RasMol 2.7.5 is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules, based on Roger Sayles' RasMol_2.6. The program is aimed at display, teaching and generation of publication quality images. RasMol runs on Microsoft Windows, Apple Macintosh, UNIX and VMS systems. The UNIX and VMS systems require an 8, 24 or 32 bit colour X Windows display (X11R4 or later). The program reads in a molecule coordinate file and interactively displays the molecule on the screen in a variety of colour schemes and molecule representations. Currently available representations include depth-cued wireframes, 'Dreiding' sticks, spacefilling (CPK) spheres, ball and stick, solid and strand biomolecular ribbons, atom labels and dot surfaces. The RasMol help facility can be accessed by typing "help " or "help " from the command line. A complete list of RasMol commands may be displayed by typing "help commands". A single question mark may also be used to abbreviate the keyword "help". Please type "help notices" for important notices. RasMol Copyright (C) Roger Sayle 1992-1999 Version 2.6x1 Mods Copyright (C) Arne Mueller 1998 Versions 2.5-ucb and 2.6-ucb Mods Copyright (C) UC Regents/ModularCHEM Consortium 1995, 1996 RasTop 1.3 Copyright (C) Philippe Valadon 2000 Version 2.7.0, 2.7.1, 2.7.1.1, 2.7.2, 2.7.2.1, 2.7.2.1.1, 2.7.3, 2.7.4, 2.7.4.1, 2.7.4.2 2.7.5, 2.7.5.1 Mods Copyright (C) Herbert J. Bernstein 1998-2009 rasmol@bernstein-plus-sons.com ?notice ?notices This software has been created from several sources. Much of the code is from RasMol 2.6, as created by Roger Sayle. See: http://www.dcs.ed.ac.uk/home/rasmol The torsion angle code, new POVRAY3 code and other features are derived from the RasMol2.6x1 revisions by Arne Mueller. See: ftp://nexus.roko.goe.net/pub/rasmol The Ramachandran printer plot code was derived from fisipl created by Frances C. Bernstein. See the Protein Data Bank program tape. The code to display multiple molecules and to allow bond rotation is derived in large part from the UCB mods by Gary Grossman and Marco Molinaro, included with permission of Eileen Lewis of the ModularCHEM Consortium. The CIF modifications make use of a library based in part on CBFlib by Paul J. Ellis and Herbert J. Bernstein. See: http://www.bernstein-plus-sons.com/software/CBF Parts of CBFlib is loosely based on the CIFPARSE software package from the NDB at Rutgers university. See: http://www.iucr.org/iucr-top/cif/mmcif/ndb/software/CIFPARSE Please type the RasMol commands 'help copying', 'help general', 'help IUCR', 'help CBFlib', and 'help CIFPARSE' for applicable notices. Please type 'help copyright' for copyright notices. If you use RasMol V2.6 or an earlier version, type the RasMol command 'help oldnotice'. ?copyright Copyright RasMol 2.7.5 Molecular Graphics Visualisation Tool 13 June 2009 (rev. 17 July 2009) Based on RasMol 2.6 by Roger Sayle Biomolecular Structures Group,Glaxo Wellcome Research & Development Stevenage, Hertfordshire, UK Version 2.6, August 1995, Version 2.6.4, December 1998 Copyright (C) Roger Sayle 1992-1999 and Based on Mods by Author Version, Date Copyright Arne Mueller RasMol 2.6x1 May 98 (C) Arne Mueller 1998 Gary Grossman and RasMol 2.5-ucb Nov 95 (C) UC Regents/ModularCHEM Marco Molinaro RasMol 2.5-ucb Nov 96 Consortium 1995, 1996 Philippe Valadon RasTop 1.3 Aug 00 (C) Philippe Valadon 2000 Herbert J. RasMol 2.7.0 Mar 99 (C) Herbert J. Bernstein Bernstein RasMol 2.7.1 Jun 99 1998-2001 RasMol 2.7.1.1 Jan 01 RasMol 2.7.2 Aug 00 RasMol 2.7.2.1.1 Jan 04 RasMol 2.7.3 Feb 05 RasMol 2.7.3.1 Apr 06 RasMol 2.7.4 Nov 07 RasMol 2.7.4.1 Jan 08 RasMol 2.7.4.2 Mar 08 RasMol 2.7.5 Jun 09 RasMol 2.7.5.1 Jul 09 RasMol 2.7.5 incorporates changes by T. Ikonen, G. McQuillan, N. Darakev and L. Andrews (via the neartree package). Work on RasMol 2.7.5 supported in part by grant 1R15GM078077-01 from the National Institute of General Medical Sciences (NIGMS), U.S. National Institutes of Health and by grant ER63601-1021466-0009501 from the Office of Biological & Environmental Research (BER), Office of Science, U. S. Department of Energy. RasMol 2.7.4 incorporated changes by G. Todorov, Nan Jia, N. Darakev, P. Kamburov, G. McQuillan, and J. Jemilawon. Work on RasMol 2.7.4 supported in part by grant 1R15GM078077-01 from the NIGMS/NIH and grant ER63601-1021466-0009501 from BER/DOE. RasMol 2.7.3 incorporates changes by Clarice Chigbo, Ricky Chachra, and Mamoru Yamanishi. Work on RasMol 2.7.3 supported in part by grants DBI-0203064, DBI-0315281 and EF-0312612 from the U.S. National Science Foundation and grant DE-FG02-03ER63601 from BER/DOE. The content is solely the responsibility of the authors and does not necessarily represent the official views of the funding organizations. The code for use of RasMol under GTK in RasMol 2.7.4.2 was written by Teemu Ikonen. and Incorporating Translations by Author Item Language Isabel Servan Martinez, 2.6 Manual Spanish Jose Miguel Fernandez Fernandez Jose Miguel Fernandez Fernandez 2.7.1 Manual Spanish Fernando Gabriel Ranea 2.7.1 menus and messages Spanish Jean-Pierre Demailly 2.7.1 menus and messages French Giuseppe Martini, Giovanni Paolella, 2.7.1 menus and messages A. Davassi, M. Masullo, C. Liotto 2.7.1 help file Italian G. Pozhvanov 2.7.3 menus and messages Russian G. Todorov 2.7.3 menus and messages Bulgarian Nan Jia, G. Todorov 2.7.3 menus and messages Chinese Mamoru Yamanishi, Katajima Hajime 2.7.3 menus and messages Japanese This Release by Herbert J. Bernstein, Bernstein + Sons, P.O. Box 177, Bellport, NY, USA yaya@bernstein-plus-sons.com Copyright (C) Herbert J. Bernstein 1998-2009 ?copying This version is based directly on RasMol version 2.7.4.2, on RasMol verion 2.7.4.2, on RasMol version 2.7.4, on RasMol version 2.7.3.1, on RasMol version 2.7.3, on RasMol version 2.7.2.1.1, Rasmol version 2.7.2, RasMol version 2.7.1.1 and RasTop version 1.3 and indirectly on the RasMol 2.5-ucb and 2.6-ucb versions and version 2.6_CIF.2, RasMol 2.6x1 and RasMol_2.6.4. RasMol 2.7.5 may be distributed under the terms of the GNU General Public License (the GPL), see http://www.gnu.org/licenses/gpl.txt or the file GPL or type the command 'help GPL' or RasMol 2.7.5 may be distributed under the RASMOL license. See the file NOTICE or type the command 'help RASLIC' ?gpl GPL GNU GENERAL PUBLIC LICENSE Version 2, June 1991 Copyright (C) 1989, 1991 Free Software Foundation, Inc. 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change free software--to make sure the software is free for all its users. This General Public License applies to most of the Free Software Foundation's software and to any other program whose authors commit to using it. (Some other Free Software Foundation software is covered by the GNU Library General Public License instead.) You can apply it to your programs, too. When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for this service if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs; and that you know you can do these things. To protect your rights, we need to make restrictions that forbid anyone to deny you these rights or to ask you to surrender the rights. These restrictions translate to certain responsibilities for you if you distribute copies of the software, or if you modify it. For example, if you distribute copies of such a program, whether gratis or for a fee, you must give the recipients all the rights that you have. