Provided by: rasmol_2.7.6.0-1build1_amd64 bug

NAME

       rasmol - Molecular Graphics Visualisation Tool v2.7.5

SYNOPSIS

       rasmol [-nodiplay] [[-format ] filename] [-script scriptfile]

FORMATS

       -pdb        Protein Data Bank
       -mdl        MDL's MOL File Format
       -mol2       Tripos' Sybyl MOL2 Format
       -xyz        MSC's XYZ (XMol) Format
       -mopac      MOPAC Input or Output File Format
       -alchemy    Alchemy File Format
       -charmm     CHARMm File Format
       -cif        IUCr CIF or CIF File Format

NOTICES

       This  software has been created from several sources.  Much of the code is from RasMol 2.6, as created by
       Roger Sayle.  The torsion angle  code,  new  POVRAY3  code  and  other  features  are  derived  from  the
       RasMol2.6x1  revisions  by  Arne  Mueller.   The  Ramachandran  printer plot code was derived from fisipl
       created by Frances C.  Bernstein.  See the Protein Data Bank program tape.

       The code to display multiple molecules and to allow bond rotation is derived in large part from  the  UCB
       mods  by  Gary  Grossman  and Marco Molinaro, included with permission of Eileen Lewis of the ModularCHEM
       Consortium.

       The CIF modifications make use of a library based in part on CBFlib by  Paul  J.  Ellis  and  Herbert  J.
       Bernstein.   Parts  of  CBFlib  is loosely based on the CIFPARSE software package from the NDB at Rutgers
       university.  Please type the RasMol commands help copying, help general, help IUCR, help CBFlib,
        and help CIFPARSE for applicable notices.  Please type help copyright for copyright notices.  If you use
       RasMol V2.6 or an earlier version, type the RasMol command help oldnotice.

COPYING

       This  version  is  based directly on RasMol version 2.7.4.2, on RasMol version 2.7.4.2, on RasMol version
       2.7.4, on RasMol version 2.7.3.1, on RasMol version 2.7.3, on RasMol version  2.7.2.1.1,  Rasmol  version
       2.7.2,  RasMol  version  2.7.1.1  and RasTop version 1.3 and indirectly on the RasMol 2.5-ucb and 2.6-ucb
       versions and version 2.6_CIF.2, RasMol 2.6x1 and RasMol_2.6.4.

       RasMol 2.7.5 may be distributed under the terms of the GNU General Public License (the GPL), see

                 http://www.gnu.org/licenses/gpl.txt

       or the file GPL or type the command help GPL

       or RasMol 2.7.5 may be distributed under the RASMOL license.  See the file NOTICE  or  type  the  command
       help RASLIC

       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.  If,  as  a  consequence  of a court judgment or allegation of patent infringement or for any
              other reason (not limited to patent issues), conditions are  imposed  on  you  (whether  by  court
              order,  agreement or otherwise) that contradict the conditions of this License, they do not excuse
              you from the conditions of this License.  If you cannot distribute so as to satisfy simultaneously
              your obligations under this License and any other pertinent obligations, then as a consequence you
              may not distribute the Program at all.  For example, if a patent license would not permit royalty-
              free  redistribution of the Program by all those who receive copies directly or indirectly through
              you, then the only way you could satisfy both it and this License would  be  to  refrain  entirely
              from distribution of the Program.

              If any portion of this section is held invalid or unenforceable under any particular circumstance,
              the balance of the section is intended to apply and the section as a whole is intended to apply in
              other circumstances.

              It  is  not  the  purpose  of this section to induce you to infringe any patents or other property
              right claims or to contest validity of any such claims; this  section  has  the  sole  purpose  of
              protecting  the integrity of the free software distribution system, which is implemented by public
              license practices.  Many people have made generous contributions to the  wide  range  of  software
              distributed  through that system in reliance on consistent application of that system; it is up to
              the author/donor to decide if he or she is willing to distribute software through any other system
              and a licensee cannot impose that choice.

              This section is intended to make thoroughly clear what is believed to be a consequence of the rest
              of this License.

                8. If the distribution and/or use of the Program is restricted in certain  countries  either  by
              patents  or  by copyrighted interfaces, the original copyright holder who places the Program under
              this License may add an explicit geographical distribution limitation excluding  those  countries,
              so  that  distribution  is  permitted only in or among countries not thus excluded.  In such case,
              this License incorporates the limitation as if written in the body of this License.

                9. The Free Software Foundation may publish revised and/or new versions of  the  General  Public
              License  from  time  to time.  Such new versions will be similar in spirit to the present version,
              but may differ in detail to address new problems or concerns.

              Each version is given a distinguishing version number.  If the Program specifies a version  number
              of  this License which applies to it and "any later version", you have the option of following the
              terms and conditions either of that version or of any later version published by the Free Software
              Foundation.   If the Program does not specify a version number of this License, you may choose any
              version ever published by the Free Software Foundation.

                10. If you wish to incorporate parts of the Program into other free programs whose  distribution
              conditions  are  different,  write  to  the  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.

                  <one line to give the program's name and a brief idea of what it does.>
                  Copyright (C) <year>  <name of author>

                  This program is free software; you can redistribute it and/or modify
                  it under the terms of the GNU General Public License as published by
                  the Free Software Foundation; either version 2 of the License, or
                  (at your option) any later version.

                  This program is distributed in the hope that it will be useful,
                  but WITHOUT ANY WARRANTY; without even the implied warranty of
                  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
                  GNU General Public License for more details.

                  You should have received a copy of the GNU General Public License
                  along with this program; if not, write to the Free Software
                  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA

              Also add information on how to contact you by electronic and paper mail.

              If  the  program  is  interactive,  make  it  output a short notice like this when it starts in an
              interactive mode:

                  Gnomovision version 69, Copyright (C) year name of author
                  Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
                  This is free software, and you are welcome to redistribute it
                  under certain conditions; type `show c' for details.

              The hypothetical commands `show w' and `show c' should show the appropriate parts of  the  General
              Public  License.   Of course, the commands you use may be called something other than `show w' and
              `show c'; they could even be mouse-clicks or menu items--whatever suits your program.

              You should also get your employer (if you work as a programmer) or your school, if any, to sign  a
              "copyright disclaimer" for the program, if necessary.  Here is a sample; alter the names:

                Yoyodyne, Inc., hereby disclaims all copyright interest in the program
                `Gnomovision' (which makes passes at compilers) written by James Hacker.

                <signature of Ty Coon>, 1 April 1989
                Ty Coon, President of Vice

              This  General Public License does not permit incorporating your program into proprietary programs.
              If your program is a subroutine library, you  may  consider  it  more  useful  to  permit  linking
              proprietary  applications  with  the library.  If this is what you want to do, use the GNU Library
              General Public License instead of this License.

       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 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.

       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.

       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 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
              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.

DESCRIPTION

       RasMol  is  a  molecular  graphics  program intended for the visualisation of proteins, nucleic acids and
       small molecules.  The program is aimed at display, teaching and generation of publication quality images.
       RasMol  runs  on  wide  range  of  architectures and operating systems including Microsoft Windows, Apple
       Macintosh, UNIX and VMS systems. UNIX and VMS versions require an 8,  24  or  32  bit  colour  X  Windows
       display (X11R4 or later).  The X Windows version of RasMol provides optional support for a hardware dials
       box and accelerated shared memory communication (via the XInput and MIT-SHM extensions) if  available  on
       the current X Server.

       The  program reads in a molecule coordinate file and interactively displays the molecule on the screen in
       a variety of colour schemes and molecule representations.  Currently  available  representations  include
       depth-cued  wireframes,  'Dreiding'  sticks, spacefilling (CPK) spheres, ball and stick, solid and strand
       biomolecular ribbons, atom labels and dot surfaces.

       Up to 5 molecules may be loaded and displayed at once.  Any one or all of
        the molecules may be rotated and translated.

       The RasMol help facility can be accessed by typing "help <topic>" or "help <topic> <subtopic>"  from  the
       command  line.  A  complete  list of RasMol commands may be displayed by typing "help commands". A single
       question mark may also be used to  abbreviate  the  keyword  "help".   Please  type  "help  notices"  for
       important notices.

COMMANDS

       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.

       Backbone
              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
              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   The  RasMol  command  bond <number> <number> + adds the designated bond to the drawing, increasing
              the bond order if the bond already exists.  The command bond <number> <number>  pick  selects  the
              two  atoms  specified by the atom serial numbers as the two ends of a bond around which the rotate
              bond <angle> command will be applied.  If no bond exists, it is created.

              Rotation around a previously picked bond may be specified by the rotate bond <angle>  command,  or
              may  also be controlled with the mouse, using the bond rotate on/off or the equivalent rotate bond
              on/off commands.

       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
              The  RasMol  cartoon  command does a display of a molecule ribbons as Richardson (MolScript) style
              protein cartoons, implemented as thick (deep)  ribbons.  The  easiest  way  to  obtain  a  cartoon
              representation of a protein is to use the Cartoons option on the Display menu. The cartoon command
              represents the currently selected residues as a deep ribbon with width specified by the  command's
              argument.   Using  the  command without a parameter results in the ribbon's width being taken from
              the protein's secondary structure, as described in the ribbons command. By default, the  C-termini
              of  beta-sheets  are  displayed  as  arrow  heads.  This may be enabled and disabled using the set
              cartoons command.  The depth of the cartoon may  be  adjusted  using  the  set  cartoons  <number>
              command.  The  set  cartoons  command  without  any  parameters returns these two options to their
              default values.

       Centre 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
              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
              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  transferring  images  between  applications  easier  under  Microsoft Windows or on an Apple
              Macintosh.

              When using RasMol on a UNIX or VMS system this functionality  may  be  achieved  by  generating  a
              raster image in a format that can be read by the receiving program using the RasMol write command.

       Colour Colour  the  atoms  (or other objects) of the selected region. The colour may be given as either a
              colour name or a comma separated triple of Red, Green and Blue (RGB) components enclosed in square
              brackets.  Typing  the  command  help  colours will give a list of all the predefined colour names
              recognised by RasMol.

              Allowed objects are atoms, bonds, backbone, ribbons, labels, dots, hbonds, map, and  ssbonds.   If
              no  object is specified, the default keyword atom is assumed.  Some colour schemes are defined for
              certain object types. The colour scheme none can be applied to all objects except atoms and  dots,
              stating  that  the  selected  objects  have  no  colour  of their own, but use the colour of their
              associated atoms (i.e. the atoms they connect).  Atom objects can also be coloured by alt,  amino,
              chain,  charge,  cpk,  group,  model, shapely, structure, temperature or user.  Hydrogen bonds can
              also be coloured by type and dot surfaces can also be coloured by  electrostatic  potential.   For
              more  information  type help colour <colour>.  Map objects may be coloured by specific color of by
              nearest atom.

       ColourMode
              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
              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  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 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  The RasMol depth command enables, disables or positions the back-clipping plane of  the  molecule.
              The  program  only  draws  those  portions  of the molecule that are closer to the viewer than the
              clipping plane.  Integer values range from zero at the very back of the molecule to 100  which  is
              completely  in front of the molecule. Intermediate values determine the percentage of the molecule
              to be drawn.

              This command interacts with the slab <value> command, which clips to  the  front  of  a  given  z-
              clipping plane.

       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   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
              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
              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 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.

       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   The RasMol help command provides on-line help on the given topic.

       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
              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.

       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.

       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 <n> command.

