| RASMOL(1) | General Commands Manual | RASMOL(1) |
rasmol - Molecular Graphics Visualisation Tool v2.7.5
rasmol [-nodiplay] [[-format ] filename] [-script scriptfile]
This software has been created from several sources. Much of the code is from RasMol 2.6, as created by Roger Sayle. The torsion angle code, new POVRAY3 code and other features are derived from the RasMol2.6x1 revisions by Arne Mueller. 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.
The CIF modifications make use of a library based in part on
CBFlib by Paul J. Ellis and Herbert J. Bernstein. Parts of CBFlib is loosely
based on the CIFPARSE software package from the NDB at Rutgers university.
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 version 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
Copyright (C) 1989, 1991 Free Software Foundation, Inc.
59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
Preamble
The licenses for most software are designed to take away your freedom to
share and change it. By contrast, the GNU General Public License is
intended to guarantee your freedom to share and change free software--to
make sure the software is free for all its users. This General Public
License applies to most of the Free Software Foundation's software and
to any other program whose authors commit to using it. (Some other Free
Software Foundation software is covered by the GNU Library General
Public License instead.) You can apply it to your programs, too.
When we speak of free software, we are referring to freedom, not price.
Our General Public Licenses are designed to make sure that you have the
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free programs; and that you know you can do these things.
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For example, if you distribute copies of such a program, whether gratis
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You must make sure that they, too, receive or can get the source code.
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We protect your rights with two steps: (1) copyright the software, and
(2) offer you this license which gives you legal permission to copy,
distribute and/or modify the software.
Also, for each author's protection and ours, we want to make certain that
everyone understands that there is no warranty for this free software.
If the software is modified by someone else and passed on, we want its
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Finally, any free program is threatened constantly by software patents.
We wish to avoid the danger that redistributors of a free program will
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proprietary. To prevent this, we have made it clear that any patent must
be licensed for everyone's free use or not licensed at all.
The precise terms and conditions for copying, distribution and
modification follow.
GNU GENERAL PUBLIC LICENSE
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 under
the terms of this General Public License. The "Program",
below, refers to any such program or work, and a "work based on the
Program" means either the Program or any derivative work under
copyright law: that is to say, a work containing the Program or a
portion of it, either verbatim or with modifications and/or translated
into another language. (Hereinafter, translation is included without
limitation in the term "modification".) Each licensee is
addressed as "you".
Activities other than copying, distribution and modification are not covered by this License; they are outside its scope. The act of running the Program is not restricted, and the output from the Program is covered only if its contents constitute a work based on the Program (independent of having been made by running the Program). Whether that is true depends on what the Program does.
1. You may copy and distribute verbatim copies of the Program's source
code as you receive it, in any medium, provided that you conspicuously
and appropriately publish on each copy an appropriate copyright notice
and disclaimer of warranty; keep intact all the notices that refer to
this License and to the absence of any warranty; and give any other
recipients of the Program a copy of this License along with the
Program.
You may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in exchange for a fee.
2. You may modify your copy or copies of the Program or any portion of
it, thus forming a work based on the Program, and copy and distribute
such modifications or work under the terms of Section 1 above, provided
that you also meet all of these conditions:
a) You must cause the modified files to carry prominent notices
stating that you changed the files and the date of any change.
b) You must cause any work that you distribute or publish, that in
whole or in part contains or is derived from the Program or any
part thereof, to be licensed as a whole at no charge to all third
parties under the terms of this License.
c) If the modified program normally reads commands interactively
when run, you must cause it, when started running for such
interactive use in the most ordinary way, to print or display an
announcement including an appropriate copyright notice and a
notice that there is no warranty (or else, saying that you provide
a warranty) and that users may redistribute the program under
these conditions, and telling the user how to view a copy of this
License. (Exception: if the Program itself is interactive but
does not normally print such an announcement, your work based on
the Program is not required to print an announcement.)
These requirements apply to the modified work as a whole. If identifiable sections of that work are not derived from the Program, and can be reasonably considered independent and separate works in themselves, then this License, and its terms, do not apply to those sections when you distribute them as separate works. But when you distribute the same sections as part of a whole which is a work based on the Program, the distribution of the whole must be on the terms of this License, whose permissions for other licensees extend to the entire whole, and thus to each and every part regardless of who wrote it.
Thus, it is not the intent of this section to claim rights or contest your rights to work written entirely by you; rather, the intent is to exercise the right to control the distribution of derivative or collective works based on the Program.