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights. We protect your rights with two steps: (1) copyright the software, and (2) offer you this license which gives you legal permission to copy, distribute and/or modify the software. Also, for each author's protection and ours, we want to make certain that everyone understands that there is no warranty for this free software. If the software is modified by someone else and passed on, we want its recipients to know that what they have is not the original, so that any problems introduced by others will not reflect on the original authors' reputations. Finally, any free program is threatened constantly by software patents. We wish to avoid the danger that redistributors of a free program will individually obtain patent licenses, in effect making the program proprietary. To prevent this, we have made it clear that any patent must be licensed for everyone's free use or not licensed at all. The precise terms and conditions for copying, distribution and modification follow. GNU GENERAL PUBLIC LICENSE TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION 0. This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License. The "Program", below, refers to any such program or work, and a "work based on the Program" means either the Program or any derivative work under copyright law: that is to say, a work containing the Program or a portion of it, either verbatim or with modifications and/or translated into another language. (Hereinafter, translation is included without limitation in the term "modification".) Each licensee is addressed as "you". Activities other than copying, distribution and modification are not covered by this License; they are outside its scope. The act of running the Program is not restricted, and the output from the Program is covered only if its contents constitute a work based on the Program (independent of having been made by running the Program). Whether that is true depends on what the Program does. 1. You may copy and distribute verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty; keep intact all the notices that refer to this License and to the absence of any warranty; and give any other recipients of the Program a copy of this License along with the Program. You may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in exchange for a fee. 2. You may modify your copy or copies of the Program or any portion of it, thus forming a work based on the Program, and copy and distribute such modifications or work under the terms of Section 1 above, provided that you also meet all of these conditions: a) You must cause the modified files to carry prominent notices stating that you changed the files and the date of any change. b) You must cause any work that you distribute or publish, that in whole or in part contains or is derived from the Program or any part thereof, to be licensed as a whole at no charge to all third parties under the terms of this License. c) If the modified program normally reads commands interactively when run, you must cause it, when started running for such interactive use in the most ordinary way, to print or display an announcement including an appropriate copyright notice and a notice that there is no warranty (or else, saying that you provide a warranty) and that users may redistribute the program under these conditions, and telling the user how to view a copy of this License. (Exception: if the Program itself is interactive but does not normally print such an announcement, your work based on the Program is not required to print an announcement.) These requirements apply to the modified work as a whole. If identifiable sections of that work are not derived from the Program, and can be reasonably considered independent and separate works in themselves, then this License, and its terms, do not apply to those sections when you distribute them as separate works. But when you distribute the same sections as part of a whole which is a work based on the Program, the distribution of the whole must be on the terms of this License, whose permissions for other licensees extend to the entire whole, and thus to each and every part regardless of who wrote it. Thus, it is not the intent of this section to claim rights or contest your rights to work written entirely by you; rather, the intent is to exercise the right to control the distribution of derivative or collective works based on the Program. In addition, mere aggregation of another work not based on the Program with the Program (or with a work based on the Program) on a volume of a storage or distribution medium does not bring the other work under the scope of this License. 3. You may copy and distribute the Program (or a work based on it, under Section 2) in object code or executable form under the terms of Sections 1 and 2 above provided that you also do one of the following: a) Accompany it with the complete corresponding machine-readable source code, which must be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, b) Accompany it with a written offer, valid for at least three years, to give any third party, for a charge no more than your cost of physically performing source distribution, a complete machine-readable copy of the corresponding source code, to be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, c) Accompany it with the information you received as to the offer to distribute corresponding source code. (This alternative is allowed only for noncommercial distribution and only if you received the program in object code or executable form with such an offer, in accord with Subsection b above.) The source code for a work means the preferred form of the work for making modifications to it. For an executable work, complete source code means all the source code for all modules it contains, plus any associated interface definition files, plus the scripts used to control compilation and installation of the executable. However, as a special exception, the source code distributed need not include anything that is normally distributed (in either source or binary form) with the major components (compiler, kernel, and so on) of the operating system on which the executable runs, unless that component itself accompanies the executable. If distribution of executable or object code is made by offering access to copy from a designated place, then offering equivalent access to copy the source code from the same place counts as distribution of the source code, even though third parties are not compelled to copy the source along with the object code. 4. You may not copy, modify, sublicense, or distribute the Program except as expressly provided under this License. Any attempt otherwise to copy, modify, sublicense or distribute the Program is void, and will automatically terminate your rights under this License. However, parties who have received copies, or rights, from you under this License will not have their licenses terminated so long as such parties remain in full compliance. 5. You are not required to accept this License, since you have not signed it. However, nothing else grants you permission to modify or distribute the Program or its derivative works. These actions are prohibited by law if you do not accept this License. Therefore, by modifying or distributing the Program (or any work based on the Program), you indicate your acceptance of this License to do so, and all its terms and conditions for copying, distributing or modifying the Program or works based on it. 6. Each time you redistribute the Program (or any work based on the Program), the recipient automatically receives a license from the original licensor to copy, distribute or modify the Program subject to these terms and conditions. You may not impose any further restrictions on the recipients' exercise of the rights granted herein. You are not responsible for enforcing compliance by third parties to this License. 7. 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If the distribution and/or use of the Program is restricted in certain countries either by patents or by copyrighted interfaces, the original copyright holder who places the Program under this License may add an explicit geographical distribution limitation excluding those countries, so that distribution is permitted only in or among countries not thus excluded. In such case, this License incorporates the limitation as if written in the body of this License. 