1RASMOL(1) General Commands Manual RASMOL(1)
2
6 rasmol - Molecular Graphics Visualisation Tool v2.7.5
7
10 rasmol [-nodiplay] [[-format ] filename] [-script scriptfile]
11
14 -pdb Protein Data Bank
15 -mdl MDL's MOL File Format
16 -mol2 Tripos' Sybyl MOL2 Format
17 -xyz MSC's XYZ (XMol) Format
18 -mopac MOPAC Input or Output File Format
19 -alchemy Alchemy File Format
20 -charmm CHARMm File Format
21 -cif IUCr CIF or CIF File Format
22
24 This software has been created from several sources. Much of the code
25 is from RasMol 2.6, as created by Roger Sayle. The torsion angle code,
26 new POVRAY3 code and other features are derived from the RasMol2.6x1
27 revisions by Arne Mueller. The Ramachandran printer plot code was
28 derived from fisipl created by Frances C. Bernstein. See the Protein
29 Data Bank program tape.
30 The code to display multiple molecules and to allow bond rotation is
32 derived in large part from the UCB mods by Gary Grossman and Marco
33 Molinaro, included with permission of Eileen Lewis of the ModularCHEM
34 Consortium.
35 The CIF modifications make use of a library based in part on CBFlib by
37 Paul J. Ellis and Herbert J. Bernstein. Parts of CBFlib is loosely
38 based on the CIFPARSE software package from the NDB at Rutgers univer‐
39 sity. Please type the RasMol commands help copying, help general, help
40 IUCR, help CBFlib,
41 and help CIFPARSE for applicable notices. Please type help copyright
42 for copyright notices. If you use RasMol V2.6 or an earlier version,
43 type the RasMol command help oldnotice.
44
47 This version is based directly on RasMol version 2.7.4.2, on RasMol
48 verion 2.7.4.2, on RasMol version 2.7.4, on RasMol version 2.7.3.1, on
49 RasMol version 2.7.3, on RasMol version 2.7.2.1.1, Rasmol version
50 2.7.2, RasMol version 2.7.1.1 and RasTop version 1.3 and indirectly on
51 the RasMol 2.5-ucb and 2.6-ucb versions and version 2.6_CIF.2, RasMol
52 2.6x1 and RasMol_2.6.4.
53 RasMol 2.7.5 may be distributed under the terms of the GNU General Pub‐
55 lic License (the GPL), see
56 http://www.gnu.org/licenses/gpl.txt
58 or the file GPL or type the command help GPL
60 or RasMol 2.7.5 may be distributed under the RASMOL license. See the
62 file NOTICE or type the command help RASLIC
63 GPL
66 GNU GENERAL PUBLIC LICENSE
67 Version 2, June 1991
68 Copyright (C) 1989, 1991 Free Software Foundation, Inc.
70 59 Temple Place, Suite 330, Boston, MA
71 02111-1307 USA
72 Everyone is permitted to copy and distribute verbatim copies
73 of this license document, but changing it is not allowed.
74 Preamble
76 The licenses for most software are designed to take away your
78 freedom to share and change it. By contrast, the GNU General
79 Public License is intended to guarantee your freedom to share
80 and change free software--to make sure the software is free for
81 all its users. This General Public License applies to most of
82 the Free Software Foundation's software and to any other program
83 whose authors commit to using it. (Some other Free Software
84 Foundation software is covered by the GNU Library General Public
85 License instead.) You can apply it to your programs, too.
86 When we speak of free software, we are referring to freedom,
88 not price. Our General Public Licenses are designed to make
89 sure that you have the freedom to distribute copies of free
90 software (and charge for this service if you wish), that you
91 receive source code or can get it if you want it, that you can
92 change the software or use pieces of it in new free programs;
93 and that you know you can do these things.
94 To protect your rights, we need to make restrictions that for‐
96 bid anyone to deny you these rights or to ask you to surrender
97 the rights. These restrictions translate to certain responsi‐
98 bilities for you if you distribute copies of the software, or if
99 you modify it.
100 For example, if you distribute copies of such a program,
102 whether gratis or for a fee, you must give the recipients all
103 the rights that you have. You must make sure that they, too,
104 receive or can get the source code. And you must show them
105 these terms so they know their rights.
106 We protect your rights with two steps: (1) copyright the soft‐
108 ware, and (2) offer you this license which gives you legal per‐
109 mission to copy, distribute and/or modify the software.
110 Also, for each author's protection and ours, we want to make
112 certain that everyone understands that there is no warranty for
113 this free software. If the software is modified by someone else
114 and passed on, we want its recipients to know that what they
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127 GNU GENERAL PUBLIC LICENSE
129 TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICA‐
130 TION
131 0. This License applies to any program or other work which
133 contains a notice placed by the copyright holder saying it may
134 be distributed under the terms of this General Public License.
135 The "Program", below, refers to any such program or work, and a
136 "work based on the Program" means either the Program or any de‐
137 rivative work under copyright law: that is to say, a work con‐
138 taining the Program or a portion of it, either verbatim or with
139 modifications and/or translated into another language. (Here‐
140 inafter, translation is included without limitation in the term
141 "modification".) Each licensee is addressed as "you".
142 Activities other than copying, distribution and modification are
144 not covered by this License; they are outside its scope. The
145 act of running the Program is not restricted, and the output
146 from the Program is covered only if its contents constitute a
147 work based on the Program (independent of having been made by
148 running the Program). Whether that is true depends on what the
149 Program does.
150 1. You may copy and distribute verbatim copies of the Pro‐
152 gram's source code as you receive it, in any medium, provided
153 that you conspicuously and appropriately publish on each copy an
154 appropriate copyright notice and disclaimer of warranty; keep
155 intact all the notices that refer to this License and to the
156 absence of any warranty; and give any other recipients of the
157 Program a copy of this License along with the Program.
158 You may charge a fee for the physical act of transferring a
160 copy, and you may at your option offer warranty protection in
161 exchange for a fee.
162 2. You may modify your copy or copies of the Program or any
164 portion of it, thus forming a work based on the Program, and
165 copy and distribute such modifications or work under the terms
166 of Section 1 above, provided that you also meet all of these
167 conditions:
168 a) You must cause the modified files to carry prominent
170 notices
171 stating that you changed the files and the date of any
172 change.
173 b) You must cause any work that you distribute or publish,
175 that in
176 whole or in part contains or is derived from the Program or
177 any
178 part thereof, to be licensed as a whole at no charge to all
179 third
180 parties under the terms of this License.
181 c) If the modified program normally reads commands interac‐
183 tively
184 when run, you must cause it, when started running for such
185 interactive use in the most ordinary way, to print or dis‐
186 play an
187 announcement including an appropriate copyright notice and a
188 notice that there is no warranty (or else, saying that you
189 provide
190 a warranty) and that users may redistribute the program
191 under
192 these conditions, and telling the user how to view a copy of
193 this
194 License. (Exception: if the Program itself is interactive
195 but
196 does not normally print such an announcement, your work
197 based on
198 the Program is not required to print an announcement.)
199 These requirements apply to the modified work as a whole. If
201 identifiable sections of that work are not derived from the Pro‐
202 gram, and can be reasonably considered independent and separate
203 works in themselves, then this License, and its terms, do not
204 apply to those sections when you distribute them as separate
205 works. But when you distribute the same sections as part of a
206 whole which is a work based on the Program, the distribution of
207 the whole must be on the terms of this License, whose permis‐
208 sions for other licensees extend to the entire whole, and thus
209 to each and every part regardless of who wrote it.
210 Thus, it is not the intent of this section to claim rights or
212 contest your rights to work written entirely by you; rather, the
213 intent is to exercise the right to control the distribution of
214 derivative or collective works based on the Program.
215 In addition, mere aggregation of another work not based on the
217 Program with the Program (or with a work based on the Program)
218 on a volume of a storage or distribution medium does not bring
219 the other work under the scope of this License.
220 3. You may copy and distribute the Program (or a work based on
222 it, under Section 2) in object code or executable form under the
223 terms of Sections 1 and 2 above provided that you also do one of
224 the following:
225 a) Accompany it with the complete corresponding machine-
227 readable
228 source code, which must be distributed under the terms of
229 Sections
230 1 and 2 above on a medium customarily used for software
231 interchange; or,
232 b) Accompany it with a written offer, valid for at least
234 three
235 years, to give any third party, for a charge no more than
236 your
237 cost of physically performing source distribution, a com‐
238 plete
239 machine-readable copy of the corresponding source code, to
240 be
241 distributed under the terms of Sections 1 and 2 above on a
242 medium
243 customarily used for software interchange; or,
244 c) Accompany it with the information you received as to the
246 offer
247 to distribute corresponding source code. (This alternative
248 is
249 allowed only for noncommercial distribution and only if you
250 received the program in object code or executable form with
251 such
252 an offer, in accord with Subsection b above.)
253 The source code for a work means the preferred form of the work
255 for making modifications to it. For an executable work, com‐
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268 access to copy the source code from the same place counts as
269 distribution of the source code, even though third parties are
270 not compelled to copy the source along with the object code.
271 4. You may not copy, modify, sublicense, or distribute the
273 Program except as expressly provided under this License. Any
274 attempt otherwise to copy, modify, sublicense or distribute the
275 Program is void, and will automatically terminate your rights
276 under this License. However, parties who have received copies,
277 or rights, from you under this License will not have their
278 licenses terminated so long as such parties remain in full com‐
279 pliance.
280 5. You are not required to accept this License, since you have
282 not signed it. However, nothing else grants you permission to
283 modify or distribute the Program or its derivative works. These
284 actions are prohibited by law if you do not accept this License.
285 Therefore, by modifying or distributing the Program (or any work
286 based on the Program), you indicate your acceptance of this
287 License to do so, and all its terms and conditions for copying,
288 distributing or modifying the Program or works based on it.
289 6. Each time you redistribute the Program (or any work based
291 on the Program), the recipient automatically receives a license
292 from the original licensor to copy, distribute or modify the
293 Program subject to these terms and conditions. You may not
294 impose any further restrictions on the recipients' exercise of
295 the rights granted herein. You are not responsible for enforc‐
296 ing compliance by third parties to this License.
297 7. If, as a consequence of a court judgment or allegation of
299 patent infringement or for any other reason (not limited to
300 patent issues), conditions are imposed on you (whether by court
301 order, agreement or otherwise) that contradict the conditions of
302 this License, they do not excuse you from the conditions of this
303 License. If you cannot distribute so as to satisfy simultane‐
304 ously your obligations under this License and any other perti‐
305 nent obligations, then as a consequence you may not distribute
306 the Program at all. For example, if a patent license would not
307 permit royalty-free redistribution of the Program by all those
308 who receive copies directly or indirectly through you, then the
309 only way you could satisfy both it and this License would be to
310 refrain entirely from distribution of the Program.
311 If any portion of this section is held invalid or unenforceable
313 under any particular circumstance, the balance of the section is
314 intended to apply and the section as a whole is intended to
315 apply in other circumstances.
316 It is not the purpose of this section to induce you to infringe
318 any patents or other property right claims or to contest valid‐
319 ity of any such claims; this section has the sole purpose of
320 protecting the integrity of the free software distribution sys‐
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325 decide if he or she is willing to distribute software through
326 any other system and a licensee cannot impose that choice.
327 This section is intended to make thoroughly clear what is
329 believed to be a consequence of the rest of this License.
330 8. If the distribution and/or use of the Program is restricted
332 in certain countries either by patents or by copyrighted inter‐
333 faces, the original copyright holder who places the Program
334 under this License may add an explicit geographical distribution
335 limitation excluding those countries, so that distribution is
336 permitted only in or among countries not thus excluded. In such
337 case, this License incorporates the limitation as if written in
338 the body of this License.
339 9. The Free Software Foundation may publish revised and/or new
341 versions of the General Public License from time to time. Such
342 new versions will be similar in spirit to the present version,
343 but may differ in detail to address new problems or concerns.
344 Each version is given a distinguishing version number. If the
346 Program specifies a version number of this License which applies
347 to it and "any later version", you have the option of following
348 the terms and conditions either of that version or of any later
349 version published by the Free Software Foundation. If the Pro‐
350 gram does not specify a version number of this License, you may
351 choose any version ever published by the Free Software Founda‐
352 tion.
353 10. If you wish to incorporate parts of the Program into other
355 free programs whose distribution conditions are different, write
356 to the author to ask for permission. For software which is
357 copyrighted by the Free Software Foundation, write to the Free
358 Software Foundation; we sometimes make exceptions for this. Our
359 decision will be guided by the two goals of preserving the free
360 status of all derivatives of our free software and of promoting
361 the sharing and reuse of software generally.
362 NO WARRANTY
364 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS
366 NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICA‐
367 BLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
368 HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT
369 WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING,
370 BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY
371 AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE
372 QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE
373 PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY
374 SERVICING, REPAIR OR CORRECTION.
375 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO
377 IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY
378 MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE
379 LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCI‐
380 DENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR
381 INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS
382 OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
383 YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH
384 ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN
385 ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
386 END OF TERMS AND CONDITIONS
388 How to Apply These Terms to Your New Programs
390 If you develop a new program, and you want it to be of the
392 greatest possible use to the public, the best way to achieve
393 this is to make it free software which everyone can redistribute
394 and change under these terms.
395 To do so, attach the following notices to the program. It is
397 safest to attach them to the start of each source file to most
398 effectively convey the exclusion of warranty; and each file
399 should have at least the "copyright" line and a pointer to where
400 the full notice is found.
401 <one line to give the program's name and a brief idea of
403 what it does.>
404 Copyright (C) <year> <name of author>
405 This program is free software; you can redistribute it
407 and/or modify
408 it under the terms of the GNU General Public License as pub‐
409 lished by
410 the Free Software Foundation; either version 2 of the
411 License, or
412 (at your option) any later version.
413 This program is distributed in the hope that it will be use‐
415 ful,
416 but WITHOUT ANY WARRANTY; without even the implied warranty
417 of
418 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See
419 the
420 GNU General Public License for more details.
421 You should have received a copy of the GNU General Public
423 License
424 along with this program; if not, write to the Free Software
425 Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
426 02111-1307 USA
427 Also add information on how to contact you by electronic and
429 paper mail.
430 If the program is interactive, make it output a short notice
432 like this when it starts in an interactive mode:
433 Gnomovision version 69, Copyright (C) year name of author
435 Gnomovision comes with ABSOLUTELY NO WARRANTY; for details
436 type `show w'.
437 This is free software, and you are welcome to redistribute
438 it
439 under certain conditions; type `show c' for details.
440 The hypothetical commands `show w' and `show c' should show the
442 appropriate parts of the General Public License. Of course, the
443 commands you use may be called something other than `show w' and
444 `show c'; they could even be mouse-clicks or menu items--what‐
445 ever suits your program.
446 You should also get your employer (if you work as a programmer)
448 or your school, if any, to sign a "copyright disclaimer" for the
449 program, if necessary. Here is a sample; alter the names:
450 Yoyodyne, Inc., hereby disclaims all copyright interest in the
452 program
453 `Gnomovision' (which makes passes at compilers) written by
454 James Hacker.
455 <signature of Ty Coon>, 1 April 1989
457 Ty Coon, President of Vice
458 This General Public License does not permit incorporating your
460 program into proprietary programs. If your program is a subrou‐
461 tine library, you may consider it more useful to permit linking
462 proprietary applications with the library. If this is what you
463 want to do, use the GNU Library General Public License instead
464 of this License.
465 RASLIC If you do not use the GPL, the following license terms apply:
468 RasMol License
470 Even though the authors of the various documents and software
472 found here have made a good faith effort to ensure that the doc‐
473 uments are correct and that the software performs according to
474 its documentation, and we would greatly appreciate hearing of
475 any problems you may encounter, the programs and documents any
476 files created by the programs are provided **AS IS** without any
477 warranty as to correctness, merchantability or fitness for any
478 particular or general use.
479 THE RESPONSIBILITY FOR ANY ADVERSE CONSEQUENCES FROM THE USE OF
481 PROGRAMS OR DOCUMENTS OR ANY FILE OR FILES CREATED BY USE OF THE
482 PROGRAMS OR DOCUMENTS LIES SOLELY WITH THE USERS OF THE PROGRAMS
483 OR DOCUMENTS OR FILE OR FILES AND NOT WITH AUTHORS OF THE PRO‐
484 GRAMS OR DOCUMENTS.
485 Subject to your acceptance of the conditions stated above, and
487 your respect for the terms and conditions stated in the notices
488 below, if you are not going to make any modifications or create
489 derived works, you are given permission to freely copy and dis‐
490 tribute this package, provided you do the following:
491 1. Either include the complete documentation, especially the
493 file NOTICE, with what you distribute or provide a clear indica‐
494 tion where people can get a copy of the documentation; and
495 2. Please give credit where credit is due citing the version
497 and original authors properly; and
498 3. Please do not give anyone the impression that the original
500 authors are providing a warranty of any kind.