              The load command selects all the atoms in the molecule, centres it on the screen and renders it as
              a CPK coloured wireframe model. If the molecule  contains  no  bonds  (i.e.  contains  only  alpha
              carbons),  it  is drawn as an alpha carbon backbone. If the file specifies fewer bonds than atoms,
              RasMol determines connectivity using the connect command.

              The load inline command also allows the storing of atom coordinates in  scripts  to  allow  better
              integration  with  WWW  browsers.  A  load  command  executed inside a script file may specify the
              keyword inline instead of a conventional filename. This option specifies that the  coordinates  of
              the molecule to load are stored in the same file as the currently executing commands.

       Map    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 between contour lines of
              selected maps, map spread, to set the variance of the Gaussians for map generation as  a  fraction
              of the atomic radius, and map zap to delete previously generated or loaded maps.

              The  effect of map generate and map load commands is modified by the map mask command which limits
              the portion of the display space that can be considered for display of maps.

       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.

       Map generate
              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.

       Map level
              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.

       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.

       Map mask
              The RasMol map mask command specifies a mask to be used to limit the display space to be used  for
              making representations of other maps or removes an earlier mask specification.

              The  'selected' option indicates that the mask is to be created from the currently selected atoms.
              The '<number>' option indicates that the mask  is  to  be  copied  from  the  map  of  the  number
              specified.  The 'none' option removes the previously specified mask, if any.

              The  map  selector  specifies  the  map or maps to which the specified mask will the applied.  For
              example, 'map next mask selected' specifies that the currently selected atoms are to  be  used  to
              generate  a  mask  to  be  applied  to any maps created by subsequent 'map load' or 'map generate'
              commands.

              Any map may be used as a mask.  The portions of the mask map greater than than  or  equal  to  the
              average  value  of the mask map allow the values of the map being masked to be used as given.  The
              portions of the mask map lower than the average value of the mask map cause the values of the  map
              being masked to be treated as if they were equal to the lowest data value of the map being masked.

       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.

       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.

       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.

       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.

       Map select
              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.

       Map show
              The RasMol map show command causes information about the maps specified by the map selector to  be
              written to the command window.

       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.

       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.

       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
              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
              The RasMol monitor command allows the display of distance monitors. A distance monitor is a dashed
              (dotted) line between an arbitrary pair of atoms, optionally  labelled  by  the  distance  between
              them.   The  RasMol command monitor <number> <number> adds such a distance monitor between the two
              atoms specified by the atom serial numbers given as parameters

              Distance monitors are turned off with the command monitors off.  By default, monitors display  the
              distance between its two end points as a label at the centre of the monitor. These distance labels
              may be turned off with the command set monitors off, and re-enabled with the command set  monitors
              on.   Like most other representations, the colour of a monitor is taken from the colour of its end
              points unless specified by the colour monitors command.

              Distance monitors may also be added to a molecule interactively with  the  mouse,  using  the  set
              picking monitor command. Clicking on an atom results in its being identified on the rasmol command
              line. In addition every atom picked increments a modulo counter such that, in monitor mode,  every
              second  atom  displays  the  distance between this atom and the previous one. The shift key may be
              used to form distance monitors between a fixed atom and several consecutive positions. A  distance
              monitor  may  also  be  removed  (toggled)  by selecting the appropriate pair of atom end points a
              second time.

       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  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   The RasMol play command specifies the recording medium from which  to  play  back  a  movie.   The
              playback  frame  start time is given in seconds to millisecond precision.  Since we are working on
              computers, the medium is specified as a set of files, each marked with the  playback  frame  start
              time  in milliseconds as part of the name. The place in the name at which to look for the playback
              frame start time in milliseconds is marked by the characters "ssssss" with an  appropriate  number
              of  digits.  RasMol accepts either upper or lower case s's or decimal digits to mark the place for
              the time.  The play off and play eject commands effectively remove the specified medium from  use.
              If  no  medium is specified, play off suspends playing and play on resumes playing.  Normally play
              starts immediately and runs to the end of  the  medium.  However,  if  play  off  and/or  or  some
              combination of play from and play until is entered before play type medium, those settings will be
              used.

              As of release 2.7.5, RasMol support play from scripts and data files.

       Print  The RasMol print command sends the currently displayed image to the local  default  printer  using
              the  operating  system's native printer driver. Note: this command is not yet supported under UNIX
              or VMS. It is intended to take advantage of Microsoft Windows and Apple Macintosh printer drivers.
              For example, this allows images to be printed directly on a dot matrix printer.

              When  using RasMol on a UNIX or VMS system this functionality may be achieved by either generating
              a PostScript file using the RasMol write  ps  or  write  vectps  commands  and  printing  that  or
              generating a raster image file and using a utility to dump that to the local printer.

       Quit   Exit  from  the  RasMol  program.  The RasMol commands exit and quit are synonymous, except within
              nested scripts.  In that case, exit terminates only the current level, while quit  terminates  all
              nested levels of scripts.

       Record The  RasMol  record command specifies the recording medium to hold the movie. Since we are working
              on computers, the medium is specified as a template for a set  of  files,  each  marked  with  the
              playback  frame  start  time  in milliseconds (rather than as seconds to avoid embedding a decimal
              point) as part of the name. The place in the name to be replaced with  the  playback  frame  start
              time  in  milliseconds  is marked by the characters "ssssss" with an appropriate number of digits.
              RasMol accepts either upper or lower case s's or decimal digits to mark the place  for  the  time.
              The  record  off  commands remove the specified medium from use. If no medium is specified, record
              off suspends recording and record on resumes recording with the next available time  on  the  same
              medium.  The  screen  is  the  default  medium  and  is,  by  default, on. Writing to disk must be
              explicitly specified so that the disk does not get  filled  up  unintentionally.  The  type  of  a
              recording  medium may be an image type such as gif, pict or png to record the actual screen images
              or script to record the RasMol commands used to generate the frames.

              Normally recording starts at playback frame start time 0 seconds.  A  non-zero  starting  time  in
              seconds can be specified with the record from command as in record from 25 or record from 37.25 to
              help in organizing scenes of movies to be assembled later in an  appropriate  order.   The  record
              until  command  allows  an  upper limit to be set on recording time in seconds.  The default is to
              have no limit. Issuing the commands

              record from 600

              record until 1800

              would result in a 20 minute movie segment intended to start 10 minutes into a longer movie.  These
              commands allow control over rewriting selected time segments.

       Refresh
              The  RasMol  refresh  command  redraws  the  current  image.   This is useful in scripts to ensure
              application of a complex list of parameter changes.

       Renumber
              The RasMol renumber command sequentially numbers the residues  in  a  macromolecular  chain.   The
              optional  parameter  specifies  the  value  of the first residue in the sequence. By default, this
              value is one. For proteins, each amino acid is numbered consecutively from the N terminus to the C
              terminus.  For  nucleic  acids, each base is numbered from the 5' terminus to the 3' terminus. All
              chains in the current database are renumbered and gaps in the original sequence are  ignored.  The
              starting value for numbering may be negative.

       Reset  The  RasMol reset command restores the original viewing transformation and centre of rotation. The
              scale is set to its default value, zoom 100, the centre of rotation is set to the geometric centre
              of  the  currently  loaded  molecule,  centre  all, this centre is translated to the middle of the
              screen and the viewpoint set to the default orientation.

              This command should not be mistaken for the RasMol zap command which deletes the currently  stored
              molecule, returning the program to its initial state.

       Restrict
              The  RasMol  restrict  command  both  defines  the  currently  selected region of the molecule and
              disables the representation of (most of) those parts of the  molecule  no  longer  selected.   All
              subsequent  RasMol  commands  that  modify  a  molecule's colour or representation affect only the
              currently selected region. The parameter of a restrict command is a RasMol atom expression that is
              evaluated  for  every  atom  of  the  current molecule. This command is very similar to the RasMol
              select command, except restrict disables the wireframe, spacefill and backbone representations  in
              the non-selected region.

              Type  "help  expression"  for  more  information  on  RasMol  atom expressions or see section Atom
              Expressions.

       Ribbons
              The RasMol ribbons command displays the currently loaded protein or nucleic acid as a smooth solid
              "ribbon"  surface  passing  along  the  backbone of the protein.  The ribbon is drawn between each
              amino acid whose alpha carbon is currently selected. The colour of the ribbon is  changed  by  the
              RasMol  colour  ribbon  command. If the current ribbon colour is none (the default), the colour is
              taken from the alpha carbon at each position along its length.

              The width of the ribbon at each position is determined by the  optional  parameter  in  the  usual
              RasMol  units.  By  default  the  width of the ribbon is taken from the secondary structure of the
              protein or a constant value of 720 (2.88 Angstroms) for  nucleic  acids.   The  default  width  of
              protein  alpha  helices  and beta sheets is 380 (1.52 Angstroms) and 100 (0.4 Angstroms) for turns
              and random coil. The secondary structure assignment is either from  the  PDB  file  or  calculated
              using  the  DSSP algorithm as used by the structure command. This command is similar to the RasMol
              command strands which renders the biomolecular ribbon as parallel depth-cued curves.

       Rotate Rotate the molecule about the specified axis.  Permitted values for the axis  parameter  are  "x",
              "y",  "z"  and  "bond".  The integer parameter states the angle in degrees for the structure to be
              rotated. For the X and Y axes, positive values move the closest point up and right,  and  negative
              values move it down and left, respectively. For the Z axis, a positive rotation acts clockwise and
              a negative angle anti-clockwise.

              Alternatively, this command may be used to  specify  which  rotations  the  mouse  or  dials  will
              control.   If rotate bond true is selected, the horizontal scroll bar will control rotation around
              the axis selected by the bond src dst pick command.  If rotate all true is selected, and  multiple
              molecules  have  been  loaded,  then  all molecules will rotate together.  In all other cases, the
              mouseand dials control the the rotation of the molecule selected by the molecule n command.

       Russian
              The RasMol Russian command sets the menus and messages to the Russian versions.

              This command may not work correctly unless appropriate fonts have been  installed.   The  commands
              Bulgarian, Chinese, English, French, Italian, Russian and Spanish may be used to select Bulgarian,
              Chinese, English, French, Italian, Japanese,  Russian  and  Spanish  menus  and  messages  if  the
              appropriate fonts have been installed.

       Save   Save  the  currently  selected  set  of atoms in a Protein Data Bank (PDB), Wide PDB (WPDB), mmCIF
              (CIF), MDL, Alchemy(tm) or XYZ format file.  Some of the implementations are are  only  sufficient
              for reloading in RasMol and may need to be supplemented for use by programs other than RasMol.

              Atom  serial  numbers  are  regenerated.   When  this  will result in more than 99,999 atoms being
              written in PDB format, numbers may be repeated.  If possible the repeats are  done  by  using  the
              same numbers in different NMR models.

              The  distinction  between  this  command  and  the RasMol write command has been dropped. The only
              difference is that without a format specifier the save command generates a PDB file and the  write
              command generates a GIF image.

       Script The  RasMol  script  command  reads  a  set  of  RasMol commands sequentially from a text file and
              executes them. This allows sequences of commonly used commands  to  be  stored  and  performed  by
              single  command. A RasMol script file may contain a further script command up to a maximum "depth"
              of 10, allowing complicated sequences of actions to be executed.  RasMol  ignores  all  characters
              after  the first '#' character on each line allowing the scripts to be annotated. Script files are
              often also annotated using the RasMol echo command.

              The most common way to generate a RasMol script file is to use the write script  or  write  rasmol
              commands  to  output  the  sequence  of  commands  that are needed to regenerate the current view,
              representation and colouring of the currently displayed molecule.