9. The Free Software Foundation may publish revised and/or new versions of the General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. Each version is given a distinguishing version number. If the Program specifies a version number of this License which applies to it and "any later version", you have the option of following the terms and conditions either of that version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of this License, you may choose any version ever published by the Free Software Foundation. 10. If you wish to incorporate parts of the Program into other free programs whose distribution conditions are different, write to the author to ask for permission. For software which is copyrighted by the Free Software Foundation, write to the Free Software Foundation; we sometimes make exceptions for this. Our decision will be guided by the two goals of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally. NO WARRANTY 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. END OF TERMS AND CONDITIONS How to Apply These Terms to Your New Programs If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms. To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively convey the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found. Copyright (C) This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA Also add information on how to contact you by electronic and paper mail. If the program is interactive, make it output a short notice like this when it starts in an interactive mode: Gnomovision version 69, Copyright (C) year name of author Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, the commands you use may be called something other than `show w' and `show c'; they could even be mouse-clicks or menu items--whatever suits your program. You should also get your employer (if you work as a programmer) or your school, if any, to sign a "copyright disclaimer" for the program, if necessary. Here is a sample; alter the names: Yoyodyne, Inc., hereby disclaims all copyright interest in the program `Gnomovision' (which makes passes at compilers) written by James Hacker. , 1 April 1989 Ty Coon, President of Vice This General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Library General Public License instead of this License. ?raslic RASLIC If you do not use the GPL, the following license terms apply: RasMol License Even though the authors of the various documents and software found here have made a good faith effort to ensure that the documents are correct and that the software performs according to its documentation, and we would greatly appreciate hearing of any problems you may encounter, the programs and documents any files created by the programs are provided **AS IS** without any warranty as to correctness, merchantability or fitness for any particular or general use. THE RESPONSIBILITY FOR ANY ADVERSE CONSEQUENCES FROM THE USE OF PROGRAMS OR DOCUMENTS OR ANY FILE OR FILES CREATED BY USE OF THE PROGRAMS OR DOCUMENTS LIES SOLELY WITH THE USERS OF THE PROGRAMS OR DOCUMENTS OR FILE OR FILES AND NOT WITH AUTHORS OF THE PROGRAMS OR DOCUMENTS. Subject to your acceptance of the conditions stated above, and your respect for the terms and conditions stated in the notices below, if you are not going to make any modifications or create derived works, you are given permission to freely copy and distribute this package, provided you do the following: 1. Either include the complete documentation, especially the file NOTICE, with what you distribute or provide a clear indication where people can get a copy of the documentation; and 2. Please give credit where credit is due citing the version and original authors properly; and 3. Please do not give anyone the impression that the original authors are providing a warranty of any kind. If you would like to use major pieces of RasMol in some other program, make modifications to RasMol, or in some other way make what a lawyer would call a "derived work", you are not only permitted to do so, you are encouraged to do so. In addition to the things we discussed above, please do the following: 4. Please explain in your documentation how what you did differs from this version of RasMol; and 5. Please make your modified source code available. This version of RasMol is _not_ in the public domain, but it is given freely to the community in the hopes of advancing science. If you make changes, please make them in a responsible manner, and please offer us the opportunity to include those changes in future versions of RasMol. ?general ?generalnotice ?general notice General Notice The following notice applies to this work as a whole and to the works included within it: * Creative endeavors depend on the lively exchange of ideas. There are laws and customs which establish rights and responsibilities for authors and the users of what authors create. This notice is not intended to prevent you from using the software and documents in this package, but to ensure that there are no misunderstandings about terms and conditions of such use. * Please read the following notice carefully. If you do not understand any portion of this notice, please seek appropriate professional legal advice before making use of the software and documents included in this software package. In addition to whatever other steps you may be obliged to take to respect the intellectual property rights of the various parties involved, if you do make use of the software and documents in this package, please give credit where credit is due by citing this package, its authors and the URL or other source from which you obtained it, or equivalent primary references in the literature with the same authors. * Some of the software and documents included within this software package are the intellectual property of various parties, and placement in this package does not in any way imply that any such rights have in any way been waived or diminished. * With respect to any software or documents for which a copyright exists, ALL RIGHTS ARE RESERVED TO THE OWNERS OF SUCH COPYRIGHT. * Even though the authors of the various documents and software found here have made a good faith effort to ensure that the documents are correct and that the software performs according to its documentation, and we would greatly appreciate hearing of any problems you may encounter, the programs and documents and any files created by the programs are provided **AS IS** without any warranty as to correctness, merchantability or fitness for any particular or general use. * THE RESPONSIBILITY FOR ANY ADVERSE CONSEQUENCES FROM THE USE OF PROGRAMS OR DOCUMENTS OR ANY FILE OR FILES CREATED BY USE OF THE PROGRAMS OR DOCUMENTS LIES SOLELY WITH THE USERS OF THE PROGRAMS OR DOCUMENTS OR FILE OR FILES AND NOT WITH AUTHORS OF THE PROGRAMS OR DOCUMENTS. See the files GPL and RASLIC for two alternate ways to license this package. ?old ?oldnotice ?rasmol v2.6 notice RasMol V2.6 Notice The following notice applies to RasMol V 2.6 and older RasMol versions. Information in this document is subject to change without notice and does not represent a commitment on the part of the supplier. This package is sold/distributed subject to the condition that it shall not, by way of trade or otherwise, be lent, re-sold, hired out or otherwise circulated without the supplier's prior consent, in any form of packaging or cover other than that in which it was produced. No part of this manual or accompanying software may be reproduced, stored in a retrieval system on optical or magnetic disk, tape or any other medium, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording or otherwise for any purpose other than the purchaser's personal use. This product is not to