501 If you would like to use major pieces of RasMol in some other
503 program, make modifications to RasMol, or in some other way make
504 what a lawyer would call a "derived work", you are not only per‐
505 mitted to do so, you are encouraged to do so. In addition to the
506 things we discussed above, please do the following:
507 4. Please explain in your documentation how what you did dif‐
509 fers from this version of RasMol; and
510 5. Please make your modified source code available.
512 This version of RasMol is _not_ in the public domain, but it is
514 given freely to the community in the hopes of advancing science.
515 If you make changes, please make them in a responsible manner,
516 and please offer us the opportunity to include those changes in
517 future versions of RasMol.
518 General Notice
521 The following notice applies to this work as a whole and to the
522 works included within it:
523 * Creative endeavors depend on the lively exchange of ideas.
525 There are laws and customs which establish rights and responsi‐
526 bilities for authors and the users of what authors create. This
527 notice is not intended to prevent you from using the software
528 and documents in this package, but to ensure that there are no
529 misunderstandings about terms and conditions of such use.
530 * Please read the following notice carefully. If you do not
532 understand any portion of this notice, please seek appropriate
533 professional legal advice before making use of the software and
534 documents included in this software package. In addition to
535 whatever other steps you may be obliged to take to respect the
536 intellectual property rights of the various parties involved, if
537 you do make use of the software and documents in this package,
538 please give credit where credit is due by citing this package,
539 its authors and the URL or other source from which you obtained
540 it, or equivalent primary references in the literature with the
541 same authors.
542 * Some of the software and documents included within this soft‐
544 ware package are the intellectual property of various parties,
545 and placement in this package does not in any way imply that any
546 such rights have in any way been waived or diminished.
547 * With respect to any software or documents for which a copy‐
549 right exists, ALL RIGHTS ARE RESERVED TO THE OWNERS OF SUCH
550 COPYRIGHT.
551 * Even though the authors of the various documents and software
553 found here have made a good faith effort to ensure that the doc‐
554 uments are correct and that the software performs according to
555 its documentation, and we would greatly appreciate hearing of
556 any problems you may encounter, the programs and documents and
557 any files created by the programs are provided **AS IS** without
558 any warranty as to correctness, merchantability or fitness for
559 any particular or general use.
560 * THE RESPONSIBILITY FOR ANY ADVERSE CONSEQUENCES FROM THE USE
562 OF PROGRAMS OR DOCUMENTS OR ANY FILE OR FILES CREATED BY USE OF
563 THE PROGRAMS OR DOCUMENTS LIES SOLELY WITH THE USERS OF THE PRO‐
564 GRAMS OR DOCUMENTS OR FILE OR FILES AND NOT WITH AUTHORS OF THE
565 PROGRAMS OR DOCUMENTS.
566 See the files GPL and RASLIC for two alternate ways to license
568 this package.
569 RasMol V2.6 Notice
572 The following notice applies to RasMol V 2.6 and older RasMol
573 versions.
574 Information in this document is subject to change without notice
576 and does not represent a commitment on the part of the supplier.
577 This package is sold/distributed subject to the condition that
578 it shall not, by way of trade or otherwise, be lent, re-sold,
579 hired out or otherwise circulated without the supplier's prior
580 consent, in any form of packaging or cover other than that in
581 which it was produced. No part of this manual or accompanying
582 software may be reproduced, stored in a retrieval system on
583 optical or magnetic disk, tape or any other medium, or transmit‐
584 ted in any form or by any means, electronic, mechanical, photo‐
585 copying, recording or otherwise for any purpose other than the
586 purchaser's personal use.
587 This product is not to be used in the planning, construction,
589 maintenance, operation or use of any nuclear facility nor the
590 flight, navigation or communication of aircraft or ground sup‐
591 port equipment. The author shall not be liable, in whole or in
592 part, for any claims or damages arising from such use, including
593 death, bankruptcy or outbreak of war.
594 IUCR Policy
597 The IUCr Policy for the Protection and the Promotion of the STAR
598 File and CIF Standards for Exchanging and Archiving Electronic
599 Data.
600 Overview
602 The Crystallographic Information File (CIF)[1] is a standard for
604 information interchange promulgated by the International Union
605 of Crystallography (IUCr). CIF (Hall, Allen & Brown, 1991) is
606 the recommended method for submitting publications to Acta Crys‐
607 tallographica Section C and reports of crystal structure deter‐
608 minations to other sections of Acta Crystallographica and many
609 other journals. The syntax of a CIF is a subset of the more gen‐
610 eral STAR File[2] format. The CIF and STAR File approaches are
611 used increasingly in the structural sciences for data exchange
612 and archiving, and are having a significant influence on these
613 activities in other fields.
614 Statement of intent
616 The IUCr's interest in the STAR File is as a general data inter‐
618 change standard for science, and its interest in the CIF, a con‐
619 formant derivative of the STAR File, is as a concise data
620 exchange and archival standard for crystallography and struc‐
621 tural science.
622 Protection of the standards
624 To protect the STAR File and the CIF as standards for inter‐
626 changing and archiving electronic data, the IUCr, on behalf of
627 the scientific community,
628 * holds the copyrights on the standards themselves,
630 * owns the associated trademarks and service marks, and
632 * holds a patent on the STAR File.
634 These intellectual property rights relate solely to the inter‐
636 change formats, not to the data contained therein, nor to the
637 software used in the generation, access or manipulation of the
638 data.
639 Promotion of the standards
641 The sole requirement that the IUCr, in its protective role,
643 imposes on software purporting to process STAR File or CIF data
644 is that the following conditions be met prior to sale or distri‐
645 bution.
646 * Software claiming to read files written to either the STAR
648 File or the CIF standard must be able to extract the pertinent
649 data from a file conformant to the STAR File syntax, or the CIF
650 syntax, respectively.
651 * Software claiming to write files in either the STAR File,
653 or the CIF, standard must produce files that are conformant to
654 the STAR File syntax, or the CIF syntax, respectively.
655 * Software claiming to read definitions from a specific data
657 dictionary approved by the IUCr must be able to extract any per‐
658 tinent definition which is conformant to the dictionary defini‐
659 tion language (DDL)[3] associated with that dictionary.
660 The IUCr, through its Committee on CIF Standards, will assist
662 any developer to verify that software meets these conformance
663 conditions.
664 Glossary of terms
666 [1] CIF:
668 is a data file conformant to the file syntax defined at
670 http://www.iucr.org/iucr-top/cif/spec/index.html
671 [2] STAR File:
673 is a data file conformant to the file syntax defined at
675 http://www.iucr.org/iucr-top/cif/spec/star/index.html
676 [3] DDL:
678 is a language used in a data dictionary to define data items in
680 terms of "attributes". Dictionaries currently approved by the
681 IUCr, and the DDL versions used to construct these dictionaries,
682 are listed at http://www.iucr.org/iucr-
683 top/cif/spec/ddl/index.html
684 Last modified: 30 September 2000
686 IUCr Policy Copyright (C) 2000 International Union of Crystal‐
688 lography
689 CBFLIB The following Disclaimer Notice applies to CBFlib V0.1, from
692 which this code in part is derived.
693 * The items furnished herewith were developed under the sponsor‐
695 ship of the U.S. Government. Neither the U.S., nor the U.S.
696 D.O.E., nor the Leland Stanford Junior University, nor their
697 employees, makes any warranty, express or implied, or assumes
698 any liability or responsibility for accuracy, completeness or
699 usefulness of any information, apparatus, product or process
700 disclosed, or represents that its use will not infringe pri‐
701 vately-owned rights. Mention of any product, its manufacturer,
702 or suppliers shall not, nor is it intended to, imply approval,
703 disapproval, or fitness for any particular use. The U.S. and the
704 University at all times retain the right to use and disseminate
705 the furnished items for any purpose whatsoever.
706 Notice 91 02 01
708 CIFPARSE
711 Portions of this software are loosely based on the CIFPARSE
712 software package from the NDB at Rutgers University. See
713 http://ndbserver.rutgers.edu/NDB/mmcif/software
715 CIFPARSE is part of the NDBQUERY application, a program compo‐
717 nent of the Nucleic Acid Database Project [ H. M. Berman, W. K.
718 Olson, D. L. Beveridge, J. K. Westbrook, A. Gelbin, T. Demeny,
719 S. H. Shieh, A. R. Srinivasan, and B. Schneider. (1992). The
720 Nucleic Acid Database: A Comprehensive Relational Database of
721 Three-Dimensional Structures of Nucleic Acids. Biophys J., 63,
722 751-759.], whose cooperation is gratefully acknowledged, espe‐
723 cially in the form of design concepts created by J. Westbrook.
724 Please be aware of the following notice in the CIFPARSE API:
726 This software is provided WITHOUT WARRANTY OF MERCHANTABILITY OR
728 FITNESS FOR A PARTICULAR PURPOSE OR ANY OTHER WARRANTY, EXPRESS
729 OR IMPLIED. RUTGERS MAKE NO REPRESENTATION OR WARRANTY THAT THE
730 SOFTWARE WILL NOT INFRINGE ANY PATENT, COPYRIGHT OR OTHER PRO‐
731 PRIETARY RIGHT.
732
735 RasMol is a molecular graphics program intended for the visualisation
736 of proteins, nucleic acids and small molecules. The program is aimed
737 at display, teaching and generation of publication quality images.
738 RasMol runs on wide range of architectures and operating systems
739 including Microsoft Windows, Apple Macintosh, UNIX and VMS systems.
740 UNIX and VMS versions require an 8, 24 or 32 bit colour X Windows dis‐
741 play (X11R4 or later). The X Windows version of RasMol provides
742 optional support for a hardware dials box and accelerated shared memory
743 communication (via the XInput and MIT-SHM extensions) if available on
744 the current X Server.
745 The program reads in a molecule coordinate file and interactively dis‐
747 plays the molecule on the screen in a variety of colour schemes and
748 molecule representations. Currently available representations include
749 depth-cued wireframes, 'Dreiding' sticks, spacefilling (CPK) spheres,
750 ball and stick, solid and strand biomolecular ribbons, atom labels and
751 dot surfaces.
752 Up to 5 molecules may be loaded and displayed at once. Any one or all
754 of
755 the molecules may be rotated and translated.
756 The RasMol help facility can be accessed by typing "help <topic>" or
758 "help <topic> <subtopic>" from the command line. A complete list of
759 RasMol commands may be displayed by typing "help commands". A single
760 question mark may also be used to abbreviate the keyword "help".
761 Please type "help notices" for important notices.
762
765 RasMol allows the execution of interactive commands typed at the Ras‐
766 Mol> prompt in the terminal window. Each command must be given on a
767 separate line. Keywords are case insensitive and may be entered in
768 either upper or lower case letters. All whitespace characters are
769 ignored except to separate keywords and their arguments.
770 All commands may be prefixed by a parenthesized atom expression to tem‐
772 porarily select certain atoms just for the execution of that one com‐
773 mand. After execution of the command, the previous selection is
774 restored except for the commands select , restrict and script.
775 The commands/keywords currently recognised by RasMol are given below.
777 Backbone
780 The RasMol backbone command permits the representation of a
781 polypeptide backbone as a series of bonds connecting the adja‐
782 cent alpha carbons of each amino acid in a chain. The display of
783 these backbone 'bonds' is turned on and off by the command
784 parameter in the same way as with the wireframe command. The
785 command backbone off turns off the selected 'bonds', and back‐
786 bone on or with a number turns them on. The number can be used
787 to specify the cylinder radius of the representation in either
788 Angstrom or RasMol units. A parameter value of 500 (2.0
789 Angstroms) or above results in a "Parameter value too large"
790 error. Backbone objects may be coloured using the RasMol colour
791 backbone command.
792 The reserved word backbone is also used as a predefined set
794 ("help sets") and as a parameter to the set hbond and set ssbond
795 commands. The RasMol command trace renders a smoothed backbone,
796 in contrast to backbone which connects alpha carbons with
797 straight lines.
798 The backbone may be displayed with dashed lines by use of the
800 backbone dash command.
801 Background
804 The RasMol background command is used to set the colour of the
805 "canvas" background. The colour may be given as either a colour
806 name or a comma separated triple of Red, Green and Blue (RGB)
807 components enclosed in square brackets. Typing the command help
808 colours will give a list of the predefined colour names recog‐
809 nised by RasMol. When running under X Windows, RasMol also
810 recognises colours in the X server's colour name database.
811 The background command is synonymous with the RasMol set back‐
813 ground command.
814 Bond The RasMol command bond <number> <number> + adds the designated
817 bond to the drawing, increasing the bond order if the bond
818 already exists. The command bond <number> <number> pick selects
819 the two atoms specified by the atom serial numbers as the two
820 ends of a bond around which the rotate bond <angle> command will
821 be applied. If no bond exists, it is created.
822 Rotation around a previously picked bond may be specified by the
824 rotate bond <angle> command, or may also be controlled with the
825 mouse, using the bond rotate on/off or the equivalent rotate
826 bond on/off commands.
827 Bulgarian
830 The RasMol Bulgarian command sets the menus and messages to the
831 Bulgarian versions.
832 This command may not work correctly unless appropriate fonts
834 have been installed. The commands Bulgarian, Chinese, English,
835 French, Italian, Russian and Spanish may be used to select Bul‐
836 garian, Chinese, English, French, Italian, Japanese, Russian and
837 Spanish menus and messages if the appropriate fonts have been
838 installed.
839 Cartoon
842 The RasMol cartoon command does a display of a molecule ribbons
843 as Richardson (MolScript) style protein cartoons, implemented as
844 thick (deep) ribbons. The easiest way to obtain a cartoon repre‐
845 sentation of a protein is to use the Cartoons option on the Dis‐
846 play menu. The cartoon command represents the currently selected
847 residues as a deep ribbon with width specified by the command's
848 argument. Using the command without a parameter results in the
849 ribbon's width being taken from the protein's secondary struc‐
850 ture, as described in the ribbons command. By default, the C-
851 termini of beta-sheets are displayed as arrow heads. This may be
852 enabled and disabled using the set cartoons command. The depth
853 of the cartoon may be adjusted using the set cartoons <number>
854 command. The set cartoons command without any parameters returns
855 these two options to their default values.
856 Centre The RasMol centre command defines the point about which the
859 rotate command and the scroll bars rotate the current molecule.
860 Without a parameter the centre command resets the centre of
861 rotation to be the centre of gravity of the molecule. If an atom
862 expression is specified, RasMol rotates the molecule about the
863 centre of gravity of the set of atoms specified by the expres‐
864 sion. Hence, if a single atom is specified by the expression,
865 that atom will remain 'stationary' during rotations.
866 Type help expression for more information on RasMol atom expres‐
868 sions.
869 Alternatively the centring may be given as a comma separated
871 triple of [CenX, CenY, CenZ] offsets in RasMol units (1/250 of
872 an Angstrom) from the centre of gravity. The triple must be
873 enclosed in square brackets.
874 The optional forms centre ... translate and centre ... center
876 may be used to specify use of a translated centre of rotation
877 (not necessarily in the centre of the canvas) or a centre of
878 rotation which is placed at the centre of the canvas. Starting
879 with RasMol 2.7.2, the default is to center the new axis on the
880 canvas.
881 Chinese
884 The RasMol Chinese command sets the menus and messages to the
885 Chinese versions.
886 This command may not work correctly unless appropriate fonts
888 have been installed. The commands Bulgarian, Chinese, English,
889 French, Italian, Russian and Spanish may be used to select Bul‐
890 garian, Chinese, English, French, Italian, Japanese, Russian and
891 Spanish menus and messages if the appropriate fonts have been
892 installed.
893 Clipboard
896 The RasMol clipboard command places a copy of the currently dis‐
897 played image on the local graphics 'clipboard'. Note: this com‐
898 mand is not yet supported on UNIX or VMS machines. It is
899 intended to make transfering images between applications easier
900 under Microsoft Windows or on an Apple Macintosh.
901 When using RasMol on a UNIX or VMS system this functionality may
903 be achieved by generating a raster image in a format that can be
904 read by the receiving program using the RasMol write command.
905 Colour Colour the atoms (or other objects) of the selected region. The
908 colour may be given as either a colour name or a comma separated
909 triple of Red, Green and Blue (RGB) components enclosed in
910 square brackets. Typing the command help colours will give a
911 list of all the predefined colour names recognised by RasMol.