              The RasMol command source is synonymous with the script command.

       Select Define the currently selected  region  of  the  molecule.  All  subsequent  RasMol  commands  that
              manipulate  a  molecule  or modify its colour or representation only affect the currently selected
              region. The parameter of a select command is a RasMol expression that is evaluated for every  atom
              of  the  current  molecule. The currently selected (active) region of the molecule are those atoms
              that cause the expression to evaluate true. To select the whole molecule use  the  RasMol  command
              select  all.   The  behaviour  of  the  select command without any parameters is determined by the
              RasMol hetero and hydrogen parameters.

              Type "help expression" for more information  on  RasMol  atom  expressions  or  see  section  Atom
              Expressions.

       Set    The  RasMol set command allows the user to alter various internal program parameters such as those
              controlling rendering options. Each parameter has its own set or  permissible  parameter  options.
              Typically,  omitting  the  parameter  option resets that parameter to its default value. A list of
              valid parameter names is given below.

       Show   The RasMol show command display details of the  status  of  the  currently  loaded  molecule.  The
              command  show  information  lists  the molecule's name, classification, PDB code and the number of
              atoms, chains, groups it contains.  If hydrogen bonding, disulphide bridges or secondary structure
              have  been  determined,  the  number  of  hbonds,  ssbonds,  helices,  ladders  and turns are also
              displayed, respectively. The command show centre shows any non-zero centering values  selected  by
              the centre [CenX, CenY, CenZ] command. The command show phipsi shows the phi and psi angles of the
              currently selected residues and the omega angles of cis peptide bonds. The command  show  RamPrint
              (or  'show RPP' or 'show RamachandranPrinterPlot') shows a simple Ramachandran printer plot in the
              style of Frances Bernstein's fisipl program.  The command show rotation (or 'show  rot'  or  'show
              'rotate')  shows the currently selected values of z, y, x and bond rotations, if any.  The command
              show selected (or 'show selected group' or 'show selected chain' or  'show selected atom' )  shows
              the  groups  (default), chains or atoms of the current selection.  The command show sequence lists
              the residues that comprise each chain of the molecule.  The command show symmetry shows the  space
              group  and  unit cell of the molecule. The command show translation shows any non-zero translation
              values selected by the translate <axis> <value> command. The command show zoom shows any  non-zero
              zoom value selected by the zoom <value> command.

       Slab   The  RasMol  slab command enables, disables or positions the z-clipping plane of the molecule. The
              program only draws those portions of the molecule that  are  further  from  the  viewer  than  the
              slabbing  plane.   Integer values range from zero at the very back of the molecule to 100 which is
              completely in front of the molecule. Intermediate values determine the percentage of the  molecule
              to be drawn.

              This  command  interacts  with  the  depth  <value> command, which clips to the rear of a given z-
              clipping plane.

       Spacefill
              The RasMol spacefill command is used to represent all of the currently  selected  atoms  as  solid
              spheres.  This  command  is  used  to produce both union-of-spheres and ball-and-stick models of a
              molecule. The command, spacefill true, the default, represents each atom as a sphere  of  van  der
              Waals  radius.   The  command  spacefill  off turns off the representation of the selected atom as
              spheres. A sphere radius may be specified as an integer in RasMol units (1/250th  Angstrom)  or  a
              value  containing  a  decimal  point.  A  value  of  500  (2.0  Angstroms) or greater results in a
              "Parameter value too large" error.

              The temperature option sets the radius of each sphere to  the  value  stored  in  its  temperature
              field.  Zero  or  negative values have no effect and values greater than 2.0 are truncated to 2.0.
              The user option allows the radius of each sphere to  be  specified  by  additional  lines  in  the
              molecule's PDB file using Raster 3D's COLOUR record extension.

              The RasMol command cpk is synonymous with the spacefill command.

              The  RasMol  command  cpknew  is  synonymous  with  the  spacefill command, except that a slightly
              different set of colours is used.

       Spanish
              The RasMol Spanish command sets the menus and messages to the Spanish versions.

              This command may not work correctly unless appropriate fonts have been  installed.   The  commands
              Bulgarian, Chinese, English, French, Italian, Russian and Spanish may be used to select Bulgarian,
              Chinese, English, French, Italian, Japanese,  Russian  and  Spanish  menus  and  messages  if  the
              appropriate fonts have been installed.

       SSBonds
              The  RasMol ssbonds command is used to represent the disulphide bridges of the protein molecule as
              either dotted lines or cylinders between the connected cysteines. The first time that the  ssbonds
              command  is  used,  the  program searches the structure of the protein to find half-cysteine pairs
              (cysteines whose sulphurs are within 3 Angstroms of each other) and reports the number of  bridges
              to the user. The command ssbonds on displays the selected "bonds" as dotted lines, and the command
              ssbonds off disables the  display  of  ssbonds  in  the  currently  selected  area.  Selection  of
              disulphide bridges is identical to normal bonds, and may be adjusted using the RasMol set bondmode
              command. The colour of disulphide bonds may be  changed  using  the  colour  ssbonds  command.  By
              default, each disulphide bond has the colours of its connected atoms.

              By  default  disulphide  bonds  are drawn between the sulphur atoms within the cysteine groups. By
              using the set ssbonds command the position of the cysteine's alpha carbons may be used instead.

       Star   The RasMol star command is used to represent all of the currently selected  atoms  as  stars  (six
              strokes,  one  each  in  the  x,  -x, y, -y, z and -z directions).  The commands select not bonded
              followed by star 75 are useful to mark unbonded atoms in a wireframe display  with  less  overhead
              than  provided  by  spacefill  75.   This  can  be done automatically for all subsequent wireframe
              displays with the command set bondmode not bonded.

              The command star true, the default, represents each atom as a star with strokes  length  equal  to
              van  der  Waals radius.  The command star off turns off the representation of the selected atom as
              stars. A star stroke length may be specified as an integer in RasMol units (1/250th Angstrom) or a
              value  containing  a  decimal  point.  A  value  of  500  (2.0  Angstroms) or greater results in a
              "Parameter value too large" error.

              The temperature option sets the stroke length of each star to the value stored in its  temperature
              field.  Zero  or  negative values have no effect and values greater than 2.0 are truncated to 2.0.
              The user option allows the stroke length of each star to be specified by additional lines  in  the
              molecule's PDB file using Raster 3D's COLOUR record extension.

              The RasMol spacefill command can be used for more artistic rendering of atoms as spheres.

       Stereo The  RasMol  stereo  command  provides  side-by-side stereo display of images. Stereo viewing of a
              molecule may be turned on (and off) either by selecting Stereo from the Options menu, or by typing
              the commands stereo on or stereo off.

              Starting  with  RasMol  version  2.7.2.1, the Stereo menu selection and the command stereo without
              arguments cycle from the initial state of stereo off to stereo on in cross-eyed mode to stereo  on
              in wall-eyed mode and then back to stereo off.

              The  separation  angle  between  the  two  views  may be adjusted with the set stereo [-] <number>
              command, where positive values result in crossed eye viewing and negative values in relaxed (wall-
              eyed) viewing.  The inclusion of [-] <number> in the stereo command, as for example in stereo 3 or
              stereo -5, also controls angle and direction.

              The stereo command is only partially implemented. When stereo is  turned  on,  the  image  is  not
              properly recentred. (This can be done with a translate x -<number>
               command.)   It  is  not  supported  in  vector PostScript output files, is not saved by the write
              script command, and in general is not yet properly interfaced with several other features  of  the
              program.

       Strands
              The  RasMol  strands  command  displays  the  currently loaded protein or nucleic acid as a smooth
              "ribbon" of depth-cued curves passing along the backbone of the protein. The ribbon is composed of
              a  number of strands that run parallel to one another along the peptide plane of each residue. The
              ribbon is drawn between each amino acid whose alpha carbon is currently selected.  The  colour  of
              the  ribbon  is  changed by the RasMol colour ribbon command. If the current ribbon colour is none
              (the default), the colour is taken from the alpha carbon at each position along  its  length.  The
              central  and  outermost  strands may be coloured independently using the colour ribbon1 and colour
              ribbon2 commands, respectively. The number of strands in the  ribbon  may  be  altered  using  the
              RasMol set strands command.

              The  width  of  the  ribbon  at each position is determined by the optional parameter in the usual
              RasMol units. By default the width of the ribbon is taken from  the  secondary  structure  of  the
              protein  or  a  constant  value  of  720 for nucleic acids (which produces a ribbon 2.88 Angstroms
              wide).  The default width of protein alpha helices and beta sheets is 380 (1.52 Angstroms) and 100
              (0.4  Angstroms)  for turns and random coil. The secondary structure assignment is either from the
              PDB file or calculated using the DSSP algorithm as used by the structure command. This command  is
              similar  to  the  RasMol  command ribbons which renders the biomolecular ribbon as a smooth shaded
              surface.

       Structure
              The RasMol structure command calculates secondary structure assignments for the  currently  loaded
              protein.  If the original PDB file contained structural assignment records (HELIX, SHEET and TURN)
              these are discarded.  Initially, the hydrogen bonds of the current molecule  are  found,  if  this
              hasn't  been  done  already.  The secondary structure is then determined using Kabsch and Sander's
              DSSP algorithm. Once finished the program reports the number of helices, strands and turns found.

       Surface
              The RasMol surface command renders a Lee-Richards molecular surface resulting from rolling a probe
              atom  on  the selected atoms.  The value given specifies the radius of the probe.  If given in the
              first form, the evolute of the surface of the probe is shown (the solvent excluded  surface).   If
              given  in  the second form, the envelope of the positions of the center of the probe is shown (the
              solvent accessible surface).

       Trace  The RasMol trace command displays a smooth spline between   consecutive  alpha  carbon  positions.
              This  spline does not pass exactly through the alpha carbon position of each residue, but  follows
              the same path as ribbons, strands and cartoons.  Note that residues may be displayed  as  ribbons,
              strands,  cartoons  or  as  a  trace.   Enabling one of these representations disables the others.
              However, a residue  may  be  displayed  simultaneously  as  backbone  and  as  one  of  the  above
              representations.   This  may change in future versions of RasMol.  Prior to version 2.6, trace was
              synonymous with backbone.

              Trace temperature displays the backbone as a  wider  cylinder  at  high  temperature  factors  and
              thinner   at   lower.    This   representation  is  useful  to  X-ray  crystallographers  and  NMR
              spectroscopists.

       Translate
              The RasMol translate command moves the position of the centre of the molecule on the  screen.  The
              axis  parameter  specifies  along which axis the molecule is to be moved and the integer parameter
              specifies the absolute position of the molecule centre from the middle of the  screen.   Permitted
              values  for the axis parameter are "x", "y" and "z".  Displacement values must be between -100 and
              100 which correspond to  moving  the  current  molecule  just  off  the  screen.  A  positive  "x"
              displacement  moves  the molecule to the right, and a positive "y" displacement moves the molecule
              down the screen. The pair of commands translate x 0 and translate y 0 centres the molecule on  the
              screen.

       UnBond The RasMol command unbond <number> <number> removes the designated bond from the drawing.

              The  command  unbond  without  arguments  removes  a  bond  previously picked by the bond <number>
              <number> pick command.

       Wireframe
              The RasMol wireframe command represents each bond within the selected region of the molecule as  a
              cylinder,  a line or a depth-cued vector. The display of bonds as depth-cued vectors (drawn darker
              the further away from the viewer) is turned on by the command  wireframe  or  wireframe  on.   The
              selected  bonds  are  displayed as cylinders by specifying a radius either as an integer in RasMol
              units or containing a decimal point as a value in  Angstroms.   A  parameter  value  of  500  (2.0
              Angstroms)  or  above results in an "Parameter value too large" error. Bonds may be coloured using
              the colour bonds command.