In addition, mere aggregation of another work not based on the Program with the Program (or with a work based on the Program) on a volume of a storage or distribution medium does not bring the other work under the scope of this License.
3. You may copy and distribute the Program (or a work based on it, under
Section 2) in object code or executable form under the terms of Sections
1 and 2 above provided that you also do one of the following:
a) Accompany it with the complete corresponding machine-readable
source code, which must be distributed under the terms of Sections
1 and 2 above on a medium customarily used for software interchange;
or,
b) Accompany it with a written offer, valid for at least three
years, to give any third party, for a charge no more than your
cost of physically performing source distribution, a complete
machine-readable copy of the corresponding source code, to be
distributed under the terms of Sections 1 and 2 above on a medium
customarily used for software interchange; or,
c) Accompany it with the information you received as to the offer
to distribute corresponding source code. (This alternative is
allowed only for noncommercial distribution and only if you
received the program in object code or executable form with such
an offer, in accord with Subsection b above.)
The source code for a work means the preferred form of the work for making modifications to it. For an executable work, complete source code means all the source code for all modules it contains, plus any associated interface definition files, plus the scripts used to control compilation and installation of the executable. However, as a special exception, the source code distributed need not include anything that is normally distributed (in either source or binary form) with the major components (compiler, kernel, and so on) of the operating system on which the executable runs, unless that component itself accompanies the executable.
If distribution of executable or object code is made by offering access to copy from a designated place, then offering equivalent access to copy the source code from the same place counts as distribution of the source code, even though third parties are not compelled to copy the source along with the object code.
4. You may not copy, modify, sublicense, or distribute the Program except
as expressly provided under this License. Any attempt otherwise to copy,
modify, sublicense or distribute the Program is void, and will
automatically terminate your rights under this License. However, parties
who have received copies, or rights, from you under this License will
not have their licenses terminated so long as such parties remain in
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5. You are not required to accept this License, since you have not signed
it. However, nothing else grants you permission to modify or distribute
the Program or its derivative works. These actions are prohibited by law
if you do not accept this License. Therefore, by modifying or
distributing the Program (or any work based on the Program), you
indicate your acceptance of this License to do so, and all its terms and
conditions for copying, distributing or modifying the Program or works
based on it.
6. Each time you redistribute the Program (or any work based on the
Program), the recipient automatically receives a license from the
original licensor to copy, distribute or modify the Program subject to
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on the recipients' exercise of the rights granted herein. You are not
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License.
7. If, as a consequence of a court judgment or allegation of patent
infringement or for any other reason (not limited to patent issues),
conditions are imposed on you (whether by court order, agreement or
otherwise) that contradict the conditions of this License, they do not
excuse you from the conditions of this License. If you cannot distribute
so as to satisfy simultaneously your obligations under this License and
any other pertinent obligations, then as a consequence you may not
distribute the Program at all. For example, if a patent license would
not permit royalty-free redistribution of the Program by all those who
receive copies directly or indirectly through you, then the only way you
could satisfy both it and this License would be to refrain entirely from
distribution of the Program.
If any portion of this section is held invalid or unenforceable under any particular circumstance, the balance of the section is intended to apply and the section as a whole is intended to apply in other circumstances.
It is not the purpose of this section to induce you to infringe any patents or other property right claims or to contest validity of any such claims; this section has the sole purpose of protecting the integrity of the free software distribution system, which is implemented by public license practices. Many people have made generous contributions to the wide range of software distributed through that system in reliance on consistent application of that system; it is up to the author/donor to decide if he or she is willing to distribute software through any other system and a licensee cannot impose that choice.
This section is intended to make thoroughly clear what is believed to be a consequence of the rest of this License.
8. If the distribution and/or use of the Program is restricted in certain
countries either by patents or by copyrighted interfaces, the original
copyright holder who places the Program under this License may add an
explicit geographical distribution limitation excluding those countries,
so that distribution is permitted only in or among countries not thus
excluded. In such case, this License incorporates the limitation as if
written in the body of this License.
9. The Free Software Foundation may publish revised and/or new versions
of the General Public License from time to time. Such new versions will
be similar in spirit to the present version, but may differ in detail to
address new problems or concerns.
Each version is given a distinguishing version number. If the Program specifies a version number of this License which applies to it and "any later version", you have the option of following the terms and conditions either of that version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of this License, you may choose any version ever published by the Free Software Foundation.