912 Allowed objects are atoms, bonds, backbone, ribbons, labels,
914 dots, hbonds, map, and ssbonds. If no object is specified, the
915 default keyword atom is assumed. Some colour schemes are
916 defined for certain object types. The colour scheme none can be
917 applied to all objects except atoms and dots, stating that the
918 selected objects have no colour of their own, but use the colour
919 of their associated atoms (i.e. the atoms they connect). Atom
920 objects can also be coloured by alt, amino, chain, charge, cpk,
921 group, model, shapely, structure, temperature or user. Hydrogen
922 bonds can also be coloured by type and dot surfaces can also be
923 coloured by electrostatic potential. For more information type
924 help colour <colour>. Map objects may be coloured by specific
925 color of by nearest atom.
926 ColourMode
929 ColourMode allows the user to switch between using the new
930 colour method. At present, the new coloring technique is the
931 same as the old one, but to preserve compatibility for older
932 scripts it may be wise to add a "colormode on" near the top of
933 your script somewhere, if the script was designed for version
934 2.7.3 of RasMol or earlier. The new color method, when com‐
935 pleted, aims to fix a few bugs in the coloring routines.
936 Connect
939 The RasMol connect command is used to force RasMol to (re)calcu‐
940 late the connectivity of the current molecule. If the original
941 input file contained connectivity information, this is dis‐
942 carded. The command connect false uses a fast heuristic algo‐
943 rithm that is suitable for determining bonding in large bio-mol‐
944 ecules such as proteins and nucleic acids. The command connect
945 true uses a slower more accurate algorithm based upon covalent
946 radii that is more suitable to small molecules containing inor‐
947 ganic elements or strained rings. If no parameters are given,
948 RasMol determines which algorithm to use based on the number of
949 atoms in the input file. Greater than 255 atoms causes RasMol to
950 use the faster implementation. This is the method used to deter‐
951 mine bonding, if necessary, when a molecule is first read in
952 using the load command.
953 Defer The RasMol defer command adds the command given to the macro
956 with given name, if no name is given, the command is added to
957 the macro with a blank name. The command zap is a special case.
958 In that case the macro is erased. If no name is given the com‐
959 mand must begin with a selection, e.g. defer (selection).space‐
960 fill
961 The deferred commands accumulated under the given name can be
963 executed using the execute command
964 Define The RasMol define command allows the user to associate an arbi‐
967 trary set of atoms with a unique identifier. This allows the
968 definition of user-defined sets. These sets are declared stati‐
969 cally, i.e. once defined the contents of the set do not change,
970 even if the expression defining them depends on the current
971 transformation and representation of the molecule.
972 Depth The RasMol depth command enables, disables or positions the
975 back-clipping plane of the molecule. The program only draws
976 those portions of the molecule that are closer to the viewer
977 than the clipping plane. Integer values range from zero at the
978 very back of the molecule to 100 which is completely in front of
979 the molecule. Intermediate values determine the percentage of
980 the molecule to be drawn.
981 This command interacts with the slab <value> command, which
983 clips to the front of a given z-clipping plane.
984 Dots The RasMol dots command is used to generate a van der Waals' dot
987 surface around the currently selected atoms. Dot surfaces dis‐
988 play regularly spaced points on a sphere of van der Waals'
989 radius about each selected atom. Dots that would are 'buried'
990 within the van der Waals' radius of any other atom (selected or
991 not) are not displayed. The command dots on deletes any exist‐
992 ing dot surface and generates a dots surface around the cur‐
993 rently selected atom set with a default dot density of 100. The
994 command dots off deletes any existing dot surface. The dot den‐
995 sity may be specified by providing a numeric parameter between 1
996 and 1000. This value approximately corresponds to the number of
997 dots on the surface of a medium sized atom.
998 By default, the colour of each point on a dot surface is the
1000 colour of its closest atom at the time the surface is generated.
1001 The colour of the whole dot surface may be changed using the
1002 colour dots command.
1003 Echo The RasMol echo command is used to display a message in the Ras‐
1006 Mol command/terminal window. The string parameter may optionally
1007 be delimited in double quote characters. If no parameter is
1008 specified, the echo command displays a blank line. This command
1009 is particularly useful for displaying text from within a RasMol
1010 script file.
1011 English
1014 The RasMol English command sets the menus and messages to the
1015 English versions.
1016 This command may not work correctly unless appropriate fonts
1018 have been installed. The commands Bulgarian, Chinese, English,
1019 French, Italian, Russian and Spanish may be used to select Bul‐
1020 garian, Chinese, English, French, Italian, Japanese, Russian and
1021 Spanish menus and messages if the appropriate fonts have been
1022 installed.
1023 Execute
1026 The RasMol execute command:
1027 1. saves the old poise of the molecule (translation, rotation
1029 and zoom)
1030 2. executes the specified macro suppressing both screen updates
1032 and recording
1033 3. animates motion of the newly rendered molecule linearly from
1035 the old poise to the new poise
1036 The macro must have been previously defined by calls to the
1038 defer command.
1039 The animation of the motion depends on the prior settings of the
1041 record command.
1042 French The RasMol French command sets the menus and messages to the
1045 French versions.
1046 This command may not work correctly unless appropriate fonts
1048 have been installed. The commands Bulgarian, Chinese, English,
1049 French, Italian, Russian and Spanish may be used to select Bul‐
1050 garian, Chinese, English, French, Italian, Japanese, Russian and
1051 Spanish menus and messages if the appropriate fonts have been
1052 installed.
1053 HBonds The RasMol hbond command is used to represent the hydrogen bond‐
1056 ing of the protein molecule's backbone. This information is use‐
1057 ful in assessing the protein's secondary structure. Hydrogen
1058 bonds are represented as either dotted lines or cylinders
1059 between the donor and acceptor residues. The first time the
1060 hbond command is used, the program searches the structure of the
1061 molecule to find hydrogen bonded residues and reports the number
1062 of bonds to the user. The command hbonds on displays the
1063 selected 'bonds' as dotted lines, and the hbonds off turns off
1064 their display. The colour of hbond objects may be changed by the
1065 colour hbond command. Initially, each hydrogen bond has the
1066 colours of its connected atoms.
1067 By default the dotted lines are drawn between the accepting oxy‐
1069 gen and the donating nitrogen. By using the set hbonds command
1070 the alpha carbon positions of the appropriate residues may be
1071 used instead. This is especially useful when examining proteins
1072 in backbone representation.
1073 Help The RasMol help command provides on-line help on the given
1076 topic.
1077 Italian
1080 The RasMol Italian command sets the menus and messages to the
1081 Italian versions.
1082 This command may not work correctly unless appropriate fonts
1084 have been installed. The commands Bulgarian, Chinese, English,
1085 French, Italian, Russian and Spanish may be used to select Bul‐
1086 garian, Chinese, English, French, Italian, Japanese, Russian and
1087 Spanish menus and messages if the appropriate fonts have been
1088 installed.
1089 Japanese
1092 The RasMol Japanese command sets the menus and messages to the
1093 Japanese versions.
1094 This command may not work correctly unless appropriate fonts
1096 have been installed. The commands Bulgarian, Chinese, English,
1097 French, Italian, Russian and Spanish may be used to select Bul‐
1098 garian, Chinese, English, French, Italian, Japanese, Russian and
1099 Spanish menus and messages if the appropriate fonts have been
1100 installed.
1101 Label The RasMol label command allows an arbitrary formatted text
1104 string to be associated with each currently selected atom. This
1105 string may contain embedded 'expansion specifiers' which display
1106 properties of the atom being labelled. An expansion specifier
1107 consists of a '%' character followed by a single alphabetic
1108 character specifying the property to be displayed. An actual
1109 '%' character may be displayed by using the expansion specifier
1110 '%%'.
1111 Atom labelling for the currently selected atoms may be turned
1113 off with the command label off. By default, if no string is
1114 given as a parameter, RasMol uses labels appropriate for the
1115 current molecule.
1116 The colour of each label may be changed using the colour label
1118 command. By default, each label is drawn in the same colour as
1119 the atom to which it is attached. The size and spacing of the
1120 displayed text may be changed using the set fontsize command.
1121 The width of the strokes in the displayed text may be changed
1122 using the set fontstroke
1123 command.
1124 Load Load a molecule coordinate file into RasMol. Valid molecule file
1127 formats are pdb (Protein Data Bank format), mdl (Molecular
1128 Design Limited's MOL file format), alchemy (Tripos' Alchemy file
1129 format), mol2 (Tripos' Sybyl Mol2 file format), charmm (CHARMm
1130 file format), xyz (MSC's XMol XYZ file format), mopac (J. P.
1131 Stewart's MOPAC file format) or cif (IUCr CIF or mmCIF file for‐
1132 mat). If no file format is specified, PDB, CIF, or mmCIF is
1133 assumed by default. Up to 20 molecules may be loaded at a time.
1134 If CHEM_COMP ligand models are included in an mmCIF file, they
1135 will be loaded as NMR models, first giving the all the NMR mod‐
1136 els for model coordinates if specified and then giving all the
1137 NMR models for ideal model coordinates.
1138 To delete a molecule prior to loading another use the RasMol zap
1140 command. To select a molecule for manipulation use the RasMol
1141 molecule <n> command.
1142 The load command selects all the atoms in the molecule, centres
1144 it on the screen and renders it as a CPK coloured wireframe
1145 model. If the molecule contains no bonds (i.e. contains only
1146 alpha carbons), it is drawn as an alpha carbon backbone. If the
1147 file specifies fewer bonds than atoms, RasMol determines connec‐
1148 tivity using the connect command.
1149 The load inline command also allows the storing of atom coordi‐
1151 nates in scripts to allow better integration with WWW browsers.
1152 A load command executed inside a script file may specify the
1153 keyword inline instead of a conventional filename. This option
1154 specifies that the coordinates of the molecule to load are
1155 stored in the same file as the currently executing commands.
1156 Map The RasMol map commands manipulate electron density maps in
1159 coordination with the display of molecules. These commands are
1160 very memory intensive and may not work on machines with limited
1161 memory. Each molecule may have as many maps as available memory
1162 permits. Maps may be read from files or generated from Gaussian
1163 density distributions around atoms.
1164 map colour, to colour a map according to a given colour scheme,
1166 map generate, to generate a map from selected atoms based on
1167 pseudo-Gaussians, map level, to set the contouring level for
1168 selected maps, map load, to load a map from a file, map mask to
1169 designate a mask for the selected maps, map resolution, to set
1170 the resolution for contouring selected maps, map restrict, to
1171 select one or more maps and to disable all others, map save, to
1172 save map information to a file, map scale, control the scaling
1173 of pseudo-Gaussians when generating maps, map select, to select
1174 one or more maps, map show, to display information about one or
1175 more maps or about the parameters to be used in generating or
1176 loading the next map, map spacing, to set the spacing betwen
1177 contour lines of selected maps, map spread, to set the variance
1178 of the Gaussians for map generation as a fraction of the atomic
1179 radius, and map zap to delete previously generated or loaded
1180 maps.
1181 The effect of map generate and map load commands is modified by
1183 the map mask command which limits the portion of the display
1184 space that can be considered for display of maps.
1185 Map colour
1188 The RasMol map colour command colours the selected maps accord‐
1189 ing to the specified colour scheme. The colour scheme may be a
1190 colour name or and RBG triple in brackets, or the keyword atom
1191 to cause the map points to be coloured by the color of the near‐
1192 est atom.
1193 Map generate
1196 The RasMol map generate command generates a map from whatever
1197 atoms are currently selected, by summing electron densities
1198 approximated by Gaussian distributions. The height of each
1199 Gaussian is determined by the setting of the map scale command.
1200 In the default of map scale true, each Gaussian has a height
1201 proportional element type of the atom. If the optional 'LRSurf'
1202 parameter is given or if map scale false has been executed, each
1203 Gaussian is scaled so that the Gaussian contour level 1 is at
1204 the van der Waals radius. In either case a standard deviation
1205 determined by the most recently specified spread or resolution
1206 is used. If a non-zero spread has been given the radius of the
1207 atom is multiplied by the spread to find the standard deviation.
1208 The default is 2/3rds. If a resolution has been given, the
1209 spread is inferred as 2/3rds of the resolution.
1210 For example, if the resolution is given as 1., and the atom in
1212 question is a Carbon with a van der Waals radius of 468 RasMol
1213 units (1.87 Angstroms), the inferred spead is .6667, and the
1214 standard deviation of the Gaussian is taken as 1.25 Angstroms.
1215 If the spread has been set to zero, the spread for each atom is
1217 determined from the van der Waals radius and the probe atom
1218 radius to simulate the effect of a Lee-Richards surface.
1219 If no specific map was given by the map selector, the new map is
1221 given the next available map number.
1222 If a specific map was given by the map selector, the new map
1224 replaces that map. If more than one map was given by the map
1225 selector, the new map replaces the lowest numbered of the
1226 selected maps. In any case the new map becomes the currently
1227 selected map.
1228 The map is displayed as dots, mesh or a surface, depending on
1230 the last map rendering mode selected or the mode selected on the
1231 command itself.
1232 Map level
1235 The RasMol map level command sets the contour level to be used
1236 in creating subsequent representations of generated or loaded
1237 maps. If the keyword MEAN in used the level is relative to the
1238 mean of the map data. Otherwise the level is absolute.
1239 In general, a lower level results in a map containing more of
1241 the displayed volume, while a higher level results in a map con‐
1242 taining less of the displayed volume.
1243 Map load
1246 The RasMol map load command loads a map file into RasMol. The
1247 valid formats are CCP4 map format and imgCIF format.
1248 If no specific map was given by the map selector, the new map is
1250 given the next available map number.
1251 If a specific map was given by the map selector, the new map
1253 replaces that map. If more than one map was given by the map
1254 selector, the new map replaces the lowest numbered of the
1255 selected maps. In any case the new map becomes the currently
1256 selected map.
1257 The map is displayed as dots, mesh or a surface depending on the
1259 last map rendering mode selected.
1260 Map mask
1263 The RasMol map mask command specifies a mask to be used to limit
1264 the display space to be used for making representations of other
1265 maps or removes an earlier mask specification.
1266 The 'selected' option indicates that the mask is to be created
1268 from the currently selected atoms. The '<number>' option indi‐
1269 cates that the mask is to be copied from the map of the number
1270 specified. The 'none' option removes the previously specified
1271 mask, if any.
1272 The map selector specifies the map or maps to which the speci‐
1274 fied mask will the applied. For example, 'map next mask
1275 selected' specifies that the currently selected atoms are to be
1276 used to generate a mask to be applied to any maps created by
1277 subsequent 'map load' or 'map generate' commands.
1278 Any map may be used as a mask. The portions of the mask map
1280 greater than than or equal to the average value of the mask map
1281 allow the values of the map being masked to be used as given.
1282 The portions of the mask map lower than the average value of the
1283 mask map cause the values of the map being masked to be treated
1284 as if they were equal to the lowest data value of the map being
1285 masked.
1286 Map resolution
1289 The RasMol map resolution command specifies the resolution in
1290 RasMol units or, if a number containing a decimal point is
1291 given, the resolution in Angstroms to be used in generating and
1292 in representing maps.
1293 The resolution is used at the map spacing for representations of
1295 maps, indicating the separation between contour levels (see the
1296 map spacing command) and to infer the map spread to be used in
1297 generated maps from selected atoms (see the map spread command).
1298 The map spread is set to two thirds of the specified resolution.
1299 Map restrict
1302 The RasMol map restrict command selects particular maps to make
1303 them active for subsequent map commands. This is similar to the
1304 map select command, but does disables the display of the maps
1305 that were not selected.
1306 Map save
1309 The RasMol map save command saves an imgCIF map file.
1310 If no specific map was given by the map selector, the currently
1312 selected maps and their masks are written to the file, one map
1313 and mask pair per data block.
1314 Map scale
1317 The RasMol map scale command selects the scaling of pseudo-Gaus‐
1318 sians in the map generate commands. In the default of map scale
1319 true, each Gaussian has a height proportional element type of
1320 the atom. If map scale false has been executed, each Gaussian
1321 is scaled so that the Gaussian contour level 1 is at the van der
1322 Waals radius. In either case a standard deviation determined by
1323 the most recently specified spread or resolution is used.
1324 Map select
1327 The RasMol map select command selects particular maps to make
1328 them active for subsequent map commands. This is similar to the
1329 map restrict command, but does not disable the display of the
1330 maps that were not selected.
1331 If the optional atom parameter is given, the command selects the
1333 atoms with centres closest to the map points. The radius of the
1334 search may be specified by the parameter search_radius. The
1335 default is to look for atoms within 4 Angstroms plus the probe
1336 radius. If the optional within parameter is given, the new
1337 selection is taken from within the currently selected atoms. If
1338 the options add parameter is given, the new selection is added
1339 to the currently selected atoms. The default is to search
1340 within all atoms.
1341 Map show
1344 The RasMol map show command causes information about the maps
1345 specified by the map selector to be written to the command win‐
1346 dow.