              If the selected bonds involved atoms of alternate conformers then the bonds are  narrowed  in  the
              middle  to  a  radius  of  .8  of the specified radius (or to the radius specified as the optional
              second parameter).

              Non-bonded atoms, which could become invisible in an ordinary wireframe display can be marked by a
              preceding  set  bondmode  not bonded command.  If nearly co-linear bonds to atoms cause them to be
              difficult to see in a wireframe display, the set bondmode all command will  add  markers  for  all
              atoms in subsequent wireframe command executions.

       Write  Write  the  current  image  to a file in a standard format. Currently supported image file formats
              include bmp (Microsoft bitmap) and gif (Compuserve GIF), iris (IRIS RGB), ppm  (Portable  Pixmap),
              ras  (Sun  rasterfile),  ps  and  epsf  (Encapsulated PostScript), monops (Monochrome Encapsulated
              PostScript), pict (Apple PICT), vectps (Vector Postscript).  The write command may also be used to
              generate  command  scripts  for  other  graphics  programs.  The  format  script writes out a file
              containing the RasMol script commands to reproduce the current image. The format molscript  writes
              out  the  commands  required to render the current view of the molecule as ribbons in Per Kraulis'
              Molscript program and the format kinemage the commands for David Richardson's program  Mage.   The
              following formats are useful for further processing: povray (POVRay 2), povray3 (POVRay 3 -- under
              development), vrml (VRML file).  Finally, several formats are provided to provide phi-psi data for
              listing  or  for  phipsi (phi-psi data as an annotated list with cis omegas), ramachan and RDF and
              RamachandranDataFile   (phi-psi   data   as   columns   of   numbers   for   gnuplot),   RPP   and
              RamachandranPrinterPlot (phi-psi data as a printer plot).

              The  distinction  between  this  command  and  the  RasMol save command has been dropped. The only
              difference is that without a format specifier the save command generates a PDB file and the  write
              command generates a GIF image.

       Zap    Deletes  the  contents  of  the  current  database and resets parameter variables to their initial
              default state.

       Zoom   Change the magnification of the currently displayed image. Boolean parameters  either  magnify  or
              reset the scale of current molecule. An integer parameter specifies the desired magnification as a
              percentage of the default scale. The minimum parameter value is 10; the maximum parameter value is
              dependent  upon  the size of the molecule being displayed. For medium sized proteins this is about
              500.

SET PARAMETERS

       RasMol has a number of internal parameters that may be modified using the set command.  These  parameters
       control a number of program options such as rendering options and mouse button mappings.

           picking         play.fps        radius          record.aps

       Set Ambient
              The  RasMol  ambient  parameter is used to control the amount of ambient (or surrounding) light in
              the scene. The ambient value must be between 0 and 100. It controls the  percentage  intensity  of
              the  darkest shade of an object. For a solid object, this is the intensity of surfaces facing away
              from the light source or in shadow.  For depth-cued objects  this  is  the  intensity  of  objects
              furthest from the viewer.

              This   parameter  is  commonly  used  to  correct  for  monitors  with  different  "gamma  values"
              (brightness), to change how light or dark a hardcopy image appears when printed or  to  alter  the
              feeling of depth for wireframe or ribbon representations.

       Set Axes
              The  RasMol  axes  parameter  controls  the  display  of orthogonal coordinate axes on the current
              display. The coordinate axes are those used in the molecule data  file,  and  the  origin  is  the
              centre  of  the  molecule's  bounding  box.  The  set  axes command is similar to the commands set
              boundbox and set unitcell that display the  bounding  box  and  the  crystallographic  unit  cell,
              respectively.

       Set Backfade
              The  RasMol  backfade  parameter  is  used to control backfade to the specified background colour,
              rather than black.  This is controlled by the commands set backfade on and set backfade off.   For
              example, this may be used to generate depth-cued images that fade to white, rather than black.

       Set Background
              The  RasMol  background parameter is used to set the colour of the "canvas" background. The colour
              may be given as either a colour name or a  comma  separated  triple  of  Red,  Green,  Blue  (RGB)
              components  enclosed  in  square brackets. Typing the command help colours will give a list of the
              predefined colour names  recognised  by  RasMol.   When  running  under  X  Windows,  RasMol  also
              recognises colours in the X server's colour name database.

              The command set background is synonymous with the RasMol command background.

       Set BondMode
              The  RasMol  set  bondmode  command  controls  the  mechanism  used to select individual bonds and
              modifies the display of bonded and non-bonded atoms by subsequent wireframe commands.

              When using the select and restrict commands, a given bond will be selected if i) the  bondmode  is
              or  and  either  of  the  connected  atoms  is selected, or ii) the bondmode is and and both atoms
              connected by the bond are selected. Hence an individual bond may be uniquely identified  by  using
              the command set bondmode and and then uniquely selecting the atoms at both ends.

              The  bondmode  [all  |  none  |  not  bonded] commands add star 75 or spacefill 75 markers for the
              designated atoms to wireframe displays.  Stars are used when the  specified  wireframe  radius  is
              zero.

       Set Bonds
              The  RasMol  bonds  parameter  is  used  to control display of double and triple bonds as multiple
              lines or cylinders.  Currently bond orders are only read from  MDL Mol files,  Sybyl  Mol2  format
              files,  Tripos  Alchemy format files, CIF and mmCIF,  and suitable PDB files.  Double (and triple)
              bonds are specified in some  PDB files by specifying a given bond  twice   (and  three  times)  in
              CONECT  records.   The   command set bonds on enables the display of bond orders, and  the command
              set bonds off disables them.

       Set BoundBox
              The RasMol boundbox parameter controls the display of the current molecule's bounding box  on  the
              display.  The  bounding  box  is  orthogonal  to the data file's original coordinate axes. The set
              boundbox command is similar to the commands set axes and  set  unitcell  that  display  orthogonal
              coordinate axes and the bounding box, respectively.

       Set Cartoon
              The  RasMol  cartoon  parameter  is  used to control display of the cartoon version of the ribbons
              display.  By default, the C-termini of beta-sheets are displayed  as  arrow  heads.  This  may  be
              enabled  and  disabled  using  the set cartoons <boolean> command. The depth of the cartoon may be
              adjusted using the cartoons <number> command. The set  cartoons  command  without  any  parameters
              returns these two options to
               their default values.

       Set CisAngle
              The RasMol cisangle parameter controls the cutoff angle for identifying cis peptide
               bonds.  If no value is given, the cutoff is set to 90 degrees.

       Set Display
              This  command  controls  the  display  mode  within RasMol. By default, set display normal, RasMol
              displays the molecule in the representation  specified  by  the  user.  The  command  set  display
              selected  changes  the  display mode such that the molecule is temporarily drawn so as to indicate
              currently selected portion of the molecule. The user specified colour  scheme  and  representation
              remains  unchanged.   In  this  representation  all selected atoms are shown in yellow and all non
              selected atoms are shown in blue. The colour of the background is also changed to a dark  grey  to
              indicate  the  change  of display mode.  This command is typically only used by external Graphical
              User Interfaces (GUIs).

       Set FontSize
              The RasMol set fontsize command is used to control the size  of  the  characters  that  form  atom
              labels.  This  value  corresponds  to the height of the displayed character in pixels. The maximum
              value of fontsize is 48 pixels, and the default value is 8 pixels  high.   Fixed  or  proportional
              spacing  may  be  selected  by appending the "FS" or "PS" modifiers, respectively.  The default is
              "FS".  To display atom labels on the screen use the RasMol label command and to change the  colour
              of displayed labels, use the colour labels command.

       Set FontStroke
              The  RasMol  set  fontstroke  command  is  used  to  control  the  size of the stroke width of the
              characters that form atom labels.  This value is the radius in pixels of cylinders  used  to  form
              the  strokes.   The  special  value  of "0" is the default used for the normal single pixel stroke
              width, which allows for rapid drawing and rotation of the image.  Non-zero values are provided  to
              allow  for more artistic atom labels for publication at the expense of extra time in rendering the
              image.

              When wider strokes are used, a larger font size is  recommend,  e.g.   by  using  the  RasMol  set
              fontsize 24 PS command, followed by set fontstroke 2

              To  display  atom  labels  on the screen use the RasMol label command, and to change the colour of
              displayed labels use the colour labels command.

       Set HBonds
              The RasMol hbonds parameter determines whether hydrogen bonds are  drawn  between  the  donor  and
              acceptor atoms of the hydrogen bond, set hbonds sidechain or between the alpha carbon atoms of the
              protein backbone and between the phosphorous atoms  of  the  nucleic  acid  backbone,  set  hbonds
              backbone.   The  actual  display  of  hydrogen  bonds is controlled by the hbonds command. Drawing
              hydrogen bonds between protein alpha carbons or nucleic acid phosphorous atoms is useful when  the
              rest  of  the  molecule  is  shown in only a schematic representation such as backbone, ribbons or
              strands.  This parameter is similar to the RasMol ssbonds parameter.

       Set Hetero
              The RasMol hetero parameter is used to  modify  the  'default'  behaviour  of  the  RasMol  select
              command,  i.e.  the  behaviour  of  select  without  any parameters. When this value is false, the
              default select region does not include any heterogeneous atoms (refer to the predefined set hetero
              ).  When this value is true, the default select region may contain hetero atoms. This parameter is
              similar to the RasMol hydrogen  parameter  which  determines  whether  hydrogen  atoms  should  be
              included  in  the default set. If both hetero and hydrogen are true, select without any parameters
              is equivalent to select all.

       Set HourGlass
              The RasMol hourglass parameter allows the user to enable and disable the use of the  'hour  glass'
              cursor  used  by RasMol to indicate that the program is currently busy drawing the next frame. The
              command set hourglass on enables the indicator, whilst set  hourglass  off  prevents  RasMol  from
              changing  the  cursor.  This  is useful when spinning the molecule, running a sequence of commands
              from a script file or using interprocess communication to execute complex sequences  of  commands.
              In these cases a 'flashing' cursor may be distracting.

       Set Hydrogen
              The  RasMol  hydrogen  parameter  is  used  to modify the "default" behaviour of the RasMol select
              command, i.e. the behaviour of select without any  parameters.  When  this  value  is  false,  the
              default  select  region  does  not  include any hydrogen, deuterium or tritium atoms (refer to the
              predefined set hydrogen ). When this value is true, the default select region may contain hydrogen
              atoms.  This  parameter  is  similar  to  the  RasMol  hetero  parameter  which determines whether
              heterogeneous atoms should be included in the default set. If both hydrogen and hetero  are  true,
              select without any parameters is equivalent to select all.

       Set Kinemage
              The  RasMol  set  kinemage  command controls the amount of detail stored in a Kinemage output file
              generated by the RasMol write kinemage command. The output  kinemage  files  are  intended  to  be
              displayed  by  David  Richardson's Mage program.  set kinemage false, the default, only stores the
              currently displayed representation in the generated output file. The command  set  kinemage  true,
              generates a more complex Kinemage that contains both the wireframe and backbone representations as
              well as the coordinate axes, bounding box and crystal unit cell.

       Set Menus
              The RasMol set menus command enables the canvas window's menu buttons or menu bar. This command is
              typically  only  used by graphical user interfaces or to create as large an image as possible when
              using Microsoft Windows.