be used in the planning, construction, maintenance, operation or use of any nuclear facility nor the flight, navigation or communication of aircraft or ground support equipment. The author shall not be liable, in whole or in part, for any claims or damages arising from such use, including death, bankruptcy or outbreak of war. ?iucrpolicy ?iucr policy ?iucr policy IUCR Policy The IUCr Policy for the Protection and the Promotion of the STAR File and CIF Standards for Exchanging and Archiving Electronic Data. Overview The Crystallographic Information File (CIF)[1] is a standard for information interchange promulgated by the International Union of Crystallography (IUCr). CIF (Hall, Allen & Brown, 1991) is the recommended method for submitting publications to Acta Crystallographica Section C and reports of crystal structure determinations to other sections of Acta Crystallographica and many other journals. The syntax of a CIF is a subset of the more general STAR File[2] format. The CIF and STAR File approaches are used increasingly in the structural sciences for data exchange and archiving, and are having a significant influence on these activities in other fields. Statement of intent The IUCr's interest in the STAR File is as a general data interchange standard for science, and its interest in the CIF, a conformant derivative of the STAR File, is as a concise data exchange and archival standard for crystallography and structural science. Protection of the standards To protect the STAR File and the CIF as standards for interchanging and archiving electronic data, the IUCr, on behalf of the scientific community, * holds the copyrights on the standards themselves, * owns the associated trademarks and service marks, and * holds a patent on the STAR File. These intellectual property rights relate solely to the interchange formats, not to the data contained therein, nor to the software used in the generation, access or manipulation of the data. Promotion of the standards The sole requirement that the IUCr, in its protective role, imposes on software purporting to process STAR File or CIF data is that the following conditions be met prior to sale or distribution. * Software claiming to read files written to either the STAR File or the CIF standard must be able to extract the pertinent data from a file conformant to the STAR File syntax, or the CIF syntax, respectively. * Software claiming to write files in either the STAR File, or the CIF, standard must produce files that are conformant to the STAR File syntax, or the CIF syntax, respectively. * Software claiming to read definitions from a specific data dictionary approved by the IUCr must be able to extract any pertinent definition which is conformant to the dictionary definition language (DDL)[3] associated with that dictionary. The IUCr, through its Committee on CIF Standards, will assist any developer to verify that software meets these conformance conditions. Glossary of terms [1] CIF: is a data file conformant to the file syntax defined at http://www.iucr.org/iucr-top/cif/spec/index.html [2] STAR File: is a data file conformant to the file syntax defined at http://www.iucr.org/iucr-top/cif/spec/star/index.html [3] DDL: is a language used in a data dictionary to define data items in terms of "attributes". Dictionaries currently approved by the IUCr, and the DDL versions used to construct these dictionaries, are listed at http://www.iucr.org/iucr-top/cif/spec/ddl/index.html Last modified: 30 September 2000 IUCr Policy Copyright (C) 2000 International Union of Crystallography ?cbflib CBFLIB The following Disclaimer Notice applies to CBFlib V0.1, from which this code in part is derived. * The items furnished herewith were developed under the sponsorship of the U.S. Government. Neither the U.S., nor the U.S. D.O.E., nor the Leland Stanford Junior University, nor their employees, makes any warranty, express or implied, or assumes any liability or responsibility for accuracy, completeness or usefulness of any information, apparatus, product or process disclosed, or represents that its use will not infringe privately-owned rights. Mention of any product, its manufacturer, or suppliers shall not, nor is it intended to, imply approval, disapproval, or fitness for any particular use. The U.S. and the University at all times retain the right to use and disseminate the furnished items for any purpose whatsoever. Notice 91 02 01 ?cifparse CIFPARSE Portions of this software are loosely based on the CIFPARSE software package from the NDB at Rutgers University. See http://ndbserver.rutgers.edu/NDB/mmcif/software CIFPARSE is part of the NDBQUERY application, a program component of the Nucleic Acid Database Project [ H. M. Berman, W. K. Olson, D. L. Beveridge, J. K. Westbrook, A. Gelbin, T. Demeny, S. H. Shieh, A. R. Srinivasan, and B. Schneider. (1992). The Nucleic Acid Database: A Comprehensive Relational Database of Three-Dimensional Structures of Nucleic Acids. Biophys J., 63, 751-759.], whose cooperation is gratefully acknowledged, especially in the form of design concepts created by J. Westbrook. Please be aware of the following notice in the CIFPARSE API: This software is provided WITHOUT WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR ANY OTHER WARRANTY, EXPRESS OR IMPLIED. RUTGERS MAKE NO REPRESENTATION OR WARRANTY THAT THE SOFTWARE WILL NOT INFRINGE ANY PATENT, COPYRIGHT OR OTHER PROPRIETARY RIGHT. RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images. RasMol runs on wide range of architectures and operating systems including Microsoft Windows, Apple Macintosh, UNIX and VMS systems. UNIX and VMS versions require an 8, 24 or 32 bit colour X Windows display (X11R4 or later). The X Windows version of RasMol provides optional support for a hardware dials box and accelerated shared memory communication (via the XInput and MIT-SHM extensions) if available on the current X Server. The program reads in a molecule coordinate file and interactively displays the molecule on the screen in a variety of colour schemes and molecule representations. Currently available representations include depth-cued wireframes, 'Dreiding' sticks, spacefilling (CPK) spheres, ball and stick, solid and strand biomolecular ribbons, atom labels and dot surfaces. Up to 5 molecules may be loaded and displayed at once. Any one or all of the molecules may be rotated and translated. The RasMol help facility can be accessed by typing "help " or "help " from the command line. A complete list of RasMol commands may be displayed by typing "help commands". A single question mark may also be used to abbreviate the keyword "help". Please type "help notices" for important notices. RasMol Copyright (C) Roger Sayle 1992-1999 Version 2.6x1 Mods Copyright (C) Arne Mueller 1998 Version 2.5-ucb, 2.6-ucb Mods Copyright (C) UC Regents/ModularCHEM Consortium 1995, 1996 RasTop 1.3 Copyright (C) Philippe Valadon 2000 Version 2.7.0, 2.7.1, 2.7.1.1, 2.7.2, 2.7.2.1, 2.7.2.1.1, 2.7.3, 2.7.3.1, 2.7.4, 2.7.4.1, 2.7.4.2, 2.7.5, 2.7.5.1 Mods Copyright (C) Herbert J. Bernstein 1998-2009 (yaya@bernstein-plus-sons.com) ?commands ?keywords RasMol allows the execution of interactive commands typed at the 'RasMol>' prompt in the terminal window. Each command must be given on a separate line. Keywords are case insensitive and may be entered in either upper or lower case letters. All whitespace characters are ignored except to separate keywords and their arguments. All commands may be prefixed by a parenthesized 'atom expression' to temporarily select certain atoms just for the execution of that one command. After execution of the command, the previous selection is restored except for the commands 'select' , 'restrict' and 'script'. The commands/keywords currently recognised by RasMol are given below. Type "help " for more information on each RasMol