1347 Map spacing
1350 The RasMol map spacing command specifies the spacing to be used
1351 between contour lines in creating representations of maps. The
1352 spacing is typically
1353 given in Angstroms with a decimal point, but may also be speci‐
1354 fied in RasMol units (250ths of an Angstom) as an integer. For
1355 maps loaded in grid coordinates that spacing is parallel to the
1356 cell edges. The default spacing is one half Angstrom.
1357 Map spread
1360 The RasMol map spread command specifies the reciprocal of the
1361 number of standard deviations per radius to be used in generat‐
1362 ing maps as sums of Gaussians centered on atomic positions. The
1363 default spread is one two thirds (i.e. each radius covers 1.5
1364 standard deviations).
1365 If the spread has been set to zero, the spread for each atom is
1367 determined from the van der Waals radius and the probe atom
1368 radius to simulate the effect of a Lee-Richards surface.
1369 Map zap
1372 The RasMol map zap command removes the data and representations
1373 of the maps specified by the map selector. The map numbers of
1374 maps that have not been removed are not changed.
1375 Molecule
1378 The RasMol molecule command selects one of up to 5 previously
1379 loaded molecules for active manipulation. While all the mol‐
1380 cules are displayed and may be rotated collectively (see the
1381 rotate all command), only one molecule at a time time is active
1382 for manipulation by the commands which control the details of
1383 rendering.
1384 Monitor
1387 The RasMol monitor command allows the display of distance moni‐
1388 tors. A distance monitor is a dashed (dotted) line between an
1389 arbitrary pair of atoms, optionally labelled by the distance
1390 between them. The RasMol command monitor <number> <number> adds
1391 such a distance monitor between the two atoms specified by the
1392 atom serial numbers given as parameters
1393 Distance monitors are turned off with the command monitors off.
1395 By default, monitors display the distance between its two end
1396 points as a label at the centre of the monitor. These distance
1397 labels may be turned off with the command set monitors off, and
1398 re-enabled with the command set monitors on. Like most other
1399 representations, the colour of a monitor is taken from the
1400 colour of its end points unless specified by the colour monitors
1401 command.
1402 Distance monitors may also be added to a molecule interactively
1404 with the mouse, using the set picking monitor command. Clicking
1405 on an atom results in its being identified on the rasmol command
1406 line. In addition every atom picked increments a modulo counter
1407 such that, in monitor mode, every second atom displays the dis‐
1408 tance between this atom and the previous one. The shift key may
1409 be used to form distance monitors between a fixed atom and sev‐
1410 eral consecutive positions. A distance monitor may also be
1411 removed (toggled) by selecting the appropriate pair of atom end
1412 points a second time.
1413 Notoggle
1416 The RasMol NoToggle command enables or disables the use of the
1417 toggle ability that is used by some of the other RasMol com‐
1418 mands. When no boolean value is specified, NoToggle mode is
1419 ENABLED. When NoToggle mode is ENABLED, all toggle functional‐
1420 ity is DISABLED. To turn it off, one must explicitly set notog‐
1421 gle off.
1422 Some commands which use the toggle feature are: ColourMode.
1424 More functions that utilize this capability may be added at a
1425 later date.
1426 Pause The RasMol pause command is used in script files to stop the
1429 script file for local manipulation by a mouse, until any key is
1430 pushed to restart the script file. Wait is synonymous with
1431 pause. This command may be executed in RasMol script files to
1432 suspend the sequential execution of commands and allow the user
1433 to examine the current image. When RasMol executes a pause
1434 command in a script file, it suspends execution of the rest of
1435 the file, refreshes the image on the screen and allows the
1436 manipulation of the image using the mouse and scroll bars, or
1437 resizing of the graphics window. Once a key is pressed, control
1438 returns to the script file at the line following the pause com‐
1439 mand. While a script is suspended the molecule may be rotated,
1440 translated, scaled, slabbed and picked as usual, but all menu
1441 commands are disabled.
1442 Play The RasMol play command specifies the recording medium from
1445 which to play back a movie. The playback frame start time is
1446 given in seconds to millisecond precision. Since we are working
1447 on computers, the medium is specified as a set of files, each
1448 marked with the playback frame start time in milliseconds as
1449 part of the name. The place in the name at which to look for the
1450 playback frame start time in milliseconds is marked by the char‐
1451 acters "ssssss" with an appropriate number of digits. RasMol
1452 accepts either upper or lower case s's or decimal digits to mark
1453 the place for the time. The play off and play eject commands
1454 effectively remove the specified medium from use. If no medium
1455 is specified, play off suspends playing and play on resumes
1456 playing. Normally play starts immediately and runs to the end
1457 of the medium. However, if play off and/or or some combination
1458 of play from and play until is entered before play type medium,
1459 those settings will be used.
1460 As of release 2.7.5, RasMol support play from scripts and data
1462 files.
1463 Print The RasMol print command sends the currently displayed image to
1466 the local default printer using the operating system's native
1467 printer driver. Note: this command is not yet supported under
1468 UNIX or VMS. It is intended to take advantage of Microsoft Win‐
1469 dows and Apple Macintosh printer drivers. For example, this
1470 allows images to be printed directly on a dot matrix printer.
1471 When using RasMol on a UNIX or VMS system this functionality may
1473 be achieved by either generating a PostScript file using the
1474 RasMol write ps or write vectps commands and printing that or
1475 generating a raster image file and using a utility to dump that
1476 to the local printer.
1477 Quit Exit from the RasMol program. The RasMol commands exit and quit
1480 are synonymous, except within nested scripts. In that case,
1481 exit terminates only the current level, while quit terminates
1482 all nested levels of scripts.
1483 Record The RasMol record command specifies the recording medium to hold
1486 the movie. Since we are working on computers, the medium is
1487 specified as a template for a set of files, each marked with the
1488 playback frame start time in milliseconds (rather than as sec‐
1489 onds to avoid embedding a decimal point) as part of the name.
1490 The place in the name to be replaced with the playback frame
1491 start time in milliseconds is marked by the characters "ssssss"
1492 with an appropriate number of digits. RasMol accepts either
1493 upper or lower case s's or decimal digits to mark the place for
1494 the time. The record off commands remove the specified medium
1495 from use. If no medium is specified, record off suspends record‐
1496 ing and record on resumes recording with the next available time
1497 on the same medium. The screen is the default medium and is, by
1498 default, on. Writing to disk must be explicitly specified so
1499 that the disk does not get filled up unintentionally. The type
1500 of a recording medium may be an image type such as gif, pict or
1501 png to record the actual screen images or script to record the
1502 RasMol commands used to generate the frames.
1503 Normally recording starts at playback frame start time 0 sec‐
1505 onds. A non-zero starting time in seconds can be specified with
1506 the record from command as in record from 25 or record from
1507 37.25 to help in organizing scenes of movies to be assembled
1508 later in an appropriate order. The record until command allows
1509 an upper limit to be set on recording time in seconds. The
1510 default is to have no limit. Issuing the commands
1511 record from 600
1513 record until 1800
1515 would result in a 20 minute movie segment intended to start 10
1517 minutes into a longer movie. These commands allow control over
1518 rewriting selected time segments.
1519 Refresh
1522 The RasMol refresh command redraws the current image. This is
1523 useful in scripts to ensure application of a complex list of
1524 parameter changes.
1525 Renumber
1528 The RasMol renumber command sequentially numbers the residues in
1529 a macromolecular chain. The optional parameter specifies the
1530 value of the first residue in the sequence. By default, this
1531 value is one. For proteins, each amino acid is numbered consecu‐
1532 tively from the N terminus to the C terminus. For nucleic acids,
1533 each base is numbered from the 5' terminus to the 3' terminus.
1534 All chains in the current database are renumbered and gaps in
1535 the original sequence are ignored. The starting value for num‐
1536 bering may be negative.
1537 Reset The RasMol reset command restores the original viewing transfor‐
1540 mation and centre of rotation. The scale is set to its default
1541 value, zoom 100, the centre of rotation is set to the geometric
1542 centre of the currently loaded molecule, centre all, this centre
1543 is translated to the middle of the screen and the viewpoint set
1544 to the default orientation.
1545 This command should not be mistaken for the RasMol zap command
1547 which deletes the currently stored molecule, returning the pro‐
1548 gram to its initial state.
1549 Restrict
1552 The RasMol restrict command both defines the currently selected
1553 region of the molecule and disables the representation of (most
1554 of) those parts of the molecule no longer selected. All subse‐
1555 quent RasMol commands that modify a molecule's colour or repre‐
1556 sentation affect only the currently selected region. The parame‐
1557 ter of a restrict command is a RasMol atom expression that is
1558 evaluated for every atom of the current molecule. This command
1559 is very similar to the RasMol select command, except restrict
1560 disables the wireframe, spacefill and backbone representations
1561 in the non-selected region.
1562 Type "help expression" for more information on RasMol atom
1564 expressions or see section Atom Expressions.
1565 Ribbons
1568 The RasMol ribbons command displays the currently loaded protein
1569 or nucleic acid as a smooth solid "ribbon" surface passing along
1570 the backbone of the protein. The ribbon is drawn between each
1571 amino acid whose alpha carbon is currently selected. The colour
1572 of the ribbon is changed by the RasMol colour ribbon command. If
1573 the current ribbon colour is none (the default), the colour is
1574 taken from the alpha carbon at each position along its length.
1575 The width of the ribbon at each position is determined by the
1577 optional parameter in the usual RasMol units. By default the
1578 width of the ribbon is taken from the secondary structure of the
1579 protein or a constant value of 720 (2.88 Angstroms) for nucleic
1580 acids. The default width of protein alpha helices and beta
1581 sheets is 380 (1.52 Angstroms) and 100 (0.4 Angstroms) for turns
1582 and random coil. The secondary structure assignment is either
1583 from the PDB file or calculated using the DSSP algorithm as used
1584 by the structure command. This command is similar to the RasMol
1585 command strands which renders the biomolecular ribbon as paral‐
1586 lel depth-cued curves.
1587 Rotate Rotate the molecule about the specified axis. Permitted values
1590 for the axis parameter are "x", "y", "z" and "bond". The inte‐
1591 ger parameter states the angle in degrees for the structure to
1592 be rotated. For the X and Y axes, positive values move the clos‐
1593 est point up and right, and negative values move it down and
1594 left, respectively. For the Z axis, a positive rotation acts
1595 clockwise and a negative angle anti-clockwise.
1596 Alternatively, this command may be used to specify which rota‐
1598 tions the mouse or dials will control. If rotate bond true is
1599 selected, the horizontal scroll bar will control rotation around
1600 the axis selected by the bond src dst pick command. If rotate
1601 all true is selected, and multiple molecules have been loaded,
1602 then all molecules will rotate together. In all other cases,
1603 the mouseand dials control the the rotation of the molecule
1604 selected by the molecule n command.
1605 Russian
1608 The RasMol Russian command sets the menus and messages to the
1609 Russian versions.
1610 This command may not work correctly unless appropriate fonts
1612 have been installed. The commands Bulgarian, Chinese, English,
1613 French, Italian, Russian and Spanish may be used to select Bul‐
1614 garian, Chinese, English, French, Italian, Japanese, Russian and
1615 Spanish menus and messages if the appropriate fonts have been
1616 installed.
1617 Save Save the currently selected set of atoms in a Protein Data Bank
1620 (PDB), MDL, Alchemy(tm) or XYZ format file. The distinction
1621 between this command and the RasMol write command has been
1622 dropped. The only difference is that without a format specifier
1623 the save command generates a PDB file and the write command gen‐
1624 erates a GIF image.
1625 Script The RasMol script command reads a set of RasMol commands sequen‐
1628 tially from a text file and executes them. This allows sequences
1629 of commonly used commands to be stored and performed by single
1630 command. A RasMol script file may contain a further script com‐
1631 mand up to a maximum "depth" of 10, allowing complicated
1632 sequences of actions to be executed. RasMol ignores all charac‐
1633 ters after the first '#' character on each line allowing the
1634 scripts to be annotated. Script files are often also annotated
1635 using the RasMol echo command.
1636 The most common way to generate a RasMol script file is to use
1638 the write script or write rasmol commands to output the sequence
1639 of commands that are needed to regenerate the current view, rep‐
1640 resentation and colouring of the currently displayed molecule.
1641 The RasMol command source is synonymous with the script command.
1643 Select Define the currently selected region of the molecule. All subse‐
1646 quent RasMol commands that manipulate a molecule or modify its
1647 colour or representation only affect the currently selected
1648 region. The parameter of a select command is a RasMol expression
1649 that is evaluated for every atom of the current molecule. The
1650 currently selected (active) region of the molecule are those
1651 atoms that cause the expression to evaluate true. To select the
1652 whole molecule use the RasMol command select all. The behaviour
1653 of the select command without any parameters is determined by
1654 the RasMol hetero and hydrogen parameters.
1655 Type "help expression" for more information on RasMol atom
1657 expressions or see section Atom Expressions.
1658 Set The RasMol set command allows the user to alter various internal
1661 program parameters such as those controlling rendering options.
1662 Each parameter has its own set or permissible parameter options.
1663 Typically, omitting the paramter option resets that parameter to
1664 its default value. A list of valid parameter names is given
1665 below.
1666 Show The RasMol show command display details of the status of the
1669 currently loaded molecule. The command show information lists
1670 the molecule's name, classification, PDB code and the number of
1671 atoms, chains, groups it contains. If hydrogen bonding, disul‐
1672 phide bridges or secondary structure have been determined, the
1673 number of hbonds, ssbonds, helices, ladders and turns are also
1674 displayed, respectively. The command show centre shows any non-
1675 zero centering values selected by the centre [CenX, CenY, CenZ]
1676 command. The command show phipsi shows the phi and psi angles of
1677 the currently selected residues and the omega angles of cis pep‐
1678 tide bonds. The command show RamPrint (or 'show RPP' or 'show
1679 RamachandranPrinterPlot') shows a simple Ramachandran printer
1680 plot in the style of Frances Bernstein's fisipl program. The
1681 command show rotation (or 'show rot' or 'show 'rotate') shows
1682 the currently selected values of z, y, x and bond rotations, if
1683 any. The command show selected (or 'show selected group' or
1684 'show selected chain' or 'show selected atom' ) shows the
1685 groups (default), chains or atoms of the current selection. The
1686 command show sequence lists the residues that comprise each
1687 chain of the molecule. The command show symmetry shows the
1688 space group and unit cell of the molecule. The command show
1689 translation shows any non-zero translation values selected by
1690 the translate <axis> <value> command. The command show zoom
1691 shows any non-zero zoom value selected by the zoom <value> com‐
1692 mand.
1693 Slab The RasMol slab command enables, disables or positions the z-
1696 clipping plane of the molecule. The program only draws those
1697 portions of the molecule that are further from the viewer than
1698 the slabbing plane. Integer values range from zero at the very
1699 back of the molecule to 100 which is completely in front of the
1700 molecule. Intermediate values determine the percentage of the
1701 molecule to be drawn.
1702 This command interacts with the depth <value> command, which
1704 clips to the rear of a given z-clipping plane.
1705 Spacefill
1708 The RasMol spacefill command is used to represent all of the
1709 currently selected atoms as solid spheres. This command is used
1710 to produce both union-of-spheres and ball-and-stick models of a
1711 molecule. The command, spacefill true, the default, represents
1712 each atom as a sphere of van der Waals radius. The command
1713 spacefill off turns off the representation of the selected atom
1714 as spheres. A sphere radius may be specified as an integer in
1715 RasMol units (1/250th Angstrom) or a value containing a decimal
1716 point. A value of 500 (2.0 Angstroms) or greater results in a
1717 "Parameter value too large" error.
1718 The temperature option sets the radius of each sphere to the
1720 value stored in its temperature field. Zero or negative values
1721 have no effect and values greater than 2.0 are truncated to 2.0.
1722 The user option allows the radius of each sphere to be specified
1723 by additional lines in the molecule's PDB file using Raster 3D's
1724 COLOUR record extension.
1725 The RasMol command cpk is synonymous with the spacefill command.
1727 The RasMol command cpknew is synonymous with the spacefill com‐
1729 mand, except that a slightly different set of colours is used.
1730 Spanish
1733 The RasMol Spanish command sets the menus and messages to the
1734 Spanish versions.
1735 This command may not work correctly unless appropriate fonts
1737 have been installed. The commands Bulgarian, Chinese, English,
1738 French, Italian, Russian and Spanish may be used to select Bul‐
1739 garian, Chinese, English, French, Italian, Japanese, Russian and
1740 Spanish menus and messages if the appropriate fonts have been
1741 installed.
1742 SSBonds
1745 The RasMol ssbonds command is used to represent the disulphide
1746 bridges of the protein molecule as either dotted lines or cylin‐
1747 ders between the connected cysteines. The first time that the
1748 ssbonds command is used, the program searches the structure of
1749 the protein to find half-cysteine pairs (cysteines whose sul‐
1750 phurs are within 3 Angstroms of each other) and reports the num‐
1751 ber of bridges to the user. The command ssbonds on displays the
1752 selected "bonds" as dotted lines, and the command ssbonds off
1753 disables the display of ssbonds in the currently selected area.