       Set Monitor
              The RasMol set monitor command enables monitors.  The distance monitor labels may  be  turned  off
              with the command set monitor off, and re-enabled with the command set monitor on.

       Set Mouse
              The  RasMol  set mouse command sets the rotation, translation, scaling and zooming mouse bindings.
              The default value is rasmol which is suitable for two button  mice  (for  three  button  mice  the
              second  and third buttons are synonymous); X-Y rotation is controlled by the first button, and X-Y
              translation by the second. Additional functions are controlled by holding a modifier  key  on  the
              keyboard.   [Shift]  and the first button performs scaling, [shift] and the second button performs
              Z-rotation, and [control] and the first mouse button controls the clipping plane. The insight  and
              quanta options provide the same mouse bindings as other packages for experienced users.

       Set Picking
              The  RasMol  set  picking  series  of  commands  affects  how  a user may interact with a molecule
              displayed on the screen in RasMol.

              Enabling/Disabling Atom Identification Picking: Clicking on an atom  with  the  mouse  results  in
              identification  and the display of its residue name, residue number, atom name, atom serial number
              and chain in the command window. This behavior may be disabled with the command set  picking  none
              and  restored  with  the command set picking ident.  The command set picking coord adds the atomic
              coordinates of the atom to the display.

              Disabling picking, by using set picking off is useful when executing the pause command  in  RasMol
              scripts  as  it  prevents  the display of spurious message on the command line while the script is
              suspended.

              Measuring Distances, Angles  and  Torsions:  Interactive  measurement  of  distances,  angles  and
              torsions  is  achieved  using the commands: set picking distance, set picking monitor, set picking
              angle and set picking torsion, respectively. In these modes, clicking on an  atom  results  in  it
              being  identified  on  the  rasmol command line. In addition every atom picked increments a modulo
              counter such that in distance mode, every second atom displays the distance (or distance  monitor)
              between this atom and the previous one. In angle mode, every third atom displays the angle between
              the previous three atoms and in torsion mode every fourth atom displays the  torsion  between  the
              last  four  atoms. By holding down the shift key while picking an atom, this modulo counter is not
              incremented and allows, for example, the distances of consecutive atoms from a fixed  atom  to  be
              displayed.  See  the  monitor command for how to control the display of distance monitor lines and
              labels.

              Labelling Atoms with the Mouse: The mouse may also be used to toggle the display of an atom  label
              on  a  given  atom.  The RasMol command set picking label removes a label from a picked atom if it
              already has one or displays a concise label at that atom position otherwise.

              Centring Rotation with the Mouse: A molecule may be centred on a specified atom position using the
              RasMol  commands  set  picking centre or set picking center.  In this mode, picking an atom causes
              all further rotations to be about that point.

              Picking a Bond as a Rotation Axis: Any bond may be picked as an axis of rotation for  the  portion
              of the molecule beyond the second atom selected.  This feature should be used with caution, since,
              naturally, it changes the conformation of the molecule.  After executing set picking bond or using
              the  equivalent  "Pick  Bond" in the "Settings" menu, a bond to be rotated is picked with the same
              sort of mouse clicks as are used for picking atoms for  a  distance  measurement.   Normally  this
              should  be  done where a bond exists, but if no bond exists, it will be added.  The bond cannot be
              used for rotation if it is part of a ring of any  size.   All  bonds  selected  for  rotation  are
              remembered so that they can be properly reported when writing a script, but only the most recently
              selected bond may be actively rotated.

              Enabling Atom/Group/Chain Selection Picking: Atoms, groups and chains may be selected (as if  with
              the  select  command),  with  the set picking atom, set picking group, set picking chain commands.
              For each of these commands, the shift key may be used to have a new selection added  to  the  old,
              and the control key may be used to have a new selection deleted from the old. When the set picking
              atom command is given, the mouse can be used to pick or to drag a box around the atoms  for  which
              selection is desired.  When the set picking group command is given, picking any an atom will cause
              selection of all atoms which agree in residue number with the picked atom, even  if  in  different
              chains.  When the set picking chain command is given, picking any atom will cause selection of all
              atoms which agree in chain identifier with the picked atom.

       Set Play
              The RasMol set play.fps command gives the number of frames per second for  playback  by  the  play
              command (default 24 frames per second).

              In the current release of RasMol, the play timing is not controlled by this parameter.

       Set Radius
              The  RasMol set radius command is used to alter the behaviour of the RasMol dots command depending
              upon the value of the solvent parameter.  When solvent is  true,  the  radius  parameter  controls
              whether  a true van der Waals' surface is generated by the dots command. If the value of radius is
              anything other than zero, that value is used as the radius of each atom instead of  its  true  vdW
              value.  When  the value of solvent is true, this parameter determines the 'probe sphere' (solvent)
              radius.  The parameter may be given as an integer in rasmol units or containing a decimal point in
              Angstroms.  The default value of this parameter is determined by the value of solvent and changing
              solvent resets radius to its new default value.

       Set Record
              The RasMol set record.aps gives  the  maximum  on-screen  velocity  in  Angstroms  per  second  in
              animating translations, rotations and zooms (default 10 A/second).

              The  RasMol  set  record.aps command gives number of frames per second for recording by the record
              command (default 24 frames per second).

              The RasMol set record.dwell command sets the time in seconds to dwell on a  change  in  appearance
              (default .5 sec).

       Set ShadePower
              The  shadepower  parameter  (adopted  from RasTop) determines the shade repartition (the contrast)
              used in rendering solid objects. This value between 0 and 100 adjusts shading on an object surface
              oriented  along  the  direction  to  the light source.  Changing the shadepower parameter does not
              change the maximum or the minimum values of this shading, as does changing the ambient  parameter.
              A  value  of  100  concentrates  the light on the top of spheres, giving a highly specular, glassy
              rendering (see the specpower parameter).  A value of 0 distributes the light on the entire object.

              This implementation of shadepower differs from the one in RasTop only in the choice of range (0 to
              100 versus -20 to 20 in RasTop).

       Set Shadow
              The  RasMol  set  shadow command enables and disables ray-tracing of the currently rendered image.
              Currently only the spacefilling representation is shadowed or can cast shadows. Enabling shadowing
              will  automatically  disable  the  Z-clipping  (slabbing)  plane using the command slab off.  Ray-
              tracing typically takes about several seconds for a moderately sized protein.  It  is  recommended
              that  shadowing  be normally disabled whilst the molecule is being transformed or manipulated, and
              only enabled once an appropriate viewpoint is selected, to provide a greater impression of depth.

       Set SlabMode
              The RasMol slabmode parameter controls the rendering method of objects cut  by  the  slabbing  (z-
              clipping) plane. Valid slabmode parameters are "reject", "half", "hollow", "solid" and "section".

       Set Solvent
              The  RasMol  set  solvent  command  is  used  to control the behaviour of the RasMol dots command.
              Depending upon the value of the solvent parameter, the dots command either  generates  a  van  der
              Waals'  or  a solvent accessible surface around the currently selected set of atoms. Changing this
              parameter automatically resets the value of the RasMol radius parameter.  The command set  solvent
              false,  the  default value, indicates that a van der Waals' surface should be generated and resets
              the value of radius to zero.  The  command  set  solvent  true  indicates  that  a  'Connolly'  or
              'Richards'  solvent  accessible surface should be drawn and sets the radius parameter, the solvent
              radius, to 1.2 Angstroms (or 300 RasMol units).

       Set Specular
              The RasMol set specular command enables and disables the display of specular highlights  on  solid
              objects  drawn  by  RasMol. Specular highlights appear as white reflections of the light source on
              the surface of the object. The current RasMol implementation uses  an  approximation  function  to
              generate this highlight.

              The  specular  highlights  on  the  surfaces of solid objects may be altered by using the specular
              reflection coefficient, which is altered using the RasMol set specpower command.

       Set SpecPower
              The specpower parameter determines the shininess of solid objects rendered by RasMol.  This  value
              between  0 and 100 adjusts the reflection coefficient used in specular highlight calculations. The
              specular highlights are enabled and disabled by the RasMol set specular command. Values around  20
              or 30 produce plastic looking surfaces.  High values represent more shiny surfaces such as metals,
              while lower values produce more diffuse/dull surfaces.

       Set SSBonds
              The RasMol ssbonds parameter determines whether disulphide bridges are drawn between  the  sulphur
              atoms  in  the  sidechain  (the  default) or between the alpha carbon atoms in the backbone of the
              cysteines residues. The actual display of disulphide bridges is controlled by the ssbonds command.
              Drawing  disulphide  bridges between alpha carbons is useful when the rest of the protein is shown
              in only a schematic representation such as  backbone,  ribbons  or  strands.   This  parameter  is
              similar to the RasMol hbonds parameter.

       Set Stereo
              The RasMol set stereo parameter controls the separation between the left and right images. Turning
              stereo on and off doesn't reposition the centre of the molecule.

              Stereo viewing of a molecule may be turned on (and  off)  either  by  selecting  Stereo  from  the
              Options menu, or by typing the commands stereo on or stereo off.

              The  separation  angle  between  the  two  views  may be adjusted with the set stereo [-] <number>
              command, where positive values result in crossed eye viewing and negative values in relaxed (wall-
              eyed) viewing. Currently, stereo viewing is not supported in vector PostScript output files.

       Set Strands
              The  RasMol  strands  parameter  controls the number of parallel strands that are displayed in the
              ribbon representations of proteins. The permissible values for this parameter are 1, 2,  3,  4,  5
              and  9. The default value is 5. The number of strands is constant for all ribbons being displayed.
              However, the ribbon width (the separation between strands) may  be  controlled  on  a  residue  by
              residue basis using the RasMol ribbons command.

       Set Transparent
              The  RasMol  transparent  parameter  controls  the  writing  of  transparent GIFs by the write gif
              <filename> command.  This may be controlled by the set transparent  on  and  set  transparent  off
              commands.

       Set UnitCell
              The  RasMol  unitcell  parameter  controls  the  display  of the crystallographic unit cell on the
              current display. The crystal cell is only enabled if the appropriate crystal symmetry  information
              is  contained in the PDB, CIF or mmCIF data file. The RasMol command show symmetry display details
              of the crystal's space group and unit cell axes. The  set  unitcell  command  is  similar  to  the
              commands  set  axes and set boundbox that display orthogonal coordinate axes and the bounding box,
              respectively.

       Set VectPS
              The RasMol vectps parameter is use to control the way in which the RasMol write command  generates
              vector PostScript output files. The command set vectps on enables the use of black outlines around
              spheres and cylinder bonds producing "cartoon-like" high resolution output. However,  the  current
              implementation  of RasMol incorrectly cartoons spheres that are intersected by more than one other
              sphere. Hence "ball and stick" models are rendered correctly but not  large  spacefilling  spheres
              models. Cartoon outlines can be disabled, the default, by the command set vectps off.

       Set Write
              The  RasMol write parameter controls the use of the save and write commands within scripts, but it
              may only be executed from the command line.  By default, this  value  is  false,  prohibiting  the
              generation  of  files  in  any  scripts  executed  at  start-up (such as those launched from a WWW
              browser). However, animators may start up RasMol interactively: type set write on and then execute
              a script to generate each frame using the source command.

ATOM EXPRESSIONS

       RasMol atom expressions uniquely identify an arbitrary group of atoms within a molecule. Atom expressions
       are composed of either primitive expressions, predefined sets, comparison operators, within  expressions,
       or logical (boolean) combinations of the above expression types.