function. backbone background bond bulgarian cartoon centre chinese clipboard colour colourmode connect cpk cpknew define depth dots echo english exit french hbonds help italian japanese label load map molecule monitor notoggle pause print quit refresh renumber reset restrict ribbons rotate save script select set show slab source spacefill spanish ssbonds star stereo strands structure surface trace translate unbond wireframe write zap zoom ?backbone Backbone Syntax: backbone {} backbone backbone dash The RasMol 'backbone' command permits the representation of a polypeptide backbone as a series of bonds connecting the adjacent alpha carbons of each amino acid in a chain. The display of these backbone 'bonds' is turned on and off by the command parameter in the same way as with the 'wireframe' command. The command 'backbone off' turns off the selected 'bonds', and 'backbone on' or with a number turns them on. The number can be used to specify the cylinder radius of the representation in either Angstrom or RasMol units. A parameter value of 500 (2.0 Angstroms) or above results in a "Parameter value too large" error. Backbone objects may be coloured using the RasMol 'colour backbone' command. The reserved word backbone is also used as a predefined set ("help sets") and as a parameter to the 'set hbond' and 'set ssbond' commands. The RasMol command 'trace' renders a smoothed backbone, in contrast to 'backbone' which connects alpha carbons with straight lines. The backbone may be displayed with dashed lines by use of the 'backbone dash' command. ?background Background Syntax: background The RasMol 'background' command is used to set the colour of the "canvas" background. The colour may be given as either a colour name or a comma separated triple of Red, Green and Blue (RGB) components enclosed in square brackets. Typing the command 'help colours' will give a list of the predefined colour names recognised by RasMol. When running under X Windows, RasMol also recognises colours in the X server's colour name database. The 'background' command is synonymous with the RasMol 'set background' command. ?bond Bond Syntax: bond + bond pick bond rotate {} The RasMol command 'bond +' adds the designated bond to the drawing, increasing the bond order if the bond already exists. The command 'bond pick' selects the two atoms specified by the atom serial numbers as the two ends of a bond around which the 'rotate bond ' command will be applied. If no bond exists, it is created. Rotation around a previously picked bond may be specified by the 'rotate bond ' command, or may also be controlled with the mouse, using the 'bond rotate on/off' or the equivalent 'rotate bond on/off' commands. ?bulgarian Bulgarian Syntax: Bulgarian The RasMol 'Bulgarian' command sets the menus and messages to the Bulgarian versions. This command may not work correctly unless appropriate fonts have been installed. The commands 'Bulgarian', 'Chinese', 'English', 'French', 'Italian', 'Russian' and 'Spanish' may be used to select Bulgarian, Chinese, English, French, Italian, Japanese, Russian and Spanish menus and messages if the appropriate fonts have been installed. ?cartoon Cartoon Syntax: cartoon {} The RasMol 'cartoon' command does a display of a molecule 'ribbons' as Richardson (MolScript) style protein 'cartoons', implemented as thick (deep) ribbons. The easiest way to obtain a cartoon representation of a protein is to use the 'Cartoons' option on the 'Display' menu. The 'cartoon' command represents the currently selected residues as a deep ribbon with width specified by the command's argument. Using the command without a parameter results in the ribbon's width being taken from the protein's secondary structure, as described in the 'ribbons' command. By default, the C-termini of beta-sheets are displayed as arrow heads. This may be enabled and disabled using the 'set cartoons' command. The depth of the cartoon may be adjusted using the 'set cartoons ' command. The 'set cartoons' command without any parameters returns these two options to their default values. ?center ?centre Centre Syntax: centre {} {translate|center} center {} {translate|center} The RasMol 'centre' command defines the point about which the 'rotate' command and the scroll bars rotate the current molecule. Without a parameter the centre command resets the centre of rotation to be the centre of gravity of the molecule. If an atom expression is specified, RasMol rotates the molecule about the centre of gravity of the set of atoms specified by the expression. Hence, if a single atom is specified by the expression, that atom will remain 'stationary' during rotations. Type 'help expression' for more information on RasMol atom expressions. Alternatively the centring may be given as a comma separated triple of [CenX, CenY, CenZ] offsets in RasMol units (1/250 of an Angstrom) from the centre of gravity. The triple must be enclosed in square brackets. The optional forms 'centre ... translate' and 'centre ... center' may be used to specify use of a translated centre of rotation (not necessarily in the centre of the canvas) or a centre of rotation which is placed at the centre of the canvas. Starting with RasMol 2.7.2, the default is to center the new axis on the canvas. ?chinese Chinese Syntax: Chinese The RasMol 'Chinese' command sets the menus and messages to the Chinese versions. This command may not work correctly unless appropriate fonts have been installed. The commands 'Bulgarian', 'Chinese', 'English', 'French', 'Italian', 'Russian' and 'Spanish' may be used to select Bulgarian, Chinese, English, French, Italian, Japanese, Russian and Spanish menus and messages if the appropriate fonts have been installed. ?clipboard Clipboard Syntax: clipboard The RasMol 'clipboard' command places a copy of the currently displayed image on the local graphics 'clipboard'. Note: this command is not yet supported on UNIX or VMS machines. It is intended to make transfering images between applications easier under Microsoft Windows or on an Apple Macintosh. When using RasMol on a UNIX or VMS system this functionality may be achieved by generating a raster image in a format that can be read by the receiving program using the RasMol 'write' command. ?color ?colour Colour Syntax: colour {} color {} Colour the atoms (or other objects) of the selected region. The colour may be given as either a colour name or a comma separated triple of Red, Green and Blue (RGB) components enclosed in square brackets. Typing the command 'help colours' will give a list of all the predefined colour names recognised by RasMol. Allowed objects are 'atoms', 'bonds', 'backbone', 'ribbons', 'labels', 'dots', 'hbonds', 'map', and 'ssbonds'. If no object is specified, the default keyword 'atom' is assumed. Some colour schemes are defined for certain object types. The colour scheme 'none' can be applied to all objects except atoms and dots, stating that the selected objects have no colour of their own, but use the colour of their associated atoms (i.e. the atoms they connect). 