1754 Selection of disulphide bridges is identical to normal bonds,
1755 and may be adjusted using the RasMol set bondmode command. The
1756 colour of disulphide bonds may be changed using the colour
1757 ssbonds command. By default, each disulphide bond has the
1758 colours of its connected atoms.
1759 By default disulphide bonds are drawn between the sulphur atoms
1761 within the cysteine groups. By using the set ssbonds command the
1762 position of the cysteine's alpha carbons may be used instead.
1763 Star The RasMol star command is used to represent all of the cur‐
1766 rently selected atoms as stars (six strokes, one each in the x,
1767 -x, y, -y, z and -z directions). The commands select not bonded
1768 followed by star 75 are useful to mark unbonded atoms in a wire‐
1769 frame display with less overhead than provided by spacefill 75.
1770 This can be done automatically for all subsequent wireframe dis‐
1771 plays with the command set bondmode not bonded.
1772 The command star true, the default, represents each atom as a
1774 star with strokes length equal to van der Waals radius. The
1775 command star off turns off the representation of the selected
1776 atom as stars. A star stroke length may be specified as an inte‐
1777 ger in RasMol units (1/250th Angstrom) or a value containing a
1778 decimal point. A value of 500 (2.0 Angstroms) or greater results
1779 in a "Parameter value too large" error.
1780 The temperature option sets the stroke length of each star to
1782 the value stored in its temperature field. Zero or negative val‐
1783 ues have no effect and values greater than 2.0 are truncated to
1784 2.0. The user option allows the stroke length of each star to
1785 be specified by additional lines in the molecule's PDB file
1786 using Raster 3D's COLOUR record extension.
1787 The RasMol spacefill command can be used for more artistic ren‐
1789 dering of atoms as spheres.
1790 Stereo The RasMol stereo command provides side-by-side stereo display
1793 of images. Stereo viewing of a molecule may be turned on (and
1794 off) either by selecting Stereo from the Options menu, or by
1795 typing the commands stereo on or stereo off.
1796 Starting with RasMol version 2.7.2.1, the Stereo menu selection
1798 and the command stereo without arguments cycle from the initial
1799 state of stereo off to stereo on in cross-eyed mode to stereo on
1800 in wall-eyed mode and then back to stereo off.
1801 The separation angle between the two views may be adjusted with
1803 the set stereo [-] <number> command, where positive values
1804 result in crossed eye viewing and negative values in relaxed
1805 (wall-eyed) viewing. The inclusion of [-] <number> in the
1806 stereo command, as for example in stereo 3 or stereo -5, also
1807 controls angle and direction.
1808 The stereo command is only partially implemented. When stereo is
1810 turned on, the image is not properly recentred. (This can be
1811 done with a translate x -<number>
1812 command.) It is not supported in vector PostScript output
1813 files, is not saved by the write script command, and in general
1814 is not yet properly interfaced with several other features of
1815 the program.
1816 Strands
1819 The RasMol strands command displays the currently loaded protein
1820 or nucleic acid as a smooth "ribbon" of depth-cued curves pass‐
1821 ing along the backbone of the protein. The ribbon is composed of
1822 a number of strands that run parallel to one another along the
1823 peptide plane of each residue. The ribbon is drawn between each
1824 amino acid whose alpha carbon is currently selected. The colour
1825 of the ribbon is changed by the RasMol colour ribbon command. If
1826 the current ribbon colour is none (the default), the colour is
1827 taken from the alpha carbon at each position along its length.
1828 The central and outermost strands may be coloured independently
1829 using the colour ribbon1 and colour ribbon2 commands, respec‐
1830 tively. The number of strands in the ribbon may be altered using
1831 the RasMol set strands command.
1832 The width of the ribbon at each position is determined by the
1834 optional parameter in the usual RasMol units. By default the
1835 width of the ribbon is taken from the secondary structure of the
1836 protein or a constant value of 720 for nucleic acids (which pro‐
1837 duces a ribbon 2.88 Angstroms wide). The default width of pro‐
1838 tein alpha helices and beta sheets is 380 (1.52 Angstroms) and
1839 100 (0.4 Angstroms) for turns and random coil. The secondary
1840 structure assignment is either from the PDB file or calculated
1841 using the DSSP algorithm as used by the structure command. This
1842 command is similar to the RasMol command ribbons which renders
1843 the biomolecular ribbon as a smooth shaded surface.
1844 Structure
1847 The RasMol structure command calculates secondary structure
1848 assignments for the currently loaded protein. If the original
1849 PDB file contained structural assignment records (HELIX, SHEET
1850 and TURN) these are discarded. Initially, the hydrogen bonds of
1851 the current molecule are found, if this hasn't been done
1852 already. The secondary structure is then determined using Kabsch
1853 and Sander's DSSP algorithm. Once finished the program reports
1854 the number of helices, strands and turns found.
1855 Surface
1858 The RasMol surface command renders a Lee-Richards molecular sur‐
1859 face resulting from rolling a probe atom on the selected atoms.
1860 The value given specifies the radius of the probe. If given in
1861 the first form, the evolute of the surface of the probe is shown
1862 (the solvent excluded surface). If given in the second form,
1863 the envelope of the positions of the center of the probe is
1864 shown (the solvent accessible surface).
1865 Trace The RasMol trace command displays a smooth spline between con‐
1868 secutive alpha carbon positions. This spline does not pass
1869 exactly through the alpha carbon position of each residue, but
1870 follows the same path as ribbons, strands and cartoons. Note
1871 that residues may be displayed as ribbons, strands, cartoons or
1872 as a trace. Enabling one of these representations disables the
1873 others. However, a residue may be displayed simultaneously as
1874 backbone and as one of the above representations. This may
1875 change in future versions of RasMol. Prior to version 2.6,
1876 trace was synonymous with backbone.
1877 Trace temperature displays the backbone as a wider cylinder at
1879 high temperature factors and thinner at lower. This representa‐
1880 tion is useful to X-ray crystallographers and NMR spectro‐
1881 scopists.
1882 Translate
1885 The RasMol translate command moves the position of the centre of
1886 the molecule on the screen. The axis parameter specifies along
1887 which axis the molecule is to be moved and the integer parameter
1888 specifies the absolute position of the molecule centre from the
1889 middle of the screen. Permitted values for the axis parameter
1890 are "x", "y" and "z". Displacement values must be between -100
1891 and 100 which correspond to moving the current molecule just off
1892 the screen. A positive "x" displacement moves the molecule to
1893 the right, and a positive "y" displacement moves the molecule
1894 down the screen. The pair of commands translate x 0 and trans‐
1895 late y 0 centres the molecule on the screen.
1896 UnBond The RasMol command unbond <number> <number> removes the desig‐
1899 nated bond from the drawing.
1900 The command unbond without arguments removes a bond previously
1902 picked by the bond <number> <number> pick command.
1903 Wireframe
1906 The RasMol wireframe command represents each bond within the
1907 selected region of the molecule as a cylinder, a line or a
1908 depth-cued vector. The display of bonds as depth-cued vectors
1909 (drawn darker the further away from the viewer) is turned on by
1910 the command wireframe or wireframe on. The selected bonds are
1911 displayed as cylinders by specifying a radius either as an inte‐
1912 ger in RasMol units or containing a decimal point as a value in
1913 Angstroms. A parameter value of 500 (2.0 Angstroms) or above
1914 results in an "Parameter value too large" error. Bonds may be
1915 coloured using the colour bonds command.
1916 If the selected bonds involved atoms of alternate conformers
1918 then the bonds are narrowed in the middle to a radius of .8 of
1919 the specified radius (or to the radius specifed as the optional
1920 second parameter).
1921 Non-bonded atoms, which could become invisible in an ordinary
1923 wireframe display can be marked by a preceding set bondmode not
1924 bonded command. If nearly co-linear bonds to atoms cause them
1925 to be difficult to see in a wireframe display, the set bondmode
1926 all command will add markers for all atoms in subsequent wire‐
1927 frame command executions.
1928 Write Write the current image to a file in a standard format. Cur‐
1931 rently supported image file formats include bmp (Microsoft bit‐
1932 map) and gif (Compuserve GIF), iris (IRIS RGB), ppm (Portable
1933 Pixmap), ras (Sun rasterfile), ps and epsf (Encapsulated Post‐
1934 Script), monops (Monochrome Encapsulated PostScript), pict
1935 (Apple PICT), vectps (Vector Postscript). The write command may
1936 also be used to generate command scripts for other graphics pro‐
1937 grams. The format script writes out a file containing the RasMol
1938 script commands to reproduce the current image. The format
1939 molscript writes out the commands required to render the current
1940 view of the molecule as ribbons in Per Kraulis' Molscript pro‐
1941 gram and the format kinemage the commands for David Richardson's
1942 program Mage. The following formats are useful for further pro‐
1943 cessing: povray (POVRay 2), povray3 (POVRay 3 -- under develop‐
1944 ment), vrml (VRML file). Finally, several formats are provided
1945 to provide phi-psi data for listing or for phipsi (phi-psi data
1946 as an annotated list with cis omegas), ramachan and RDF and
1947 RamachandranDataFile (phi-psi data as columns of numbers for
1948 gnuplot), RPP and RamachandranPrinterPlot (phi-psi data as a
1949 printer plot).
1950 The distinction between this command and the RasMol save command
1952 has been dropped. The only difference is that without a format
1953 specifier the save command generates a PDB file and the write
1954 command generates a GIF image.
1955 Zap Deletes the contents of the current database and resets parame‐
1958 ter variables to their initial default state.
1959 Zoom Change the magnification of the currently displayed image. Bool‐
1962 ean parameters either magnify or reset the scale of current mol‐
1963 ecule. An integer parameter specifies the desired magnification
1964 as a percentage of the default scale. The minimum parameter
1965 value is 10; the maximum parameter value is dependent upon the
1966 size of the molecule being displayed. For medium sized proteins
1967 this is about 500.
1968
1971 RasMol has a number of internal parameters that may be modified using
1972 the set command. These parameters control a number of program options
1973 such as rendering options and mouse button mappings.
1974 picking play.fps radius record.aps
1976 Set Ambient
1979 The RasMol ambient parameter is used to control the amount of
1980 ambient (or surrounding) light in the scene. The ambient value
1981 must be between 0 and 100. It controls the percentage intensity
1982 of the darkest shade of an object. For a solid object, this is
1983 the intensity of surfaces facing away from the light source or
1984 in shadow. For depth-cued objects this is the intensity of
1985 objects furthest from the viewer.
1986 This parameter is commonly used to correct for monitors with
1988 different "gamma values" (brightness), to change how light or
1989 dark a hardcopy image appears when printed or to alter the feel‐
1990 ing of depth for wireframe or ribbon representations.
1991 Set Axes
1994 The RasMol axes parameter controls the display of orthogonal
1995 coordinate axes on the current display. The coordinate axes are
1996 those used in the molecule data file, and the origin is the cen‐
1997 tre of the molecule's bounding box. The set axes command is sim‐
1998 ilar to the commands set boundbox and set unitcell that display
1999 the bounding box and the crystallographic unit cell, respec‐
2000 tively.
2001 Set Backfade
2004 The RasMol backfade parameter is used to control backfade to the
2005 specified background colour, rather than black. This is con‐
2006 trolled by the commands set backfade on and set backfade off.
2007 For example, this may be used to generate depth-cued images that
2008 fade to white, rather than black.
2009 Set Background
2012 The RasMol background parameter is used to set the colour of the
2013 "canvas" background. The colour may be given as either a colour
2014 name or a comma separated triple of Red, Green, Blue (RGB) com‐
2015 ponents enclosed in square brackets. Typing the command help
2016 colours will give a list of the predefined colour names recog‐
2017 nised by RasMol. When running under X Windows, RasMol also
2018 recognises colours in the X server's colour name database.
2019 The command set background is synonymous with the RasMol command
2021 background.
2022 Set BondMode
2025 The RasMol set bondmode command controls the mechanism used to
2026 select individual bonds and modifies the display of bonded and
2027 non-bonded atoms by subsequent wireframe commands.
2028 When using the select and restrict commands, a given bond will
2030 be selected if i) the bondmode is or and either of the connected
2031 atoms is selected, or ii) the bondmode is and and both atoms
2032 connected by the bond are selected. Hence an individual bond may
2033 be uniquely identified by using the command set bondmode and and
2034 then uniquely selecting the atoms at both ends.
2035 The bondmode [all | none | not bonded] commands add star 75 or
2037 spacefill 75 markers for the designated atoms to wireframe dis‐
2038 plays. Stars are used when the specified wireframe radius is
2039 zero.
2040 Set Bonds
2043 The RasMol bonds parameter is used to control display of double
2044 and triple bonds as multiple lines or cylinders. Currently
2045 bond orders are only read from MDL Mol files, Sybyl Mol2 format
2046 files, Tripos Alchemy format files, CIF and mmCIF, and suitable
2047 PDB files. Double (and triple) bonds are specified in some
2048 PDB files by specifying a given bond twice (and three times) in
2049 CONECT records. The command set bonds on enables the display
2050 of bond orders, and the command set bonds off disables them.
2051 Set BoundBox
2054 The RasMol boundbox parameter controls the display of the cur‐
2055 rent molecule's bounding box on the display. The bounding box is
2056 orthogonal to the data file's original coordinate axes. The set
2057 boundbox command is similar to the commands set axes and set
2058 unitcell that display orthogonal coordinate axes and the bound‐
2059 ing box, respectively.
2060 Set Cartoon
2063 The RasMol cartoon parameter is used to control display of the
2064 cartoon version of the ribbons display. By default, the C-ter‐
2065 mini of beta-sheets are displayed as arrow heads. This may be
2066 enabled and disabled using the set cartoons <boolean> command.
2067 The depth of the cartoon may be adjusted using the cartoons
2068 <number> command. The set cartoons command without any parame‐
2069 ters returns these two options to
2070 their default values.
2071 Set CisAngle
2074 The RasMol cisangle parameter controls the cutoff angle for
2075 identifying cis peptide
2076 bonds. If no value is given, the cutoff is set to 90 degrees.
2077 Set Display
2080 This command controls the display mode within RasMol. By
2081 default, set display normal, RasMol displays the molecule in the
2082 representation specified by the user. The command set display
2083 selected changes the display mode such that the molecule is tem‐
2084 porarily drawn so as to indicate currently selected portion of
2085 the molecule. The user specified colour scheme and representa‐
2086 tion remains unchanged. In this representation all selected
2087 atoms are shown in yellow and all non selected atoms are shown
2088 in blue. The colour of the background is also changed to a dark
2089 grey to indicate the change of display mode. This command is
2090 typically only used by external Graphical User Interfaces
2091 (GUIs).
2092 Set FontSize
2095 The RasMol set fontsize command is used to control the size of
2096 the characters that form atom labels. This value corresponds to
2097 the height of the displayed character in pixels. The maximum
2098 value of fontsize is 48 pixels, and the default value is 8 pix‐
2099 els high. Fixed or proportional spacing may be selected by
2100 appending the "FS" or "PS" modifiers, respectively. The default
2101 is "FS". To display atom labels on the screen use the RasMol
2102 label command and to change the colour of displayed labels, use
2103 the colour labels command.
2104 Set FontStroke
2107 The RasMol set fontstroke command is used to control the size of
2108 the stroke width of the characters that form atom labels. This
2109 value is the radius in pixels of cylinders used to form the
2110 strokes. The special value of "0" is the default used for the
2111 normal single pixel stroke width, which allows for rapid drawing
2112 and rotation of the image. Non-zero values are provided to
2113 allow for more artistic atom labels for publication at the
2114 expense of extra time in rendering the image.
2115 When wider strokes are used, a larger font size is recommend,
2117 e.g. by using the RasMol set fontsize 24 PS command, followed
2118 by set fontstroke 2
2119 To display atom labels on the screen use the RasMol label com‐
2121 mand, and to change the colour of displayed labels use the
2122 colour labels command.
2123 Set HBonds
2126 The RasMol hbonds parameter determines whether hydrogen bonds
2127 are drawn between the donor and acceptor atoms of the hydrogen
2128 bond, set hbonds sidechain or between the alpha carbon atoms of
2129 the protein backbone and between the phosphorous atoms of the
2130 nucleic acid backbone, set hbonds backbone. The actual display
2131 of hydrogen bonds is controlled by the hbonds command. Drawing
2132 hydrogen bonds between protein alpha carbons or nucleic acid
2133 phosphorous atoms is useful when the rest of the molecule is
2134 shown in only a schematic representation such as backbone, rib‐
2135 bons or strands. This parameter is similar to the RasMol
2136 ssbonds parameter.