       The  logical  operators  allow  complex  queries to be constructed out of simpler ones using the standard
       boolean connectives and, or and not.  These  may  be  abbreviated  by  the  symbols  "&",  "|"  and  "!",
       respectively.  Parentheses  (brackets)  may  be  used  to  alter  the  precedence  of  the operators. For
       convenience, a comma may also be used for boolean disjunction.

       The atom expression is evaluated for each atom, hence  protein  and  backbone  selects  protein  backbone
       atoms, not the protein and [nucleic] acid backbone atoms!

       Primitive Expressions
              RasMol  primitive  expressions  are the fundamental building blocks of atom expressions. There are
              two types of primitive expression.  The first type is used to identify a given residue  number  or
              range of residue numbers. A single residue is identified by its number (position in the sequence),
              and a range is specified by lower and upper bounds separated by a hyphen  character.  For  example
              select  5,6,7,8  is  also  select  5-8.   Note  that this selects the given residue numbers in all
              macromolecule chains.

              The second type of primitive expression specifies a sequence of fields that must match for a given
              atom.  The  first  part  specifies  a  residue  (or group of residues) and an optional second part
              specifies the atoms within those residues. The first part consists of a residue  name,  optionally
              followed by a residue number and/or chain identifier.

              The  second  part consists of a period character followed by an atom name.  An atom name may be up
              to four alphabetic or  numeric  characters.   An  optional  semicolon  followed  by  an  alternate
              conformation identifier may be appended.  An optional slash followed by a model number may also be
              appended.

              An asterisk may be used as a wild card for a whole field and a question mark as a single character
              wildcard.

       Comparison Operators
              Parts of a molecule may also be distinguished using equality, inequality and ordering operators on
              their properties. The format of such comparison expression is  a  property  name,  followed  by  a
              comparison operator and then an integer value.

              The  atom  properties that may be used in RasMol are atomno for the atom serial number, elemno for
              the atom's atomic number (element), resno for the residue number, radius for the spacefill  radius
              in  RasMol  units  (or  zero if not represented as a sphere) and temperature for the PDB isotropic
              temperature value.

              The equality operator is denoted either "=" or "==".  The inequality operator as either "<>", "!="
              or  "/=".   The  ordering operators are "<" for less than, "<=" for less than or equal to, ">" for
              greater than, and ">" for greater than or equal to.

       Within Expressions
              A RasMol within expression allows atoms to be selected on their proximity to another set of atoms.
              A  within  expression takes two parameters separated by a comma and surrounded by parentheses. The
              first argument is an integer value called the "cut-off" distance of the within expression and  the
              second argument is any  valid atom expression. The cut-off distance is expressed in either integer
              RasMol units or Angstroms containing a decimal point.  An atom is selected if  it  is  within  the
              cut-off  distance  of  any  of  the  atoms  defined  by  the  second argument. This allows complex
              expressions to be constructed containing nested within expressions.

              For example, the command select within(3.2,backbone) selects any atom within a 3.2 Angstrom radius
              of any atom in a protein or nucleic acid backbone.  Within expressions are particularly useful for
              selecting the atoms around an active site.

       Predefined Sets
              RasMol atom expressions may contain predefined sets. These sets are single keywords that represent
              portions  of  a  molecule  of interest.  Predefined sets are often abbreviations of primitive atom
              expressions.  In some cases the use of predefined sets allows selection of  areas  of  a  molecule
              that  could  not  otherwise  be  distinguished.   A list of the currently predefined sets is given
              below.  In addition to the sets listed here, RasMol also treats element names (and their  plurals)
              as  predefined  sets  containing all atoms of that element type, i.e. the command select oxygen is
              equivalent to the command select elemno=8.

Predefined Sets

       AT Set This set contains the atoms in the complementary nucleotides adenosine and  thymidine  (A  and  T,
              respectively).  All  nucleotides  are  classified  as  either the set at or the set cg This set is
              equivalent to the RasMol atom expressions a,t, and nucleic and not cg.

       Acidic Set
              The set of acidic amino acids.  These are the residue types Asp and  Glu.   All  amino  acids  are
              classified  as  either  acidic,  basic  or  neutral.   This  set  is equivalent to the RasMol atom
              expressions asp, glu and amino and not (basic or neutral).

       Acyclic Set
              The set of atoms in amino acids not containing a cycle or ring. All amino acids are classified  as
              either  cyclic  or  acyclic.   This  set is equivalent to the RasMol atom expression amino and not
              cyclic.

       Aliphatic Set
              This set contains the aliphatic amino acids.  These are the amino acids Ala,  Gly,  Ile,  Leu  and
              Val.  This set is equivalent to the RasMol atom expression ala, gly, ile, leu, val.

       Alpha Set
              The  set  of  alpha  carbons  in the protein molecule. This set is approximately equivalent to the
              RasMol atom expression *.CA.  This command should not be confused with the  predefined  set  helix
              which contains the atoms in the amino acids of the protein's alpha helices.

       Amino Set
              This  set  contains  all  the  atoms  contained  in  amino  acid  residues.   This  is  useful for
              distinguishing the protein from the nucleic acid and heterogeneous atoms in the  current  molecule
              database.

       Aromatic Set
              The  set  of  atoms in amino acids containing aromatic rings.  These are the amino acids His, Phe,
              Trp and Tyr.  Because they contain aromatic rings all members  of  this  set  are  member  of  the
              predefined  set  cyclic.  This set is equivalent to the RasMol atom expressions his, phe, trp, tyr
              and cyclic and not pro.

       Backbone Set
              This set contains the four atoms of each amino acid that form the polypeptide N-C-C-O backbone  of
              proteins,  and  the  atoms  of  the  sugar  phosphate  backbone  of nucleic acids.  Use the RasMol
              predefined sets protein and nucleic to distinguish between the two forms of  backbone.   Atoms  in
              nucleic acids and proteins are either backbone or sidechain.  This set is equivalent to the RasMol
              expression (protein or nucleic) and not sidechain.

              The predefined set mainchain is synonymous with the set backbone.

       Basic Set
              The set of basic amino acids.  These are the residue types Arg, His and Lys.  All amino acids  are
              classified  as  either  acidic,  basic  or  neutral.   This  set  is equivalent to the RasMol atom
              expressions arg, his, lys and amino and not (acidic or neutral).

       Bonded Set
              This set contain all the atoms in the current molecule database that are bonded to  at  least  one
              other atom.

       Buried Set
              This  set  contains the atoms in those amino acids that tend (prefer) to be buried inside protein,
              away from contact with solvent molecules. This set refers to the amino acids  preference  and  not
              the  actual  solvent  accessibility  for  the  current protein.  All amino acids are classified as
              either surface or buried.  This set is equivalent to the RasMol  atom  expression  amino  and  not
              surface.

       CG Set This  set  contains  the  atoms  in the complementary nucleotides cytidine and guanosine (C and G,
              respectively). All nucleotides are classified as either the set at or  the  set  cg  This  set  is
              equivalent to the RasMol atom expressions c,g and nucleic and not at.

       Charged Set
              This  set  contains  the  charged amino acids. These are the amino acids that are either acidic or
              basic.  Amino acids are classified as being either charged or neutral.  This set is equivalent  to
              the RasMol atom expressions acidic or basic and amino and not neutral.

       Cyclic Set
              The  set  of  atoms in amino acids containing a cycle or rings.  All amino acids are classified as
              either cyclic or acyclic.  This set consists of the amino acids His, Phe, Pro, Trp and  Tyr.   The
              members  of the predefined set aromatic are members of this set.  The only cyclic but non-aromatic
              amino acid is proline.  This set is equivalent to the RasMol atom expressions his, phe, pro,  trp,
              tyr and aromatic or pro and amino and not acyclic.

       Cystine Set
              This  set contains the atoms of cysteine residues that form part of a disulphide bridge, i.e. half
              cystines. RasMol automatically determines  disulphide  bridges,  if  neither  the  predefined  set
              cystine  nor  the  RasMol ssbonds command have been used since the molecule was loaded. The set of
              free cysteines may be determined using the RasMol atom expression cys and not cystine.

       Helix Set
              This set contains all atoms that form part of a protein alpha helix as determined  by  either  the
              PDB  file  author  or  Kabsch  and  Sander's DSSP algorithm. By default, RasMol uses the secondary
              structure determination given in the PDB file if it exists.  Otherwise, it uses the DSSP algorithm
              as used by the RasMol structure command.

              This  predefined set should not be confused with the predefined set alpha which contains the alpha
              carbon atoms of a protein.

       Hetero Set
              This set contains all the heterogeneous atoms in the molecule. These are the  atoms  described  by
              HETATM  entries  in  the PDB file. These typically contain water, cofactors and other solvents and
              ligands. All hetero atoms are classified as either ligand or solvent  atoms.  These  heterogeneous
              solvent atoms are further classified as either water or ions.

       Hydrogen Set
              This  predefined  set  contains  all  the  hydrogen,  deuterium  and  tritium atoms of the current
              molecule. This predefined set is equivalent to the RasMol atom expression elemno=1.

       Hydrophobic Set
              This set contains all the hydrophobic amino acids.  These are the amino acids Ala, Leu, Val,  Ile,
              Pro,  Phe,  Met and Trp.  All amino acids are classified as either hydrophobic or polar.  This set
              is equivalent to the RasMol atom expressions ala, leu, val, ile, pro, phe, met, trp and amino  and
              not polar.

       Ions Set
              This  set  contains all the heterogeneous phosphate and sulphate ions in the current molecule data
              file. A large number of these  ions  are  sometimes  associated  with  protein  and  nucleic  acid
              structures  determined  by X-ray crystallography. These atoms tend to clutter an image. All hetero
              atoms are classified as either ligand or solvent atoms. All solvent atoms are classified as either
              water or ions.

       Large Set
              All  amino  acids  are classified as either small, medium or large.  This set is equivalent to the
              RasMol atom expression amino and not (small or medium).

       Ligand Set
              This set contains all the heterogeneous cofactor and ligand moieties that  are  contained  in  the
              current  molecule  data  file.   This  set  is defined to be all hetero atoms that are not solvent
              atoms. Hence this set is equivalent to the RasMol atom expression hetero and not solvent.

       Medium Set
              All amino acids are classified as either small, medium or large.  This set is  equivalent  to  the
              RasMol atom expression amino and not (large or small).

       Neutral Set
              The  set  of  neutral  amino  acids.   All  amino  acids are classified as either acidic, basic or
              neutral.  This set is equivalent to the RasMol atom expression amino and not (acidic or basic).

       Nucleic Set
              The set of all atoms in nucleic acids, which consists of  the  four  nucleotide  bases  adenosine,
              cytidine,  guanosine  and thymidine (A, C, G and T, respectively). All neucleotides are classified
              as either purine or pyrimidine.  This set is equivalent to the RasMol atom expressions a,c,g,t and
              purine  or  pyrimidine.   The symbols for RNA nucleotides (U, +U, I, 1MA, 5MC, OMC, 1MG, 2MG, M2G,
              7MG, OMG, YG, H2U, 5MU, and PSU) are also recognized as members of this set.

       Polar Set
              This set contains the polar amino acids.  All amino acids are classified as either hydrophobic  or
              polar.  This set is equivalent to the RasMol atom expression amino and not hydrophobic.

       Protein Set
              The  set  of  all  atoms  in proteins. This consists of the RasMol predefined set amino and common
              post-translation modifications.

       Purine Set
              The set  of  purine  nucleotides.   These  are  the  bases  adenosine  and  guanosine  (A  and  G,
              respectively).   All nucleotides are either purines or pyrimidines.  This set is equivalent to the
              RasMol atom expressions a,g and nucleic and not pyrimidine.

