX sockets based IPC
Compiling RasWin with Borland and MetroWerks
Bibliography
| Changes |
Things To Do |
Introduction |
Source Code and Binaries |
| RasMol Manual |
Spanish Translation of RasMol Manual |
Italian Translation of RasMol Help File |
| Donate to Support RasMol |
Release README |
Register your RasMol |
Updated 17 April 2009.
Herbert J. Bernstein
Bernstein + Sons, 5 Brewster Lane, Bellport, NY 11713-2803, USA