2137 Set Hetero
2140 The RasMol hetero parameter is used to modify the 'default' be‐
2141 haviour of the RasMol select command, i.e. the behaviour of
2142 select without any parameters. When this value is false, the
2143 default select region does not include any heterogeneous atoms
2144 (refer to the predefined set hetero ). When this value is true,
2145 the default select region may contain hetero atoms. This parame‐
2146 ter is similar to the RasMol hydrogen parameter which determines
2147 whether hydrogen atoms should be included in the default set. If
2148 both hetero and hydrogen are true, select without any parameters
2149 is equivalent to select all.
2150 Set HourGlass
2153 The RasMol hourglass parameter allows the user to enable and
2154 disable the use of the 'hour glass' cursor used by RasMol to
2155 indicate that the program is currently busy drawing the next
2156 frame. The command set hourglass on enables the indicator,
2157 whilst set hourglass off prevents RasMol from changing the cur‐
2158 sor. This is useful when spinning the molecule, running a
2159 sequence of commands from a script file or using interprocess
2160 communication to execute complex sequences of commands. In these
2161 cases a 'flashing' cursor may be distracting.
2162 Set Hydrogen
2165 The RasMol hydrogen parameter is used to modify the "default"
2166 behaviour of the RasMol select command, i.e. the behaviour of
2167 select without any parameters. When this value is false, the
2168 default select region does not include any hydrogen, deuterium
2169 or tritium atoms (refer to the predefined set hydrogen ). When
2170 this value is true, the default select region may contain hydro‐
2171 gen atoms. This parameter is similar to the RasMol hetero param‐
2172 eter which determines whether heterogeneous atoms should be
2173 included in the default set. If both hydrogen and hetero are
2174 true, select without any parameters is equivalent to select all.
2175 Set Kinemage
2178 The RasMol set kinemage command controls the amount of detail
2179 stored in a Kinemage output file generated by the RasMol write
2180 kinemage command. The output kinemage files are intended to be
2181 displayed by David Richardson's Mage program. set kinemage
2182 false, the default, only stores the currently displayed repre‐
2183 sentation in the generated output file. The command set kinemage
2184 true, generates a more complex Kinemage that contains both the
2185 wireframe and backbone representations as well as the coordinate
2186 axes, bounding box and crystal unit cell.
2187 Set Menus
2190 The RasMol set menus command enables the canvas window's menu
2191 buttons or menu bar. This command is typically only used by
2192 graphical user interfaces or to create as large an image as pos‐
2193 sible when using Microsoft Windows.
2194 Set Monitor
2197 The RasMol set monitor command enables monitors. The distance
2198 monitor labels may be turned off with the command set monitor
2199 off, and re-enabled with the command set monitor on.
2200 Set Mouse
2204 The RasMol set mouse command sets the rotation, translation,
2205 scaling and zooming mouse bindings. The default value is rasmol
2206 which is suitable for two button mice (for three button mice the
2207 second and third buttons are synonymous); X-Y rotation is con‐
2208 trolled by the first button, and X-Y translation by the second.
2209 Additional functions are controlled by holding a modifier key on
2210 the keyboard. [Shift] and the first button performs scaling,
2211 [shift] and the second button performs Z-rotation, and [control]
2212 and the first mouse button controls the clipping plane. The
2213 insight and quanta options provide the same mouse bindings as
2214 other packages for experienced users.
2215 Set Picking
2218 The RasMol set picking series of commands affects how a user may
2219 interact with a molecule displayed on the screen in RasMol.
2220 Enabling/Disabling Atom Identification Picking: Clicking on an
2222 atom with the mouse results in identification and the display of
2223 its residue name, residue number, atom name, atom serial number
2224 and chain in the command window. This behavior may be disabled
2225 with the command set picking none and restored with the command
2226 set picking ident. The command set picking coord adds the
2227 atomic coordinates of the atom to the display.
2228 Disabling picking, by using set picking off is useful when exe‐
2230 cuting the pause command in RasMol scripts as it prevents the
2231 display of spurious message on the command line while the script
2232 is suspended.
2233 Measuring Distances, Angles and Torsions: Interactive measure‐
2235 ment of distances, angles and torsions is achieved using the
2236 commands: set picking distance, set picking monitor, set picking
2237 angle and set picking torsion, respectively. In these modes,
2238 clicking on an atom results in it being identified on the rasmol
2239 command line. In addition every atom picked increments a modulo
2240 counter such that in distance mode, every second atom displays
2241 the distance (or distance monitor) between this atom and the
2242 previous one. In angle mode, every third atom displays the angle
2243 between the previous three atoms and in torsion mode every
2244 fourth atom displays the torsion between the last four atoms. By
2245 holding down the shift key while picking an atom, this modulo
2246 counter is not incremented and allows, for example, the dis‐
2247 tances of consecutive atoms from a fixed atom to be displayed.
2248 See the monitor command for how to control the display of dis‐
2249 tance monitor lines and labels.
2250 Labelling Atoms with the Mouse: The mouse may also be used to
2252 toggle the display of an atom label on a given atom. The RasMol
2253 command set picking label removes a label from a picked atom if
2254 it already has one or displays a concise label at that atom
2255 position otherwise.
2256 Centring Rotation with the Mouse: A molecule may be centred on a
2258 specified atom position using the RasMol commands set picking
2259 centre or set picking center. In this mode, picking an atom
2260 causes all futher rotations to be about that point.
2261 Picking a Bond as a Rotation Axis: Any bond may be picked as an
2263 axis of rotation for the portion of the molecule beyond the sec‐
2264 ond atom selected. This feature should be used with caution,
2265 since, naturally, it changes the conformation of the molecule.
2266 After executing set picking bond or using the equivalent "Pick
2267 Bond" in the "Settings" menu, a bond to be rotated is picked
2268 with the same sort of mouse clicks as are used for picking atoms
2269 for a distance measurement. Normally this should be done where
2270 a bond exists, but if no bond exists, it will be added. The
2271 bond cannot be used for rotation if it is part of a ring of any
2272 size. All bonds selected for rotation are remembered so that
2273 they can be properly reported when writing a script, but only
2274 the most recently selected bond may be actively rotated.
2275 Enabling Atom/Group/Chain Selection Picking: Atoms, groups and
2277 chains may be selected (as if with the select command), with the
2278 set picking atom, set picking group, set picking chain commands.
2279 For each of these commands, the shift key may be used to have a
2280 new selection added to the old, and the control key may be used
2281 to have a new selection deleted from the old. When the set pick‐
2282 ing atom command is given, the mouse can be used to pick or to
2283 drag a box around the atoms for which selection is desired.
2284 When the set picking group command is given, picking any an atom
2285 will cause selection of all atoms which agree in residue number
2286 with the picked atom, even if in different chains. When the set
2287 picking chain command is given, picking any atom will cause
2288 selection of all atoms which agree in chain identifier with the
2289 picked atom.
2290 Set Play
2293 The RasMol set play.fps command gives the number of frames per
2294 second for playback by the play command (default 24 frames per
2295 second).
2296 In the current release of RasMol, the play timing is not con‐
2298 trolled by this parameter.
2299 Set Radius
2302 The RasMol set radius command is used to alter the behaviour of
2303 the RasMol dots command depending upon the value of the solvent
2304 parameter. When solvent is true, the radius parameter controls
2305 whether a true van der Waals' surface is generated by the dots
2306 command. If the value of radius is anything other than zero,
2307 that value is used as the radius of each atom instead of its
2308 true vdW value. When the value of solvent is true, this parame‐
2309 ter determines the 'probe sphere' (solvent) radius. The parame‐
2310 ter may be given as an integer in rasmol units or containing a
2311 decimal point in Angstroms. The default value of this parameter
2312 is determined by the value of solvent and changing solvent
2313 resets radius to its new default value.
2314 Set Record
2317 The RasMol set record.aps gives the maximum on-screen velocity
2318 in Angstroms per second in animating translations, rotations and
2319 zooms (default 10 A/second).
2320 The RasMol set record.aps command gives number of frames per
2322 second for recording by the record command (default 24 frames
2323 per second).
2324 The RasMol set record.dwell command sets the time in seconds to
2326 dwell on a change in appearance (default .5 sec).
2327 Set ShadePower
2330 The shadepower parameter (adopted from RasTop) determines the
2331 shade repartition (the contrast) used in rendering solid
2332 objects. This value between 0 and 100 adjusts shading on an
2333 object surface oriented along the direction to the light source.
2334 Changing the shadepower parameter does not change the maximum or
2335 the minimum values of this shading, as does changing the ambient
2336 parameter. A value of 100 concentrates the light on the top of
2337 spheres, giving a highly specular, glassy rendering (see the
2338 specpower parameter). A value of 0 distributes the light on the
2339 entire object.
2340 This implementation of shadepower differs from the one in RasTop
2342 only in the choice of range (0 to 100 versus -20 to 20 in
2343 RasTop).
2344 Set Shadow
2347 The RasMol set shadow command enables and disables ray-tracing
2348 of the currently rendered image. Currently only the spacefill‐
2349 ing representation is shadowed or can cast shadows. Enabling
2350 shadowing will automatically disable the Z-clipping (slabbing)
2351 plane using the command slab off. Ray-tracing typically takes
2352 about several seconds for a moderately sized protein. It is
2353 recommended that shadowing be normally disabled whilst the mole‐
2354 cule is being transformed or manipulated, and only enabled once
2355 an appropiate viewpoint is selected, to provide a greater
2356 impression of depth.
2357 Set SlabMode
2360 The RasMol slabmode parameter controls the rendering method of
2361 objects cut by the slabbing (z-clipping) plane. Valid slabmode
2362 parameters are "reject", "half", "hollow", "solid" and "sec‐
2363 tion".
2364 Set Solvent
2367 The RasMol set solvent command is used to control the behaviour
2368 of the RasMol dots command. Depending upon the value of the sol‐
2369 vent parameter, the dots command either generates a van der
2370 Waals' or a solvent accessible surface around the currently
2371 selected set of atoms. Changing this parameter automatically
2372 resets the value of the RasMol radius parameter. The command
2373 set solvent false, the default value, indicates that a van der
2374 Waals' surface should be generated and resets the value of
2375 radius to zero. The command set solvent true indicates that a
2376 'Connolly' or 'Richards' solvent accessible surface should be
2377 drawn and sets the radius parameter, the solvent radius, to 1.2
2378 Angstroms (or 300 RasMol units).
2379 Set Specular
2382 The RasMol set specular command enables and disables the display
2383 of specular highlights on solid objects drawn by RasMol. Specu‐
2384 lar highlights appear as white reflections of the light source
2385 on the surface of the object. The current RasMol implementation
2386 uses an approximation function to generate this highlight.
2387 The specular highlights on the surfaces of solid objects may be
2389 altered by using the specular reflection coefficient, which is
2390 altered using the RasMol set specpower command.
2391 Set SpecPower
2394 The specpower parameter determines the shininess of solid
2395 objects rendered by RasMol. This value between 0 and 100 adjusts
2396 the reflection coefficient used in specular highlight calcula‐
2397 tions. The specular highlights are enabled and disabled by the
2398 RasMol set specular command. Values around 20 or 30 produce
2399 plastic looking surfaces. High values represent more shiny sur‐
2400 faces such as metals, while lower values produce more dif‐
2401 fuse/dull surfaces.
2402 Set SSBonds
2405 The RasMol ssbonds parameter determines whether disulphide
2406 bridges are drawn between the sulphur atoms in the sidechain
2407 (the default) or between the alpha carbon atoms in the backbone
2408 of the cysteines residues. The actual display of disulphide
2409 bridges is controlled by the ssbonds command. Drawing disulphide
2410 bridges between alpha carbons is useful when the rest of the
2411 protein is shown in only a schematic representation such as
2412 backbone, ribbons or strands. This parameter is similar to the
2413 RasMol hbonds parameter.
2414 Set Stereo
2417 The RasMol set stereo parameter controls the separation between
2418 the left and right images. Turning stereo on and off doesn't re‐
2419 position the centre of the molecule.
2420 Stereo viewing of a molecule may be turned on (and off) either
2422 by selecting Stereo from the Options menu, or by typing the com‐
2423 mands stereo on or stereo off.
2424 The separation angle between the two views may be adjusted with
2426 the set stereo [-] <number> command, where positive values
2427 result in crossed eye viewing and negative values in relaxed
2428 (wall-eyed) viewing. Currently, stereo viewing is not supported
2429 in vector PostScript output files.
2430 Set Strands
2433 The RasMol strands parameter controls the number of parallel
2434 strands that are displayed in the ribbon representations of pro‐
2435 teins. The permissible values for this parameter are 1, 2, 3, 4,
2436 5 and 9. The default value is 5. The number of strands is con‐
2437 stant for all ribbons being displayed. However, the ribbon
2438 width (the separation between strands) may be controlled on a
2439 residue by residue basis using the RasMol ribbons command.
2440 Set Transparent
2443 The RasMol transparent parameter controls the writing of trans‐
2444 parent GIFs by the write gif <filename> command. This may be
2445 controlled by the set transparent on and set transparent off
2446 commands.
2447 Set UnitCell
2450 The RasMol unitcell parameter controls the display of the crys‐
2451 tallographic unit cell on the current display. The crystal cell
2452 is only enabled if the appropriate crystal symmetry information
2453 is contained in the PDB, CIF or mmCIF data file. The RasMol com‐
2454 mand show symmetry display details of the crystal's space group
2455 and unit cell axes. The set unitcell command is similar to the
2456 commands set axes and set boundbox that display orthogonal coor‐
2457 dinate axes and the bounding box, respectively.
2458 Set VectPS
2461 The RasMol vectps parameter is use to control the way in which
2462 the RasMol write command generates vector PostScript output
2463 files. The command set vectps on enables the use of black out‐
2464 lines around spheres and cylinder bonds producing "cartoon-like"
2465 high resolution output. However, the current implementation of
2466 RasMol incorrectly cartoons spheres that are intersected by more
2467 than one other sphere. Hence "ball and stick" models are ren‐
2468 dered correctly but not large spacefilling spheres models. Car‐
2469 toon outlines can be disabled, the default, by the command set
2470 vectps off.
2471 Set Write
2474 The RasMol write parameter controls the use of the save and
2475 write commands within scripts, but it may only be executed from
2476 the command line. By default, this value is false, prohibiting
2477 the generation of files in any scripts executed at start-up
2478 (such as those launched from a WWW browser). However, animators
2479 may start up RasMol interactively: type set write on and then
2480 execute a script to generate each frame using the source com‐
2481 mand.
2482
2485 RasMol atom expressions uniquely identify an arbitrary group of atoms
2486 within a molecule. Atom expressions are composed of either primitive
2487 expressions, predefined sets, comparison operators, within expressions,
2488 or logical (boolean) combinations of the above expression types.
2489 The logical operators allow complex queries to be constructed out of
2491 simpler ones using the standard boolean connectives and, or and not.
2492 These may be abbreviated by the symbols "&", "|" and "!", respectively.
2493 Parentheses (brackets) may be used to alter the precedence of the oper‐
2494 ators. For convenience, a comma may also be used for boolean disjunc‐
2495 tion.
2496 The atom expression is evaluated for each atom, hence protein and back‐
2498 bone selects protein backbone atoms, not the protein and [nucleic] acid
2499 backbone atoms!
2500 Primitive Expressions
2503 RasMol primitive expressions are the fundamental building blocks
2504 of atom expressions. There are two types of primitive expres‐
2505 sion. The first type is used to identify a given residue number
2506 or range of residue numbers. A single residue is identified by
2507 its number (position in the sequence), and a range is specified
2508 by lower and upper bounds separated by a hyphen character. For
2509 example select 5,6,7,8 is also select 5-8. Note that this
2510 selects the given residue numbers in all macromolecule chains.
2511 The second type of primitive expression specifies a sequence of
2513 fields that must match for a given atom. The first part speci‐
2514 fies a residue (or group of residues) and an optional second
2515 part specifies the atoms within those residues. The first part
2516 consists of a residue name, optionally followed by a residue
2517 number and/or chain identifier.
2518 The second part consists of a period character followed by an
2520 atom name. An atom name may be up to four alphabetic or numeric
2521 characters. An optional semicolon followed by an alternate con‐
2522 formation identifier may be appended. An optional slash fol‐
2523 lowed by a model number may also be appended.
2524 An asterisk may be used as a wild card for a whole field and a
2526 question mark as a single character wildcard.
2527 Comparison Operators
2530 Parts of a molecule may also be distinguished using equality,
2531 inequality and ordering operators on their properties. The for‐
2532 mat of such comparison expression is a property name, followed
2533 by a comparison operator and then an integer value.
2534 The atom properties that may be used in RasMol are atomno for
2536 the atom serial number, elemno for the atom's atomic number
2537 (element), resno for the residue number, radius for the space‐
2538 fill radius in RasMol units (or zero if not represented as a
2539 sphere) and temperature for the PDB isotropic temperature value.