       Pyrimidine Set
              The set of pyrimidine nucleotides.   These  are  the  bases  cytidine  and  thymidine  (C  and  T,
              respectively).   All nucleotides are either purines or pyrimidines.  This set is equivalent to the
              RasMol atom expressions c,t and nucleic and not purine.

       Selected Set
              This set contains the set of atoms in the currently selected region. The currently selected region
              is  defined by the preceding select or restrict command and not the atom expression containing the
              selected keyword.

       Sheet Set
              This set contains all atoms that form part of a protein beta sheet as determined by either the PDB
              file author or Kabsch and Sander's DSSP algorithm. By default, RasMol uses the secondary structure
              determination given in the PDB file if it exists.  Otherwise, it uses the DSSP algorithm  as  used
              by the RasMol structure command.

       Sidechain Set
              This  set  contains  the functional sidechains of any amino acids and the base of each nucleotide.
              These are the atoms not part of  the  polypeptide  N-C-C-O  backbone  of  proteins  or  the  sugar
              phosphate  backbone  of  nucleic  acids.   Use  the  RasMol predefined sets protein and nucleic to
              distinguish between the two forms of sidechain.  Atoms in nucleic acids and  proteins  are  either
              backbone  or  sidechain.  This set is equivalent to the RasMol expression (protein or nucleic) and
              not backbone.

       Small Set
              All amino acids are classified as either small, medium or large.  This set is  equivalent  to  the
              RasMol atom expression amino and not (medium or large).

       Solvent Set
              This  set contains the solvent atoms in the molecule coordinate file.  These are the heterogeneous
              water molecules, phosphate and sulphate ions. All hetero atoms are classified as either ligand  or
              solvent  atoms.  All solvent atoms are classified as either water or ions.  This set is equivalent
              to the RasMol atom expressions hetero and not ligand and water or ions.

       Surface Set
              This set contains the atoms in those amino acids that tend  (prefer)  to  be  on  the  surface  of
              proteins, in contact with solvent molecules. This set refers to the amino acids preference and not
              the actual solvent accessibility for the current protein.   All  amino  acids  are  classified  as
              either  surface  or  buried.   This  set is equivalent to the RasMol atom expression amino and not
              buried.

       Turn Set
              This set contains all atoms that form part of a protein turns as determined by either the PDB file
              author  or  Kabsch  and  Sander's  DSSP algorithm. By default, RasMol uses the secondary structure
              determination given in the PDB file if it exists.  Otherwise, it uses the DSSP algorithm  as  used
              by the RasMol structure command.

       Water Set
              This set contains all the heterogeneous water molecules in the current database. A large number of
              water molecules are sometimes associated with protein and nucleic acid structures determined by X-
              ray  crystallography.  These  atoms  tend to clutter an image.  All hetero atoms are classified as
              either ligand or solvent atoms. The solvent atoms are further classified as either water or ions.

       Set Summary
              The table below summarises RasMol's classification of the common amino acids.

COLOUR SCHEMES

       The RasMol colour command allows different objects (such as atoms, bonds and ribbon segments) to be given
       a  specified  colour.  Typically  this colour is either a RasMol predefined colour name or an RGB triple.
       Additionally RasMol also supports alt, amino, chain,  charge,  cpk,  group,  model,  shapely,  structure,
       temperature  or  user  colour  schemes  for  atoms,  and  hbond type colour scheme for hydrogen bonds and
       electrostatic potential colour scheme for dot surfaces.  The 24 currently  predefined  colour  names  are
       Black,  Blue,  BlueTint,  Brown, Cyan, Gold, Grey, Green, GreenBlue, GreenTint, HotPink, Magenta, Orange,
       Pink, PinkTint, Purple, Red, RedOrange, SeaGreen, SkyBlue, Violet, White, Yellow and YellowTint

       If you frequently wish to use a colour not predefined, you can write a one-line script. For  example,  if
       you  make  the  file  grey.col  containing  the line, colour [180,180,180] #grey, then the command script
       grey.col colours the currently selected atom set grey.

       Alt Colours
              The RasMol alt (Alternate Conformer) colour scheme codes the base structure with  one  colour  and
              applies  a  limited  number  of  colours to each alternate conformer.  In a RasMol built for 8-bit
              colour systems, 4  colours  are  allowed  for  alternate  conformers.  Otherwise,  8  colours  are
              available.

       Amino Colours
              The RasMol amino colour scheme colours amino acids according to traditional amino acid properties.
              The purpose of colouring is to identify amino acids in an unusual or surprising  environment.  The
              outer  parts  of  a  protein  that  are  polar are visible (bright) colours and non-polar residues
              darker. Most colours are hallowed by tradition. This colour  scheme  is  similar  to  the  shapely
              scheme.

       Chain Colours
              The  RasMol  chain  colour  scheme  assigns each macromolecular chain a unique colour. This colour
              scheme is particularly useful  for  distinguishing  the  parts  of  multimeric  structure  or  the
              individual 'strands' of a DNA chain.  Chain can be selected from the RasMol Colours menu.

       Charge Colours
              The RasMol charge colour scheme colour codes each atom according to the charge value stored in the
              input file (or beta factor field of PDB files). High values are coloured in  blue  (positive)  and
              lower  values coloured in red (negative). Rather than use a fixed scale this scheme determines the
              maximum and minimum values of the charge/temperature field  and  interpolates  from  red  to  blue
              appropriately. Hence, green cannot be assumed to be 'no net charge' charge.

              The  difference  between  the charge and temperature colour schemes is that increasing temperature
              values proceed from blue to red, whereas increasing charge values go from red to blue.

              If the charge/temperature field stores reasonable values it is possible to use the  RasMol  colour
              dots  potential  command  to  colour  code  a  dot  surface  (generated  by  the  dots command) by
              electrostatic potential.

       CPK Colours
              The RasMol cpk colour scheme is based upon the colours of the popular plastic spacefilling  models
              which  were  developed  by Corey, Pauling and later improved by Kultun. This colour scheme colours
              'atom' objects by the atom (element) type. This is the scheme  conventionally  used  by  chemists.
              The assignment of the most commonly used element types to colours is given below.

       Group Colours
              The  RasMol group colour scheme colour codes residues by their position in a macromolecular chain.
              Each chain is drawn as a smooth spectrum from blue through green, yellow and orange to red.  Hence
              the N terminus of proteins and 5' terminus of nucleic acids are coloured red and the C terminus of
              proteins and 3' terminus of nucleic acids are drawn in blue. If a chain  has  a  large  number  of
              heterogeneous molecules associated with it, the macromolecule may not be drawn in the full 'range'
              of the spectrum.  Group can be selected from the RasMol Colours menu.

              If a chain has a large number of heterogeneous molecules associated with it, the macromolecule may
              not  be  drawn  in the full range of the spectrum. When RasMol performs group colouring it decides
              the range of colours it uses from the residue numbering given in the PDB file.  Hence  the  lowest
              residue  number  is  displayed  in  blue  and  the  highest  residue  number  is displayed as red.
              Unfortunately, if a PDB file contains a large number of heteroatoms, such as water molecules, that
              occupy  the  high  residue numbers, the protein is displayed in the blue-green end of the spectrum
              and the waters in the yellow-red end of the spectrum. This is aggravated by there typically  being
              many  more  water  molecules  than amino acid residues. The solution to this problem is to use the
              command set hetero off before applying the group colour scheme.  This  can  also  be  achieved  by
              toggling  Hetero Atoms on the Options menu before selecting Group on the Colour menu. This command
              instructs RasMol to only use non-hetero residues in the group colour scaling.

       NMR Model Colours
              The RasMol model colour scheme codes each NMR model with a distinct colour.  The NMR model  number
              is  taken  as a numeric value.  High values are coloured in blue and lower values coloured in red.
              Rather than use a fixed scale this scheme determines the maximum value of the NMR model number and
              interpolates from red to blue appropriately.

       Shapely Colours
              The  RasMol  shapely  colour  scheme  colour codes residues by amino acid property. This scheme is
              based upon Bob Fletterick's "Shapely Models". Each amino acid and nucleic acid residue is given  a
              unique  colour.  The  shapely colour scheme is used by David Bacon's Raster3D program. This colour
              scheme is similar to the amino colour scheme.

       Structure Colours
              The RasMol structure colour scheme colours the molecule by  protein  secondary  structure.   Alpha
              helices are coloured magenta, [240,0,128], beta sheets are coloured yellow, [255,255,0], turns are
              coloured pale blue, [96,128,255]  and  all  other  residues  are  coloured  white.  The  secondary
              structure  is  either  read  from  the  PDB file (HELIX, SHEET and TURN records), if available, or
              determined using Kabsch and Sander's DSSP algorithm. The RasMol structure command may be  used  to
              force DSSP's structure assignment to be used.

       Temperature Colours
              The  RasMol  temperature  colour  scheme  colour  codes  each  atom  according  to the anisotropic
              temperature (beta) value  stored  in  the  PDB  file.  Typically  this  gives  a  measure  of  the
              mobility/uncertainty  of a given atom's position. High values are coloured in warmer (red) colours
              and lower values in colder (blue) colours. This feature is often used to associate a "scale" value
              [such  as  amino  acid  variability in viral mutants] with each atom in a PDB file, and colour the
              molecule appropriately.

              The difference between the temperature and charge colour schemes is  that  increasing  temperature
              values proceed from blue to red, whereas increasing charge values go from red to blue.

       User Colours
              The  RasMol  user colour scheme allows RasMol to use the colour scheme stored in the PDB file. The
              colours for each atom are stored in COLO records placed in the PDB data file. This convention  was
              introduced by David Bacon's Raster3D program.

       HBond Type Colours
              The  RasMol type colour scheme applies only to hydrogen bonds, hence is used in the command colour
              hbonds type.  This scheme colour codes each hydrogen  bond  according  to  the  distance  along  a
              protein  chain  between  hydrogen  bond  donor  and  acceptor.   This schematic representation was
              introduced by Belhadj-Mostefa and Milner-White. This representation  gives  a  good  insight  into
              protein  secondary structure (hbonds forming alpha helices appear red, those forming sheets appear
              yellow and those forming turns appear magenta).

       Potential Colours
              The RasMol potential colour scheme applies only to dot surfaces, hence  is  used  in  the  command
              colour  dots  potential.   This  scheme  colours each currently displayed dot by the electrostatic
              potential at that point in space. This potential is calculated  using  Coulomb's  law  taking  the
              temperature/charge field of the input file to be the charge associated with that atom. This is the
              same interpretation used by the colour charge command. Like the charge colour  scheme  low  values
              are blue/white and high values are red.

       Amino Acid Codes
              The  following  table  lists  the names, single letter and three letter codes of each of the amino
              acids.

       Booleans
              A boolean parameter is a truth value. Valid boolean values  are  'true'  and  'false',  and  their
              synonyms  'on'  and  'off'.  Boolean  parameters  are  commonly used by RasMol to either enable or
              disable a representation or option.

FILE FORMATS

       Protein Data Bank Files

       If you do not have the PDB documentation, you may find the following  summary  of  the  PDB  file  format
       useful.  The  Protein Data Bank is a computer-based archival database for macromolecular structures.  The
       database was established in 1971 by Brookhaven National Laboratory, Upton, New York, as a  public  domain
       repository  for  resolved  crystallographic  structures.  The  Bank uses a uniform format to store atomic
       coordinates and partial bond connectivities as  derived  from  crystallographic  studies.   In  1999  the
       Protein Data Bank moved to the Research Collaboratory for Structural Biology.