10. If you wish to incorporate parts of the Program into other free
programs whose distribution conditions are different, write to the
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sometimes make exceptions for this. Our decision will be guided by the
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NO WARRANTY
11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND,
EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE
ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH
YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL
NECESSARY SERVICING, REPAIR OR CORRECTION.
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WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR
DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL
DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM
(INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED
INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF
THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR
OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest
possible use to the public, the best way to achieve this is to make it
free software which everyone can redistribute and change under these
terms.
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
along with this program; if not, write to the Free Software
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.
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.
* 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.
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.
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 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
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.
RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images. RasMol runs on wide range of architectures and operating systems including Microsoft Windows, Apple Macintosh, UNIX and VMS systems. UNIX and VMS versions require an 8, 24 or 32 bit colour X Windows display (X11R4 or later). 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 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 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 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.
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 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 background command is synonymous with the RasMol set background command.
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.
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.
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 Angstrom) 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.
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.
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.
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.
The deferred commands accumulated under the given name can be executed using the execute command
This command interacts with the slab <value> command, which clips to the front of a given z-clipping plane.
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.
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.
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 from the old poise to the new poise
The macro must have been previously defined by calls to the defer command.
The animation of the motion depends on the prior settings of the record command.
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.
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.
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.
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.
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.
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.
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.
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 between 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.
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 Angstroms), the inferred spead is .6667, and the standard deviation of the Gaussian is taken as 1.25 Angstroms.
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.
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.
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 '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 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.
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.
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 Angstroms 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.
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.
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.
Some commands which use the toggle feature are: ColourMode. More functions that utilize this capability may be added at a later date.
As of release 2.7.5, RasMol support play from scripts and data files.
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.
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 minutes into a longer movie. These commands allow control over rewriting selected time segments.
This command should not be mistaken for the RasMol zap command which deletes the currently stored molecule, returning the program to its initial state.
Type "help expression" for more information on RasMol atom expressions or see section Atom Expressions.
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 Angstroms) for nucleic acids. The default width of protein alpha helices and beta sheets is 380 (1.52 Angstroms) and 100 (0.4 Angstroms) 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.
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.
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.
Atom serial numbers are regenerated. When this will result in more than 99,999 atoms being written in PDB format, numbers may be repeated. If possible the repeats are done by using the same numbers in different NMR models.
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 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.
Type "help expression" for more information on RasMol atom expressions or see section Atom Expressions.
This command interacts with the depth <value> command, which clips to the rear of a given z-clipping plane.
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.
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.
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 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 Angstrom) or a value containing a decimal point. A value of 500 (2.0 Angstroms) 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.
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 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 Angstroms wide). The default width of protein alpha helices and beta sheets is 380 (1.52 Angstroms) and 100 (0.4 Angstroms) 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.
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 command unbond without arguments removes a bond previously picked by the bond <number> <number> pick 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 specified 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.
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.
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.
picking play.fps radius record.aps
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 command set background is synonymous with the RasMol command background.
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.
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
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.
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 further 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.
In the current release of RasMol, the play timing is not controlled by this parameter.
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).
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 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.
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.
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.
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 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.
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 asterisk may be used as a wild card for a whole field and a question mark as a single character wildcard.
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.
For example, the command select within(3.2,backbone) selects any atom within a 3.2 Angstrom radius of any atom in a protein or nucleic acid backbone. Within expressions are particularly useful for selecting the atoms around an active site.
The predefined set mainchain is synonymous with the set backbone.
This predefined set should not be confused with the predefined set alpha which contains the alpha carbon atoms of a protein.
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 Black, Blue, BlueTint, Brown, Cyan, Gold, Grey, Green, GreenBlue, GreenTint, HotPink, Magenta, Orange, Pink, PinkTint, Purple, Red, RedOrange, SeaGreen, SkyBlue, Violet, White, Yellow and YellowTint
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 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.
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 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.
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 Angstrom 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.
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.
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.
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.
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: A search is made through multiple data blocks for the desired tags, so a single dataset may be composed from multiple data blocks, but multiple data sets may not be stacked in the same file.
In the following sections, support for Monochrome X-Windows, Tcl/Tk IPC, UNIX sockets based IPC, Compiling RasWin with Borland and MetroWerks are described.
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.
The RasMol User Manual!
1992-1998 by Roger Sayle (rasmol@ggr.co.uk)
| July 2009 |