2540 The equality operator is denoted either "=" or "==". The
2542 inequality operator as either "<>", "!=" or "/=". The ordering
2543 operators are "<" for less than, "<=" for less than or equal to,
2544 ">" for greater than, and ">" for greater than or equal to.
2545 Within Expressions
2548 A RasMol within expression allows atoms to be selected on their
2549 proximity to another set of atoms. A within expression takes two
2550 parameters separated by a comma and surrounded by parentheses.
2551 The first argument is an integer value called the "cut-off" dis‐
2552 tance of the within expression and the second argument is any
2553 valid atom expression. The cut-off distance is expressed in
2554 either integer RasMol units or Angstroms containing a decimal
2555 point. An atom is selected if it is within the cut-off distance
2556 of any of the atoms defined by the second argument. This allows
2557 complex expressions to be constructed containing nested within
2558 expressions.
2559 For example, the command select within(3.2,backbone) selects any
2561 atom within a 3.2 Angstrom radius of any atom in a protein or
2562 nucleic acid backbone. Within expressions are particularly use‐
2563 ful for selecting the atoms around an active site.
2564 Predefined Sets
2567 RasMol atom expressions may contain predefined sets. These sets
2568 are single keywords that represent portions of a molecule of
2569 interest. Predefined sets are often abbreviations of primitive
2570 atom expressions. In some cases the use of predefined sets
2571 allows selection of areas of a molecule that could not otherwise
2572 be distinguished. A list of the currently predefined sets is
2573 given below. In addition to the sets listed here, RasMol also
2574 treats element names (and their plurals) as predefined sets con‐
2575 taining all atoms of that element type, i.e. the command select
2576 oxygen is equivalent to the command select elemno=8.
2577
2580 AT Set This set contains the atoms in the complementary nucleotides
2581 adenosine and thymidine (A and T, respectively). All nucleotides
2582 are classified as either the set at or the set cg This set is
2583 equivalent to the RasMol atom expressions a,t, and nucleic and
2584 not cg.
2585 Acidic Set
2588 The set of acidic amino acids. These are the residue types Asp
2589 and Glu. All amino acids are classified as either acidic, basic
2590 or neutral. This set is equivalent to the RasMol atom expres‐
2591 sions asp, glu and amino and not (basic or neutral).
2592 Acyclic Set
2595 The set of atoms in amino acids not containing a cycle or ring.
2596 All amino acids are classified as either cyclic or acyclic.
2597 This set is equivalent to the RasMol atom expression amino and
2598 not cyclic.
2599 Aliphatic Set
2602 This set contains the aliphatic amino acids. These are the
2603 amino acids Ala, Gly, Ile, Leu and Val. This set is equivalent
2604 to the RasMol atom expression ala, gly, ile, leu, val.
2605 Alpha Set
2608 The set of alpha carbons in the protein molecule. This set is
2609 approximately equivalent to the RasMol atom expression *.CA.
2610 This command should not be confused with the predefined set
2611 helix which contains the atoms in the amino acids of the pro‐
2612 tein's alpha helices.
2613 Amino Set
2616 This set contains all the atoms contained in amino acid
2617 residues. This is useful for distinguishing the protein from
2618 the nucleic acid and heterogeneous atoms in the current molecule
2619 database.
2620 Aromatic Set
2623 The set of atoms in amino acids containing aromatic rings.
2624 These are the amino acids His, Phe, Trp and Tyr. Because they
2625 contain aromatic rings all members of this set are member of the
2626 predefined set cyclic. This set is equivalent to the RasMol
2627 atom expressions his, phe, trp, tyr and cyclic and not pro.
2628 Backbone Set
2631 This set contains the four atoms of each amino acid that form
2632 the polypeptide N-C-C-O backbone of proteins, and the atoms of
2633 the sugar phosphate backbone of nucleic acids. Use the RasMol
2634 predefined sets protein and nucleic to distinguish between the
2635 two forms of backbone. Atoms in nucleic acids and proteins are
2636 either backbone or sidechain. This set is equivalent to the
2637 RasMol expression (protein or nucleic) and not sidechain.
2638 The predefined set mainchain is synonymous with the set back‐
2640 bone.
2641 Basic Set
2644 The set of basic amino acids. These are the residue types Arg,
2645 His and Lys. All amino acids are classified as either acidic,
2646 basic or neutral. This set is equivalent to the RasMol atom
2647 expressions arg, his, lys and amino and not (acidic or neutral).
2648 Bonded Set
2651 This set contain all the atoms in the current molecule database
2652 that are bonded to at least one other atom.
2653 Buried Set
2656 This set contains the atoms in those amino acids that tend (pre‐
2657 fer) to be buried inside protein, away from contact with solvent
2658 molecules. This set refers to the amino acids preference and not
2659 the actual solvent accessibility for the current protein. All
2660 amino acids are classified as either surface or buried. This
2661 set is equivalent to the RasMol atom expression amino and not
2662 surface.
2663 CG Set This set contains the atoms in the complementary nucleotides
2666 cytidine and guanosine (C and G, respectively). All nucleotides
2667 are classified as either the set at or the set cg This set is
2668 equivalent to the RasMol atom expressions c,g and nucleic and
2669 not at.
2670 Charged Set
2673 This set contains the charged amino acids. These are the amino
2674 acids that are either acidic or basic. Amino acids are classi‐
2675 fied as being either charged or neutral. This set is equivalent
2676 to the RasMol atom expressions acidic or basic and amino and not
2677 neutral.
2678 Cyclic Set
2681 The set of atoms in amino acids containing a cycle or rings.
2682 All amino acids are classified as either cyclic or acyclic.
2683 This set consists of the amino acids His, Phe, Pro, Trp and Tyr.
2684 The members of the predefined set aromatic are members of this
2685 set. The only cyclic but non-aromatic amino acid is proline.
2686 This set is equivalent to the RasMol atom expressions his, phe,
2687 pro, trp, tyr and aromatic or pro and amino and not acyclic.
2688 Cystine Set
2691 This set contains the atoms of cysteine residues that form part
2692 of a disulphide bridge, i.e. half cystines. RasMol automatically
2693 determines disulphide bridges, if neither the predefined set
2694 cystine nor the RasMol ssbonds command have been used since the
2695 molecule was loaded. The set of free cysteines may be determined
2696 using the RasMol atom expression cys and not cystine.
2697 Helix Set
2700 This set contains all atoms that form part of a protein alpha
2701 helix as determined by either the PDB file author or Kabsch and
2702 Sander's DSSP algorithm. By default, RasMol uses the secondary
2703 structure determination given in the PDB file if it exists.
2704 Otherwise, it uses the DSSP algorithm as used by the RasMol
2705 structure command.
2706 This predefined set should not be confused with the predefined
2708 set alpha which contains the alpha carbon atoms of a protein.
2709 Hetero Set
2712 This set contains all the heterogeneous atoms in the molecule.
2713 These are the atoms described by HETATM entries in the PDB file.
2714 These typically contain water, cofactors and other solvents and
2715 ligands. All hetero atoms are classified as either ligand or
2716 solvent atoms. These heterogeneous solvent atoms are further
2717 classified as either water or ions.
2718 Hydrogen Set
2721 This predefined set contains all the hydrogen, deuterium and
2722 tritium atoms of the current molecule. This predefined set is
2723 equivalent to the RasMol atom expression elemno=1.
2724 Hydrophobic Set
2727 This set contains all the hydrophobic amino acids. These are
2728 the amino acids Ala, Leu, Val, Ile, Pro, Phe, Met and Trp. All
2729 amino acids are classified as either hydrophobic or polar. This
2730 set is equivalent to the RasMol atom expressions ala, leu, val,
2731 ile, pro, phe, met, trp and amino and not polar.
2732 Ions Set
2735 This set contains all the heterogeneous phosphate and sulphate
2736 ions in the current molecule data file. A large number of these
2737 ions are sometimes associated with protein and nucleic acid
2738 structures determined by X-ray crystallography. These atoms tend
2739 to clutter an image. All hetero atoms are classified as either
2740 ligand or solvent atoms. All solvent atoms are classified as
2741 either water or ions.
2742 Large Set
2745 All amino acids are classified as either small, medium or large.
2746 This set is equivalent to the RasMol atom expression amino and
2747 not (small or medium).
2748 Ligand Set
2751 This set contains all the heterogeneous cofactor and ligand moi‐
2752 eties that are contained in the current molecule data file.
2753 This set is defined to be all hetero atoms that are not solvent
2754 atoms. Hence this set is equivalent to the RasMol atom expres‐
2755 sion hetero and not solvent.
2756 Medium Set
2759 All amino acids are classified as either small, medium or large.
2760 This set is equivalent to the RasMol atom expression amino and
2761 not (large or small).
2762 Neutral Set
2765 The set of neutral amino acids. All amino acids are classified
2766 as either acidic, basic or neutral. This set is equivalent to
2767 the RasMol atom expression amino and not (acidic or basic).
2768 Nucleic Set
2771 The set of all atoms in nucleic acids, which consists of the
2772 four nucleotide bases adenosine, cytidine, guanosine and thymi‐
2773 dine (A, C, G and T, respectively). All neucleotides are classi‐
2774 fied as either purine or pyrimidine. This set is equivalent to
2775 the RasMol atom expressions a,c,g,t and purine or pyrimidine.
2776 The symbols for RNA nucleotides (U, +U, I, 1MA, 5MC, OMC, 1MG,
2777 2MG, M2G, 7MG, OMG, YG, H2U, 5MU, and PSU) are also recognized
2778 as members of this set.
2779 Polar Set
2782 This set contains the polar amino acids. All amino acids are
2783 classified as either hydrophobic or polar. This set is equiva‐
2784 lent to the RasMol atom expression amino and not hydrophobic.
2785 Protein Set
2788 The set of all atoms in proteins. This consists of the RasMol
2789 predefined set amino and common post-translation modifications.
2790 Purine Set
2793 The set of purine nucleotides. These are the bases adenosine
2794 and guanosine (A and G, respectively). All nucleotides are
2795 either purines or pyrimidines. This set is equivalent to the
2796 RasMol atom expressions a,g and nucleic and not pyrimidine.
2797 Pyrimidine Set
2800 The set of pyrimidine nucleotides. These are the bases cytidine
2801 and thymidine (C and T, respectively). All nucleotides are
2802 either purines or pyrimidines. This set is equivalent to the
2803 RasMol atom expressions c,t and nucleic and not purine.
2804 Selected Set
2807 This set contains the set of atoms in the currently selected
2808 region. The currently selected region is defined by the preced‐
2809 ing select or restrict command and not the atom expression con‐
2810 taining the selected keyword.
2811 Sheet Set
2814 This set contains all atoms that form part of a protein beta
2815 sheet as determined by either the PDB file author or Kabsch and
2816 Sander's DSSP algorithm. By default, RasMol uses the secondary
2817 structure determination given in the PDB file if it exists.
2818 Otherwise, it uses the DSSP algorithm as used by the RasMol
2819 structure command.
2820 Sidechain Set
2823 This set contains the functional sidechains of any amino acids
2824 and the base of each nucleotide. These are the atoms not part of
2825 the polypeptide N-C-C-O backbone of proteins or the sugar phos‐
2826 phate backbone of nucleic acids. Use the RasMol predefined sets
2827 protein and nucleic to distinguish between the two forms of
2828 sidechain. Atoms in nucleic acids and proteins are either back‐
2829 bone or sidechain. This set is equivalent to the RasMol expres‐
2830 sion (protein or nucleic) and not backbone.
2831 Small Set
2834 All amino acids are classified as either small, medium or large.
2835 This set is equivalent to the RasMol atom expression amino and
2836 not (medium or large).
2837 Solvent Set
2840 This set contains the solvent atoms in the molecule coordinate
2841 file. These are the heterogeneous water molecules, phosphate
2842 and sulphate ions. All hetero atoms are classified as either
2843 ligand or solvent atoms. All solvent atoms are classified as
2844 either water or ions. This set is equivalent to the RasMol atom
2845 expressions hetero and not ligand and water or ions.
2846 Surface Set
2849 This set contains the atoms in those amino acids that tend (pre‐
2850 fer) to be on the surface of proteins, in contact with solvent
2851 molecules. This set refers to the amino acids preference and not
2852 the actual solvent accessibility for the current protein. All
2853 amino acids are classified as either surface or buried. This
2854 set is equivalent to the RasMol atom expression amino and not
2855 buried.
2856 Turn Set
2859 This set contains all atoms that form part of a protein turns as
2860 determined by either the PDB file author or Kabsch and Sander's
2861 DSSP algorithm. By default, RasMol uses the secondary structure
2862 determination given in the PDB file if it exists. Otherwise, it
2863 uses the DSSP algorithm as used by the RasMol structure command.
2864 Water Set
2867 This set contains all the heterogeneous water molecules in the
2868 current database. A large number of water molecules are some‐
2869 times associated with protein and nucleic acid structures deter‐
2870 mined by X-ray crystallography. These atoms tend to clutter an
2871 image. All hetero atoms are classified as either ligand or sol‐
2872 vent atoms. The solvent atoms are further classified as either
2873 water or ions.
2874 Set Summary
2877 The table below summarises RasMol's classification of the common
2878 amino acids.
2879
2882 The RasMol colour command allows different objects (such as atoms,
2883 bonds and ribbon segments) to be given a specified colour. Typically
2884 this colour is either a RasMol predefined colour name or an RGB triple.
2885 Additionally RasMol also supports alt, amino, chain, charge, cpk,
2886 group, model, shapely, structure, temperature or user colour schemes
2887 for atoms, and hbond type colour scheme for hydrogen bonds and electro‐
2888 static potential colour scheme for dot surfaces. The 24 currently pre‐
2889 defined colour names are Black, Blue, BlueTint, Brown, Cyan, Gold,
2890 Grey, Green, GreenBlue, GreenTint, HotPink, Magenta, Orange, Pink,
2891 PinkTint, Purple, Red, RedOrange, SeaGreen, SkyBlue, Violet, White,
2892 Yellow and YellowTint
2893 If you frequently wish to use a colour not predefined, you can write a
2895 one-line script. For example, if you make the file grey.col containing
2896 the line, colour [180,180,180] #grey, then the command script grey.col
2897 colours the currently selected atom set grey.
2898 Alt Colours
2901 The RasMol alt (Alternate Conformer) colour scheme codes the
2902 base structure with one colour and applies a limited number of
2903 colours to each alternate conformer. In a RasMol built for
2904 8-bit colour systems, 4 colours are allowed for alternate con‐
2905 formers. Otherwise, 8 colours are available.
2906 Amino Colours
2909 The RasMol amino colour scheme colours amino acids according to
2910 traditional amino acid properties. The purpose of colouring is
2911 to identify amino acids in an unusual or surprising environment.
2912 The outer parts of a protein that are polar are visible (bright)
2913 colours and non-polar residues darker. Most colours are hallowed
2914 by tradition. This colour scheme is similar to the shapely
2915 scheme.
2916 Chain Colours
2919 The RasMol chain colour scheme assigns each macromolecular chain
2920 a unique colour. This colour scheme is particularly useful for
2921 distinguishing the parts of multimeric structure or the individ‐
2922 ual 'strands' of a DNA chain. Chain can be selected from the
2923 RasMol Colours menu.
2924 Charge Colours
2927 The RasMol charge colour scheme colour codes each atom according
2928 to the charge value stored in the input file (or beta factor
2929 field of PDB files). High values are coloured in blue (positive)
2930 and lower values coloured in red (negative). Rather than use a
2931 fixed scale this scheme determines the maximum and minimum val‐
2932 ues of the charge/temperature field and interpolates from red to
2933 blue appropriately. Hence, green cannot be assumed to be 'no net
2934 charge' charge.
2935 The difference between the charge and temperature colour schemes
2937 is that increasing temperature values proceed from blue to red,
2938 whereas increasing charge values go from red to blue.
2939 If the charge/temperature field stores reasonable values it is
2941 possible to use the RasMol colour dots potential command to
2942 colour code a dot surface (generated by the dots command) by
2943 electrostatic potential.
2944 CPK Colours
2947 The RasMol cpk colour scheme is based upon the colours of the
2948 popular plastic spacefilling models which were developed by
2949 Corey, Pauling and later improved by Kultun. This colour scheme
2950 colours 'atom' objects by the atom (element) type. This is the
2951 scheme conventionally used by chemists. The assignment of the
2952 most commonly used element types to colours is given below.
2953 Group Colours
2956 The RasMol group colour scheme colour codes residues by their
2957 position in a macromolecular chain. Each chain is drawn as a
2958 smooth spectrum from blue through green, yellow and orange to
2959 red. Hence the N terminus of proteins and 5' terminus of nucleic
2960 acids are coloured red and the C terminus of proteins and 3'
2961 terminus of nucleic acids are drawn in blue. If a chain has a
2962 large number of heterogeneous molecules associated with it, the
2963 macromolecule may not be drawn in the full 'range' of the spec‐
2964 trum. Group can be selected from the RasMol Colours menu.