'Atom' objects can also be coloured by 'alt', 'amino', 'chain', 'charge', 'cpk', 'group', 'model', 'shapely', 'structure', 'temperature' or 'user'. Hydrogen bonds can also be coloured by 'type' and dot surfaces can also be coloured by 'electrostatic potential'. For more information type 'help colour '. Map objects may be coloured by specific color of by nearest atom. ?colourmode ?colourmode ColourMode Syntax: colourmode {} colormode {} ColourMode allows the user to switch between using the new 'colour' method. At present, the new coloring technique is the same as the old one, but to preserve compatibility for older scripts it may be wise to add a "colormode on" near the top of your script somewhere, if the script was designed for version 2.7.3 of RasMol or earlier. The new color method, when completed, aims to fix a few bugs in the coloring routines. ?connect Connect Syntax: connect {} The RasMol 'connect' command is used to force RasMol to (re)calculate the connectivity of the current molecule. If the original input file contained connectivity information, this is discarded. The command 'connect false' uses a fast heuristic algorithm that is suitable for determining bonding in large bio-molecules such as proteins and nucleic acids. The command 'connect true' uses a slower more accurate algorithm based upon covalent radii that is more suitable to small molecules containing inorganic elements or strained rings. If no parameters are given, RasMol determines which algorithm to use based on the number of atoms in the input file. Greater than 255 atoms causes RasMol to use the faster implementation. This is the method used to determine bonding, if necessary, when a molecule is first read in using the 'load' command. ?defer Defer Syntax: defer The RasMol 'defer' command adds the command given to the macro with given name, if no name is given, the command is added to the macro with a blank name. The command 'zap' is a special case. In that case the macro is erased. If no name is given the command must begin with a selection, e.g. 'defer (selection).spacefill' The deferred commands accumulated under the given name can be executed using the 'execute' command ?define Define Syntax: define The RasMol 'define' command allows the user to associate an arbitrary set of atoms with a unique identifier. This allows the definition of user-defined sets. These sets are declared statically, i.e. once defined the contents of the set do not change, even if the expression defining them depends on the current transformation and representation of the molecule. ?depth Depth Syntax: depth {} depth The RasMol 'depth' command enables, disables or positions the back-clipping plane of the molecule. The program only draws those portions of the molecule that are closer to the viewer than the clipping plane. Integer values range from zero at the very back of the molecule to 100 which is completely in front of the molecule. Intermediate values determine the percentage of the molecule to be drawn. This command interacts with the 'slab ' command, which clips to the front of a given z-clipping plane. ?dot surface ?surface ?dots Dots Syntax: dots {} dots The RasMol 'dots' command is used to generate a van der Waals' dot surface around the currently selected atoms. Dot surfaces display regularly spaced points on a sphere of van der Waals' radius about each selected atom. Dots that would are 'buried' within the van der Waals' radius of any other atom (selected or not) are not displayed. The command 'dots on' deletes any existing dot surface and generates a dots surface around the currently selected atom set with a default dot density of 100. The command 'dots off' deletes any existing dot surface. The dot density may be specified by providing a numeric parameter between 1 and 1000. This value approximately corresponds to the number of dots on the surface of a medium sized atom. By default, the colour of each point on a dot surface is the colour of its closest atom at the time the surface is generated. The colour of the whole dot surface may be changed using the 'colour dots' command. ?echo Echo Syntax: echo {} The RasMol 'echo' command is used to display a message in the RasMol command/terminal window. The string parameter may optionally be delimited in double quote characters. If no parameter is specified, the 'echo' command displays a blank line. This command is particularly useful for displaying text from within a RasMol 'script' file. ?english English Syntax: English The RasMol 'English' command sets the menus and messages to the English versions. This command may not work correctly unless appropriate fonts have been installed. The commands 'Bulgarian', 'Chinese', 'English', 'French', 'Italian', 'Russian' and 'Spanish' may be used to select Bulgarian, Chinese, English, French, Italian, Japanese, Russian and Spanish menus and messages if the appropriate fonts have been installed. ?execute Execute Syntax: execute The RasMol 'execute' command: 1. saves the old poise of the molecule (translation, rotation and zoom) 2. executes the specified macro suppressing both screen updates and recording 3. animates motion of the newly rendered molecule linearly from the old poise to the new poise The macro must have been previously defined by calls to the 'defer' command. The animation of the motion depends on the prior settings of the 'record' command. ?french French Syntax: French The RasMol 'French' command sets the menus and messages to the French versions. This command may not work correctly unless appropriate fonts have been installed. The commands 'Bulgarian', 'Chinese', 'English', 'French', 'Italian', 'Russian' and 'Spanish' may be used to select Bulgarian, Chinese, English, French, Italian, Japanese, Russian and Spanish menus and messages if the appropriate fonts have been installed. ?hbond ?hbonds HBonds Syntax: hbonds {} hbonds The RasMol 'hbond' command is used to represent the hydrogen bonding of the protein molecule's backbone. This information is useful in assessing the protein's secondary structure. Hydrogen bonds are represented as either dotted lines or cylinders between the donor and acceptor residues. The first time the 'hbond' command is used, the program searches the structure of the molecule to find hydrogen bonded residues and reports the number of bonds to the user. The command 'hbonds on' displays the selected 'bonds' as dotted lines, and the 'hbonds off' turns off their display. The colour of hbond objects may be changed by the 'colour hbond' command. Initially, each hydrogen bond has the colours of its connected atoms. By default the dotted lines are drawn between the accepting oxygen and the donating nitrogen. By using the 'set hbonds' command the alpha carbon positions of the appropriate residues may be used instead. This is especially useful when examining proteins in backbone representation. ?help Help Syntax: help { {}} ? { {} The RasMol 'help' command provides on-line help on the given topic. ?italian Italian Syntax: Italian The RasMol 'Italian' command sets the menus and messages to the Italian versions. This command may not work correctly unless appropriate fonts have been installed. The commands 'Bulgarian', 'Chinese', 'English', 'French', 'Italian', 'Russian' and 'Spanish' may be used to select Bulgarian, Chinese, English, French, Italian, Japanese, Russian and Spanish menus and messages if the appropriate fonts have been installed. ?japanese Japanese Syntax: Japanese The RasMol 'Japanese' command sets the menus and messages to the Japanese versions. This command may not work correctly unless appropriate fonts have been installed. The commands 'Bulgarian', 'Chinese', 'English', 'French', 'Italian', 'Russian' and 'Spanish' may be used to select Bulgarian, Chinese, English, French, Italian, Japanese, Russian and Spanish menus and messages if the appropriate fonts have been installed. ?labels ?label Label Syntax: label {} label The RasMol 'label' command allows an arbitrary formatted text string to be associated with each currently selected atom. This string may contain embedded 'expansion specifiers' which display properties of the atom being labelled. An expansion specifier consists of a '%' character followed by a single alphabetic character specifying the property to be displayed. An actual '%' character may be displayed by using the expansion specifier '%%'. Atom labelling for the currently selected atoms may be turned off with the command 'label off'. By default, if no string is given as a parameter, RasMol uses labels appropriate for the current molecule. The colour of each label may be changed using the 'colour label' command. By default, each label is drawn in the same colour as the atom to which it is attached. The size and spacing of the displayed text may be changed using the 'set fontsize' command. The width of the strokes in the displayed text may be changed using the 'set fontstroke' command. For a list of expansion specifiers, type "help specifiers". ?expansion ?specifiers ?expansion specifiers ?label specifiers Label Specifiers Label specifiers are characters sequences that are embedded in the string parameter passed to the RasMol 'label' command. These specifiers are then expanded as the labels are drawn to display properties associated with the atom being labelled. The following table lists the current expansion specifiers. The specifier '%%' is treated as an exception and is displayed as a single '%' character. %a Atom Name %b %t B-factor/Temperature %c %s Chain Identifier %e Element Atomic Symbol %i Atom Serial Number %n Residue Name %r Residue Number %M NMR Model Number (with leading "/") %A Alternate Conformation Identifier (with leading ";") ?load Load Syntax: load {} Load a molecule coordinate file into RasMol. Valid molecule file formats are 'pdb' (Protein Data Bank format), 'mdl' (Molecular Design Limited's MOL file format), 'alchemy' (Tripos' Alchemy file format), 'mol2' (Tripos' Sybyl Mol2 file format), 'charmm' (CHARMm file format), 'xyz' (MSC's XMol XYZ file format), 'mopac' (J. P. Stewart's MOPAC file format) or 'cif' (IUCr CIF or mmCIF file format). If no file format is specified, 'PDB', 'CIF', or 'mmCIF' is assumed by default. Up to 20 molecules may be loaded at a time. If CHEM_COMP ligand models are included in an mmCIF file, they will be loaded as NMR models, first giving the all the NMR models for model coordinates if specified and then giving all the NMR models for ideal model coordinates. To delete a molecule prior to loading another use the RasMol 'zap' command. To select a molecule for manipulation use the RasMol 'molecule ' command. The 'load' command selects all the atoms in the molecule, centres it on the screen and renders it as a CPK coloured wireframe model. If the molecule contains no bonds (i.e. contains only alpha carbons), it is drawn as an alpha carbon backbone. If the file specifies fewer bonds than atoms, RasMol determines connectivity using the 'connect' command. The 'load inline' command also allows the storing of atom coordinates in scripts to allow better integration with WWW browsers. A load command executed inside a script file may specify the keyword 'inline' instead of a conventional filename. This option specifies that the coordinates of the molecule to load are stored in the same file as the currently executing commands. ?map Map Syntax: map {} { } The RasMol 'map' commands manipulate electron density maps in coordination with the display of molecules. These commands are very memory intensive and may not work on machines with limited memory. Each molecule may have as many maps as available memory permits. Maps may be read from files or generated from Gaussian density distributions around atoms. 'map colour', to colour a map according to a given colour scheme, 'map generate', to generate a map from selected atoms based on pseudo-Gaussians, 'map level', to set the contouring level for selected maps, 'map load', to load a map from a file, 'map mask' to designate a mask for the selected maps, 'map resolution', to set the resolution for contouring selected maps, 'map restrict', to select one or more maps and to disable all others, 'map save', to save map information to a file, 'map scale', 'control the scaling of pseudo-Gaussians when generating maps', 'map select', to select one or more maps, 'map show', to display information about one or more maps or about the parameters to be used in generating or loading the next map, 'map spacing', to set the spacing betwen contour lines of selected maps, 'map spread', to set the variance of the Gaussians for map generation as a fraction of the atomic radius, and 'map zap' to delete previously generated or loaded maps. The effect of 'map generate' and 'map load' commands is modified by the 'map mask' command which limits the portion of the display space that can be considered for display of maps. ?mapcolour ?map colour Map colour Syntax: map {} colour The RasMol 'map colour' command colours the selected maps according to the specified colour scheme. The colour scheme may be a colour name or and RBG triple in brackets, or the keyword 'atom' to cause the map points to be coloured by the color of the nearest atom. ?mapgenerate ?map generate Map generate Syntax: map {} generate {LRsurf} dots map {} generate {LRsurf} mesh map {} generate {LRsurf} surface The RasMol 'map generate' command generates a map from whatever atoms are currently selected, by summing electron densities approximated by Gaussian distributions. The height of each Gaussian is determined by the setting of the ' map scale' command. In the default of map scale true, each Gaussian has a height proportional element type of the atom. If the optional 'LRSurf' parameter is given or if map scale false has been executed, each Gaussian is scaled so that the Gaussian contour level 1 is at the van der Waals radius. In either case a standard deviation determined by the most recently specified spread or resolution is used. If a non-zero spread has been given the radius of the atom is multiplied by the spread to find the standard deviation. The default is 2/3rds. If a resolution has been given, the spread is inferred as 2/3rds of the resolution. For example, if the resolution is given as 1., and the atom in question is a Carbon with a van der Waals radius of 468 RasMol units (1.87 Angstroms), the inferred spead is .6667, and the standard deviation of the Gaussian is taken as 1.25 Angstroms. If the spread has been set to zero, the spread for each atom is determined from the van der Waals radius and the probe atom radius to simulate the effect of a Lee-Richards surface. If no specific map was given by the map selector, the new map is given the next available map number. If a specific map was given by the map selector, the new map replaces that map. If more than one map was given by the map selector, the new map replaces the lowest numbered of the selected maps. In any case the new map becomes the currently selected map. The map is displayed as dots, mesh or a surface, depending on the last map rendering mode selected or the mode selected on the command itself. ?maplevel ?map level Map level Syntax: map {} level {MEAN} The RasMol 'map level' command sets the contour level to be used in creating subsequent representations of generated or loaded maps. If the keyword MEAN in used the level is relative to the mean of the map data. Otherwise the level is absolute. In general, a lower level results in a map containing more of the displayed volume, while a higher level results in a map containing less of the displayed volume. ?mapload ?map load Map load Syntax: map {} load The RasMol 'map load' command loads a map file into RasMol. The valid formats are CCP4 map format and imgCIF format. If no specific map was given by the map selector, the new map is given the next available map number. If a specific map was given by the map selector, the new map replaces that map. If more than one map was given by the map selector, the new map replaces the lowest numbered of the selected maps. In any case the new map becomes the currently selected map. The map is displayed as dots, mesh or a surface depending on the last map rendering mode selected. ?mapmask ?map mask Map mask Syntax: map {} mask selected map {} mask map {} mask none The RasMol 'map mask' command specifies a mask to be used to limit the display space to be used for making representations of other maps or removes an earlier mask specification. The 'selected' option indicates that the mask is to be created