2965 If a chain has a large number of heterogeneous molecules associ‐
2967 ated with it, the macromolecule may not be drawn in the full
2968 range of the spectrum. When RasMol performs group colouring it
2969 decides the range of colours it uses from the residue numbering
2970 given in the PDB file. Hence the lowest residue number is dis‐
2971 played in blue and the highest residue number is displayed as
2972 red. Unfortunately, if a PDB file contains a large number of
2973 heteroatoms, such as water molecules, that occupy the high
2974 residue numbers, the protein is displayed in the blue-green end
2975 of the spectrum and the waters in the yellow-red end of the
2976 spectrum. This is aggravated by there typically being many more
2977 water molecules than amino acid residues. The solution to this
2978 problem is to use the command set hetero off before applying the
2979 group colour scheme. This can also be achieved by toggling Het‐
2980 ero Atoms on the Options menu before selecting Group on the
2981 Colour menu. This command instructs RasMol to only use non-het‐
2982 ero residues in the group colour scaling.
2983 NMR Model Colours
2986 The RasMol model colour scheme codes each NMR model with a dis‐
2987 tinct colour. The NMR model number is taken as a numeric value.
2988 High values are coloured in blue and lower values coloured in
2989 red. Rather than use a fixed scale this scheme determines the
2990 maximum value of the NMR model number and interpolates from red
2991 to blue appropriately.
2992 Shapely Colours
2995 The RasMol shapely colour scheme colour codes residues by amino
2996 acid property. This scheme is based upon Bob Fletterick's
2997 "Shapely Models". Each amino acid and nucleic acid residue is
2998 given a unique colour. The shapely colour scheme is used by
2999 David Bacon's Raster3D program. This colour scheme is similar to
3000 the amino colour scheme.
3001 Structure Colours
3004 The RasMol structure colour scheme colours the molecule by pro‐
3005 tein secondary structure. Alpha helices are coloured magenta,
3006 [240,0,128], beta sheets are coloured yellow, [255,255,0], turns
3007 are coloured pale blue, [96,128,255] and all other residues are
3008 coloured white. The secondary structure is either read from the
3009 PDB file (HELIX, SHEET and TURN records), if available, or
3010 determined using Kabsch and Sander's DSSP algorithm. The RasMol
3011 structure command may be used to force DSSP's structure assign‐
3012 ment to be used.
3013 Temperature Colours
3016 The RasMol temperature colour scheme colour codes each atom
3017 according to the anisotropic temperature (beta) value stored in
3018 the PDB file. Typically this gives a measure of the mobil‐
3019 ity/uncertainty of a given atom's position. High values are
3020 coloured in warmer (red) colours and lower values in colder
3021 (blue) colours. This feature is often used to associate a
3022 "scale" value [such as amino acid variability in viral mutants]
3023 with each atom in a PDB file, and colour the molecule appropri‐
3024 ately.
3025 The difference between the temperature and charge colour schemes
3027 is that increasing temperature values proceed from blue to red,
3028 whereas increasing charge values go from red to blue.
3029 User Colours
3032 The RasMol user colour scheme allows RasMol to use the colour
3033 scheme stored in the PDB file. The colours for each atom are
3034 stored in COLO records placed in the PDB data file. This conven‐
3035 tion was introduced by David Bacon's Raster3D program.
3036 HBond Type Colours
3039 The RasMol type colour scheme applies only to hydrogen bonds,
3040 hence is used in the command colour hbonds type. This scheme
3041 colour codes each hydrogen bond according to the distance along
3042 a protein chain between hydrogen bond donor and acceptor. This
3043 schematic representation was introduced by Belhadj-Mostefa and
3044 Milner-White. This representation gives a good insight into pro‐
3045 tein secondary structure (hbonds forming alpha helices appear
3046 red, those forming sheets appear yellow and those forming turns
3047 appear magenta).
3048 Potential Colours
3051 The RasMol potential colour scheme applies only to dot surfaces,
3052 hence is used in the command colour dots potential. This scheme
3053 colours each currently displayed dot by the electrostatic poten‐
3054 tial at that point in space. This potential is calculated using
3055 Coulomb's law taking the temperature/charge field of the input
3056 file to be the charge assocated with that atom. This is the same
3057 interpretation used by the colour charge command. Like the
3058 charge colour scheme low values are blue/white and high values
3059 are red.
3060 Amino Acid Codes
3063 The following table lists the names, single letter and three
3064 letter codes of each of the amino acids.
3065 Booleans
3068 A boolean parameter is a truth value. Valid boolean values are
3069 'true' and used by RasMol to either enable or disable a repre‐
3070 sentation or option.
3071
3074 Protein Data Bank Files
3075 If you do not have the PDB documentation, you may find the following
3077 summary of the PDB file format useful. The Protein Data Bank is a com‐
3078 puter-based archival database for macromolecular structures. The data‐
3079 base was established in 1971 by Brookhaven National Laboratory, Upton,
3080 New York, as a public domain repository for resolved crystallographic
3081 structures. The Bank uses a uniform format to store atomic coordinates
3082 and partial bond connectivities as derived from crystallographic stud‐
3083 ies. In 1999 the Protein Data Bank moved to the Research Collaboratory
3084 for Structural Biology.
3085 PDB file entries consist of records of 80 characters each. Using the
3087 punched card analogy, columns 1 to 6 contain a record-type identifier,
3088 the columns 7 to 70 contain data. In older entries, columns 71 to 80
3089 are normally blank, but may contain sequence information added by
3090 library management programs. In new entries conforming to the 1996 PDB
3091 format, there is other information in those columns. The first four
3092 characters of the record identifier are sufficient to identify the type
3093 of record uniquely, and the syntax of each record is independent of the
3094 order of records within any entry for a particular macromolecule.
3095 The only record types that are of major interest to the RasMol program
3097 are the ATOM and HETATM records which describe the position of each
3098 atom. ATOM/HETATM records contain standard atom names and residue
3099 abbreviations, along with sequence identifiers, coordinates in Angstrom
3100 units, occupancies and thermal motion factors. The exact details are
3101 given below as a FORTRAN format statement. The "fmt" column indicates
3102 use of the field in all PDB formats, in the 1992 and earlier formats or
3103 in the 1996 and later formats.
3104 Residues occur in order starting from the N-terminal residue for pro‐
3106 teins and 5'-terminus for nucleic acids. If the residue sequence is
3107 known, certain atom serial numbers may be omitted to allow for future
3108 insertion of any missing atoms. Within each residue, atoms are ordered
3109 in a standard manner, starting with the backbone (N-C-C-O for proteins)
3110 and proceeding in increasing remoteness from the alpha carbon, along
3111 the side chain.
3112 HETATM records are used to define post-translational modifications and
3114 cofactors associated with the main molecule. TER records are inter‐
3115 preted as breaks in the main molecule's backbone.
3116 If present, RasMol also inspects HEADER, COMPND, HELIX, SHEET, TURN,
3118 CONECT, CRYST1, SCALE, MODEL, ENDMDL, EXPDTA and END records. Informa‐
3119 tion such as the name, database code, revision date and classification
3120 of the molecule are extracted from HEADER and COMPND records, initial
3121 secondary structure assignments are taken from HELIX, SHEET and TURN
3122 records, and the end of the file may be indicated by an END record.
3123 RasMol Interpretation of PDB fields
3126 Atoms located at 9999.000, 9999.000, 9999.000 are assumed to be
3127 Insight pseudo atoms and are ignored by RasMol. Atom names
3128 beginning ' Q' are also assumed to be pseudo atoms or position
3129 markers.
3130 When a data file contains an NMR structure, multiple conforma‐
3132 tions may be placed in a single PDB file delimited by pairs of
3133 MODEL and ENDMDL records. RasMol displays all the NMR models
3134 contained in the file.
3135 Residue names "CSH", "CYH" and "CSM" are considered pseudonyms
3137 for cysteine "CYS". Residue names "WAT", "H20", "SOL" and "TIP"
3138 are considered pseudonyms for water "HOH". The residue name
3139 "D20" is consider heavy water "DOD". The residue name "SUL" is
3140 considered a sulphate ion "SO4". The residue name "CPR" is con‐
3141 sidered to be cis-proline and is translated as "PRO". The
3142 residue name "TRY" is considered a pseudonym for tryptophan
3143 "TRP".
3144 RasMol uses the HETATM fields to define the sets hetero, water,
3146 solvent and ligand. Any group with the name "HOH", "DOD", "SO4"
3147 or "PO4" (or aliased to one of these names by the preceding
3148 rules) is considered a solvent and is considered to be defined
3149 by a HETATM field.
3150 RasMol only respects CONECT connectivity records in PDB files
3152 containing fewer than 256 atoms. This is explained in more
3153 detail in the section on determining molecule connectivity.
3154 CONECT records that define a bond more than once are interpreted
3155 as specifying the bond order of that bond, i.e. a bond specified
3156 twice is a double bond and a bond specified three (or more)
3157 times is a triple bond. This is not a standard PDB feature.
3158 PDB Colour Scheme Specification
3161 RasMol also accepts the supplementary COLO record type in the
3162 PDB files. This record format was introduced by David Bacon's
3163 Raster3D program for specifying the colour scheme to be used
3164 when rendering the molecule. This extension is not currently
3165 supported by the PDB. The COLO record has the same basic record
3166 type as the ATOM and HETATM records described above.
3167 Colours are assigned to atoms using a matching process. The Mask
3169 field is used in the matching process as follows. First RasMol
3170 reads in and remembers all the ATOM, HETATM and COLO records in
3171 input order. When the user-defined ('User') colour scheme is
3172 selected, RasMol goes through each remembered ATOM/HETATM record
3173 in turn, and searches for a COLO record that matches in all of
3174 columns 7 through 30. The first such COLO record to be found
3175 determines the colour and radius of the atom.
3176 Note that the Red, Green and Blue components are in the same
3178 positions as the X, Y, and Z components of an ATOM or HETA
3179 record, and the van der Waals radius goes in the place of the
3180 Occupancy. The Red, Green and Blue components must all be in the
3181 range 0 to 1.
3182 In order that one COLO record can provide colour and radius
3184 specifications for more than one atom (e.g. based on residue,
3185 atom type, or any other criterion for which labels can be given
3186 somewhere in columns 7 through 30), a 'don't-care' character,
3187 the hash mark "#" (number or sharp sign) is used. This charac‐
3188 ter, when found in a COLO record, matches any character in the
3189 corresponding column in a ATOM/HETATM record. All other charac‐
3190 ters must match identically to count as a match. As an extension
3191 to the specification, any atom that fails to match a COLO record
3192 is displayed in white.
3193 Multiple NMR Models
3196 RasMol loads all of the NMR models from a PDB file no matter
3197 which command is used: load pdb <filename> or load nmrpdb <file‐
3198 name>
3199 Once multiple NMR conformations have been loaded they may be
3201 manipulated with the atom expression extensions described in
3202 Primitive Expressions. In particular, the command restrict */1
3203 will restrict the display to the first model only.
3204 CIF and mmCIF Format Files
3207 CIF is the IUCr standard for presentation of small molecules and
3208 mmCIF is intended as the replacement for the fixed-field PDB
3209 format for presentation of macromolecular structures. RasMol can
3210 accept data sets in either format.
3211 There are many useful sites on the World Wide Web where informa‐
3213 tion tools and software related to CIF, mmCIF and the PDB can be
3214 found. The following are good starting points for exploration:
3215 The International Union of Crystallography (IUCr) provides
3217 access to software, dictionaries, policy statements and documen‐
3218 tation relating to CIF and mmCIF at: IUCr, Chester, England
3219 (www.iucr.org/iucr-top/cif/) with many mirror sites.
3220 The Nucleic Acid Database Project provides access to its
3222 entries, software and documentation, with an mmCIF page giving
3223 access to the dictionary and mmCIF software tools at Rutgers
3224 University, New Jersey, USA (http://ndbserver.rut‐
3225 gers.edu/NDB/mmcif) with many mirror sites.
3226 This version of RasMol restricts CIF or mmCIF tag values to
3228 essentially the same conventions as are used for the fixed-field
3229 PDB format. Thus chain identifiers and alternate conformation
3230 identifiers are limited to a single character, atom names are
3231 limited to 4 characters, etc. RasMol interprets the following
3232 CIF and mmCIF tags: A search is made through multiple data
3233 blocks for the desired tags, so a single dataset may be composed
3234 from multiple data blocks, but multiple data sets may not be
3235 stacked in the same file.
3236
3239 In the following sections, support for Monochrome X-Windows, Tcl/Tk
3240 IPC, UNIX sockets based IPC, Compiling RasWin with Borland and MetroW‐
3241 erks are described.
3242 Monochrome X-Windows Support
3245 RasMol supports the many monochrome UNIX workstations typically
3246 found in academia, such as low-end SUN workstations and NCD X-
3247 terminals. The X11 version of RasMol (when compiled in 8 bit
3248 mode) now detects black and white X-Windows displays and enables
3249 dithering automatically. The use of run-time error diffusion
3250 dithering means that all display modes of RasMol are available
3251 when in monochrome mode. For best results, users should experi‐
3252 ment with the set ambient command to ensure the maximum contrast
3253 in resulting images.
3254 Tcl/Tk IPC support
3257 Version 4 of Tk graphics library changed the protocol used to
3258 communicate between Tk applications. RasMol version 2.6 was mod‐
3259 ified such that it could communicate with both this new protocol
3260 and the previous version 3 protocol supported by RasMol v2.5.
3261 Although Tcl/Tk 3.x applications may only communicate with other
3262 3.x applications and Tcl/Tk 4.x applications with other 4.x
3263 applications, these changes allow RasMol to communicate between
3264 processes with both protocols (potentially concurrently).
3265 UNIX sockets based IPC
3268 The UNIX implementation of RasMol supports BSD-style socket com‐
3269 munication. An identical socket mechanism is also being devel‐
3270 oped for VMS, Apple Macintosh and Microsoft Windows systems.
3271 This should allow RasMol to interactively display results of a
3272 computation on a remote host. The current protocol acts as a
3273 TCP/IP server on port 21069 that executes command lines until
3274 either the command exit or the command quit is typed. The com‐
3275 mand exit from the RasMol server, the command quit both discon‐
3276 nects the current session and terminates RasMol. This function‐
3277 ality may be tested using the UNIX command telnet <hostname>
3278 21069.
3279 Compiling RasWin with Borland and MetroWerks
3282 A number of changes were made to the source code in the transi‐
3283 tion from version 2.5 to 2.6 to allow the Microsoft Windows ver‐
3284 sion of RasMol to compile using the Borland C/C++ compiler.
3285 These fixes include name changes for the standard library and
3286 special code to avoid a bug in _fmemset. Additional changes
3287 were made in the transition from 2.6 to 2.7 to allow compilation
3288 with the MetroWerks compilers.
3289
3292 Molecular Graphics
3293 [1] Nelson Max, "Computer Representation of Molecular Surfaces", IEEE
3295 Computer Graphics and Applications, pp.21-29, August 1983.
3296 [2] Arthur M. Lesk, "Protein Architecture: A Practical Approach", IRL
3298 Press Publishers, 1991.
3299 Molecular Graphics Programs
3301 [3] Per J. Kraulis, "MOLSCRIPT: A Program to Produce both Detailed and
3303 Schematic Plots of Protein Structures", Journal of Applied Crystallog‐
3304 raphy, Vol.24, pp.946-950, 1991.
3305 [4] David Bacon and Wayne F. Anderson, "A Fast Algorithm for Rendering
3307 Space-Filling Molecule Pictures", Journal of Molecular Graphics, Vol.6,
3308 No.4, pp.219-220, December 1988.
3309 [5] David C. Richardson and Jane S. Richardson, "The Kinemage: A tool
3311 for Scientific Communication", Protein Science, Vol.1, No.1,pp.3-9,
3312 January 1992.
3313 [6] Mike Carson, "RIBBONS 2.0", Journal of Applied Crystallography,
3315 Vol.24, pp.958-961, 1991.
3316 [7] Conrad C. Huang, Eric F. Pettersen, Teri E. Klein, Thomas E. Fer‐
3318 rin and Robert Langridge, "Conic: A Fast Renderer for Space-Filling
3319 Molecules with Shadows", Journal of Molecular Graphics, Vol.9, No.4,
3320 pp.230-236, December 1991.
3321 Molecular Biology Algorithms
3323 [8] Wolfgang Kabsch and Christian Sander, "Dictionary of Protein Sec‐
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3395 The RasMol User Manual!
3396
3399 1992-1998 by Roger Sayle (rasmol@ggr.co.uk)
3400 July 2009 RASMOL(1)