from the currently selected atoms. The '' option indicates that the mask is to be copied from the map of the number specified. The 'none' option removes the previously specified mask, if any. The map selector specifies the map or maps to which the specified mask will the applied. For example, 'map next mask selected' specifies that the currently selected atoms are to be used to generate a mask to be applied to any maps created by subsequent 'map load' or 'map generate' commands. Any map may be used as a mask. The portions of the mask map greater than than or equal to the average value of the mask map allow the values of the map being masked to be used as given. The portions of the mask map lower than the average value of the mask map cause the values of the map being masked to be treated as if they were equal to the lowest data value of the map being masked. ?mapresolution ?map resolution Map resolution Syntax: map {} resolution The RasMol 'map resolution' command specifies the resolution in RasMol units or, if a number containing a decimal point is given, the resolution in Angstroms to be used in generating and in representing maps. The resolution is used at the map spacing for representations of maps, indicating the separation between contour levels (see the 'map spacing' command) and to infer the map spread to be used in generated maps from selected atoms (see the 'map spread' command). The map spread is set to two thirds of the specified resolution. ?maprestrict ?map restrict Map restrict Syntax: map {} restrict The RasMol 'map restrict' command selects particular maps to make them active for subsequent map commands. This is similar to the 'map select' command, but does disables the display of the maps that were not selected. ?mapsave ?map save Map save Syntax: map {} save The RasMol 'map save' command saves an imgCIF map file. If no specific map was given by the map selector, the currently selected maps and their masks are written to the file, one map and mask pair per data block. ?mapscale ?map scale Map scale Syntax: map {} scale The RasMol 'map scale' command selects the scaling of pseudo-Gaussians in the 'map generate' commands. In the default of map scale true, each Gaussian has a height proportional element type of the atom. If map scale false has been executed, each Gaussian is scaled so that the Gaussian contour level 1 is at the van der Waals radius. In either case a standard deviation determined by the most recently specified spread or resolution is used. ?mapselect ?map select Map select Syntax: map {} select {atom {within} {add} {}} The RasMol 'map select' command selects particular maps to make them active for subsequent map commands. This is similar to the 'map restrict' command, but does not disable the display of the maps that were not selected. If the optional 'atom' parameter is given, the command selects the atoms with centres closest to the map points. The radius of the search may be specified by the parameter 'search_radius'. The default is to look for atoms within 4 Angstroms plus the probe radius. If the optional 'within' parameter is given, the new selection is taken from within the currently selected atoms. If the options 'add' parameter is given, the new selection is added to the currently selected atoms. The default is to search within all atoms. ?mapshow ?map show Map show Syntax: map {} show The RasMol 'map show' command causes information about the maps specified by the map selector to be written to the command window. ?mapspacing ?map spacing Map spacing Syntax: map {} spacing The RasMol 'map spacing' command specifies the spacing to be used between contour lines in creating representations of maps. The spacing is typically given in Angstroms with a decimal point, but may also be specified in RasMol units (250ths of an Angstom) as an integer. For maps loaded in grid coordinates that spacing is parallel to the cell edges. The default spacing is one half Angstrom. ?mapspread ?map spread Map spread Syntax: map {} spread The RasMol 'map spread' command specifies the reciprocal of the number of standard deviations per radius to be used in generating maps as sums of Gaussians centered on atomic positions. The default spread is one two thirds (i.e. each radius covers 1.5 standard deviations). If the spread has been set to zero, the spread for each atom is determined from the van der Waals radius and the probe atom radius to simulate the effect of a Lee-Richards surface. ?mapzap ?map zap Map zap Syntax: map {} zap The RasMol 'map zap' command removes the data and representations of the maps specified by the map selector. The map numbers of maps that have not been removed are not changed. ?molecule Molecule Syntax: molecule The RasMol 'molecule' command selects one of up to 5 previously loaded molecules for active manipulation. While all the molcules are displayed and may be rotated collectively (see the 'rotate all' command), only one molecule at a time time is active for manipulation by the commands which control the details of rendering. ?monitor Monitor Syntax: monitor monitor {} The RasMol 'monitor' command allows the display of distance monitors. A distance monitor is a dashed (dotted) line between an arbitrary pair of atoms, optionally labelled by the distance between them. The RasMol command 'monitor ' adds such a distance monitor between the two atoms specified by the atom serial numbers given as parameters Distance monitors are turned off with the command 'monitors off'. By default, monitors display the distance between its two end points as a label at the centre of the monitor. These distance labels may be turned off with the command 'set monitors off', and re-enabled with the command 'set monitors on'. Like most other representations, the colour of a monitor is taken from the colour of its end points unless specified by the 'colour monitors' command. Distance monitors may also be added to a molecule interactively with the mouse, using the 'set picking monitor' command. Clicking on an atom results in its being identified on the rasmol command line. In addition every atom picked increments a modulo counter such that, in monitor mode, every second atom displays the distance between this atom and the previous one. The shift key may be used to form distance monitors between a fixed atom and several consecutive positions. A distance monitor may also be removed (toggled) by selecting the appropriate pair of atom end points a second time. ?notoggle Notoggle Syntax: notoggle {} The RasMol 'NoToggle' command enables or disables the use of the toggle ability that is used by some of the other RasMol commands. When no boolean value is specified, NoToggle mode is ENABLED. When NoToggle mode is ENABLED, all toggle functionality is DISABLED. To turn it off, one must explicitly set 'notoggle off'. Some commands which use the toggle feature are: 'ColourMode'. More functions that utilize this capability may be added at a later date. ?pause Pause Syntax: pause wait The RasMol 'pause' command is used in script files to stop the script file for local manipulation by a mouse, until any key is pushed to restart the script file. 'Wait' is synonymous with 'pause'. This command may be executed in RasMol script files to suspend the sequential execution of commands and allow the user to examine the current image. When RasMol executes a 'pause' command in a script file, it suspends execution of the rest of the file, refreshes the image on the screen and allows the manipulation of the image using the mouse and scroll bars, or resizing of the graphics window. Once a key is pressed, control returns to the script file at the line following the 'pause' command. While a script is suspended the molecule may be rotated, translated, scaled, slabbed and picked as usual, but all menu commands are disabled. ?play Play Syntax: play {from