       PDB file entries consist of records of 80 characters each. Using the punched card analogy, columns 1 to 6
       contain a record-type identifier, the columns 7 to 70 contain data. In older entries, columns  71  to  80
       are  normally  blank,  but may contain sequence information added by library management programs.  In new
       entries conforming to the 1996 PDB format, there is other information in those columns.  The  first  four
       characters  of  the  record  identifier  are  sufficient to identify the type of record uniquely, and the
       syntax of each record is independent  of  the  order  of  records  within  any  entry  for  a  particular
       macromolecule.

       The  only  record  types that are of major interest to the RasMol program are the ATOM and HETATM records
       which describe the position of each atom. ATOM/HETATM records contain standard  atom  names  and  residue
       abbreviations,  along  with  sequence identifiers, coordinates in Angstrom units, occupancies and thermal
       motion factors. The exact details are given below as  a  FORTRAN  format  statement.   The  "fmt"  column
       indicates  use  of the field in all PDB formats, in the 1992 and earlier formats or in the 1996 and later
       formats.

       Residues occur in order starting from the N-terminal residue for proteins  and  5'-terminus  for  nucleic
       acids.  If  the residue sequence is known, certain atom serial numbers may be omitted to allow for future
       insertion of any missing atoms. Within each residue, atoms are ordered in  a  standard  manner,  starting
       with  the  backbone (N-C-C-O for proteins) and proceeding in increasing remoteness from the alpha carbon,
       along the side chain.

       HETATM records are used to define post-translational modifications and cofactors associated with the main
       molecule. TER records are interpreted as breaks in the main molecule's backbone.

       If  present,  RasMol  also  inspects  HEADER,  COMPND,  HELIX, SHEET, TURN, CONECT, CRYST1, SCALE, MODEL,
       ENDMDL, EXPDTA and END  records.  Information  such  as  the  name,  database  code,  revision  date  and
       classification  of the molecule are extracted from HEADER and COMPND records, initial secondary structure
       assignments are taken from HELIX, SHEET and TURN records, and the end of the file may be indicated by  an
       END record.

       RasMol Interpretation of PDB fields
              Atoms  located  at  9999.000,  9999.000,  9999.000  are assumed to be Insight pseudo atoms and are
              ignored by RasMol. Atom names beginning ' Q' are also assumed  to  be  pseudo  atoms  or  position
              markers.

              When  a  data file contains an NMR structure, multiple conformations may be placed in a single PDB
              file delimited by pairs of MODEL and ENDMDL records. RasMol displays all the NMR models  contained
              in the file.

              Residue  names  "CSH", "CYH" and "CSM" are considered pseudonyms for cysteine "CYS". Residue names
              "WAT", "H20", "SOL" and "TIP" are considered pseudonyms for water "HOH". The residue name "D20" is
              consider heavy water "DOD". The residue name "SUL" is considered a sulphate ion "SO4". The residue
              name "CPR" is considered to be cis-proline and is translated as "PRO". The residue name  "TRY"  is
              considered a pseudonym for tryptophan "TRP".

              RasMol uses the HETATM fields to define the sets hetero, water, solvent and ligand. Any group with
              the name "HOH", "DOD", "SO4" or "PO4" (or aliased to one of these names by the preceding rules) is
              considered a solvent and is considered to be defined by a HETATM field.

              RasMol  only  respects  CONECT  connectivity records in PDB files containing fewer than 256 atoms.
              This is explained in more detail in the  section  on  determining  molecule  connectivity.  CONECT
              records  that  define  a  bond more than once are interpreted as specifying the bond order of that
              bond, i.e. a bond specified twice is a double bond and a bond specified three (or more) times is a
              triple bond.  This is not a standard PDB feature.

       PDB Colour Scheme Specification
              RasMol  also  accepts  the supplementary COLO record type in the PDB files. This record format was
              introduced by David Bacon's Raster3D program for specifying the colour  scheme  to  be  used  when
              rendering  the molecule. This extension is not currently supported by the PDB. The COLO record has
              the same basic record type as the ATOM and HETATM records described above.

              Colours are assigned to atoms using a matching process. The Mask field is  used  in  the  matching
              process  as  follows. First RasMol reads in and remembers all the ATOM, HETATM and COLO records in
              input order. When the user-defined ('User') colour scheme is selected, RasMol  goes  through  each
              remembered  ATOM/HETATM  record  in  turn,  and  searches for a COLO record that matches in all of
              columns 7 through 30. The first such COLO record to be found determines the colour and  radius  of
              the atom.

              Note  that  the  Red,  Green  and  Blue  components  are  in the same positions as the X, Y, and Z
              components of an ATOM or HETA record, and the van der Waals  radius  goes  in  the  place  of  the
              Occupancy. The Red, Green and Blue components must all be in the range 0 to 1.

              In  order that one COLO record can provide colour and radius specifications for more than one atom
              (e.g. based on residue, atom type, or any other criterion for which labels can be given  somewhere
              in  columns  7  through 30), a 'don't-care' character, the hash mark "#" (number or sharp sign) is
              used. This character, when found in a COLO record, matches  any  character  in  the  corresponding
              column  in  a ATOM/HETATM record. All other characters must match identically to count as a match.
              As an extension to the specification, any atom that fails to match a COLO record is  displayed  in
              white.

       Multiple NMR Models
              RasMol  loads  all  of  the  NMR  models from a PDB file no matter which command is used: load pdb
              <filename> or load nmrpdb <filename>

              Once multiple NMR conformations have been loaded they may be manipulated with the atom  expression
              extensions  described  in  Primitive  Expressions.   In  particular, the command restrict */1 will
              restrict the display to the first model only.

       CIF and mmCIF Format Files
              CIF is the IUCr standard for presentation  of  small  molecules  and  mmCIF  is  intended  as  the
              replacement  for  the fixed-field PDB format for presentation of macromolecular structures. RasMol
              can accept data sets in either format.

              There are many useful sites on the World Wide Web where information tools and software related  to
              CIF, mmCIF and the PDB can be found. The following are good starting points for exploration:

              The  International  Union  of  Crystallography  (IUCr)  provides access to software, dictionaries,
              policy statements and  documentation  relating  to  CIF  and  mmCIF  at:  IUCr,  Chester,  England
              (www.iucr.org/iucr-top/cif/) with many mirror sites.

              The Nucleic Acid Database Project provides access to its entries, software and documentation, with
              an mmCIF page giving access to the dictionary and mmCIF software tools at Rutgers University,  New
              Jersey, USA (http://ndbserver.rutgers.edu/NDB/mmcif) with many mirror sites.

              This  version  of  RasMol restricts CIF or mmCIF tag values to essentially the same conventions as
              are used for the fixed-field  PDB  format.  Thus  chain  identifiers  and  alternate  conformation
              identifiers are limited to a single character, atom names are limited to 4 characters, etc. RasMol
              interprets the following CIF and mmCIF tags: A search is made through multiple data blocks for the
              desired  tags,  so  a  single dataset may be composed from multiple data blocks, but multiple data
              sets may not be stacked in the same file.

MACHINE-SPECIFIC SUPPORT

       In the following sections, support  for  Monochrome  X-Windows,  Tcl/Tk  IPC,  UNIX  sockets  based  IPC,
       Compiling RasWin with Borland and MetroWerks are described.

       Monochrome X-Windows Support
              RasMol supports the many monochrome UNIX workstations typically found in academia, such as low-end
              SUN workstations and NCD X-terminals. The X11 version of RasMol (when compiled in 8 bit mode)  now
              detects  black  and  white X-Windows displays and enables dithering automatically. The use of run-
              time error diffusion dithering means that all display  modes  of  RasMol  are  available  when  in
              monochrome  mode. For best results, users should experiment with the set ambient command to ensure
              the maximum contrast in resulting images.

       Tcl/Tk IPC support
              Version 4 of Tk graphics library changed the protocol used to communicate between Tk applications.
              RasMol version 2.6 was modified such that it could communicate with both this new protocol and the
              previous version 3 protocol supported by RasMol v2.5. Although Tcl/Tk 3.x  applications  may  only
              communicate  with  other 3.x applications and Tcl/Tk 4.x applications with other 4.x applications,
              these changes allow RasMol to communicate  between  processes  with  both  protocols  (potentially
              concurrently).

       UNIX sockets based IPC
              The  UNIX  implementation  of  RasMol supports BSD-style socket communication. An identical socket
              mechanism is also being developed for VMS, Apple Macintosh and  Microsoft  Windows  systems.  This
              should  allow  RasMol  to  interactively  display  results  of a computation on a remote host. The
              current protocol acts as a TCP/IP server on port 21069 that executes command  lines  until  either
              the  command  exit  or  the  command  quit  is typed. The command exit from the RasMol server, the
              command quit both disconnects the current session and terminates RasMol. This functionality may be
              tested using the UNIX command telnet <hostname> 21069.

       Compiling RasWin with Borland and MetroWerks
              A  number  of  changes  were  made to the source code in the transition from version 2.5 to 2.6 to
              allow the Microsoft Windows version of RasMol to compile using the Borland C/C++  compiler.  These
              fixes  include  name changes for the standard library and special code to avoid a bug in _fmemset.
              Additional changes were made in the transition from 2.6 to  2.7  to  allow  compilation  with  the
              MetroWerks compilers.

BIBLIOGRAPHY

       Molecular Graphics

       [1] Nelson Max, "Computer Representation of Molecular Surfaces", IEEE Computer Graphics and Applications,
       pp.21-29, August 1983.

       [2] Arthur M. Lesk, "Protein Architecture: A Practical Approach", IRL Press Publishers, 1991.

       Molecular Graphics Programs

       [3] Per J. Kraulis, "MOLSCRIPT: A Program to  Produce  both  Detailed  and  Schematic  Plots  of  Protein
       Structures", Journal of Applied Crystallography, Vol.24, pp.946-950, 1991.

       [4]  David Bacon and Wayne F. Anderson, "A Fast Algorithm for Rendering Space-Filling Molecule Pictures",
       Journal of Molecular Graphics, Vol.6, No.4, pp.219-220, December 1988.

       [5] David C. Richardson and Jane S. Richardson, "The Kinemage:  A  tool  for  Scientific  Communication",
       Protein Science, Vol.1, No.1,pp.3-9, January 1992.

       [6] Mike Carson, "RIBBONS 2.0", Journal of Applied Crystallography, Vol.24, pp.958-961, 1991.

       [7]  Conrad C. Huang, Eric F. Pettersen, Teri E. Klein, Thomas E.  Ferrin and Robert Langridge, "Conic: A
       Fast Renderer for Space-Filling Molecules with Shadows", Journal  of  Molecular  Graphics,  Vol.9,  No.4,
       pp.230-236, December 1991.

       Molecular Biology Algorithms

       [8] Wolfgang Kabsch and Christian Sander, "Dictionary of Protein Secondary Structure: Pattern Recognition
       of Hydrogen-Bonded and Geometrical Features", Biopolymers, Vol.22, pp.2577-2637, 1983.

       [9] Michael L. Connolly, "Solvent-Accessible Surfaces of Proteins and Nucleic Acids",  Science,  Vol.221,
       No.4612, pp.709-713, August 1983.

       [10]  Khaled  Belhadj-Mostefa,  Ron Poet and E. James Milner-White, "Displaying Inter-Main Chain Hydrogen
       Bond Patterns in Proteins", Journal of Molecular Graphics, Vol.9, No.3, pp.194-197, September 1991.

       [11] Mike Carson, "Ribbon  Models  of  Macromolecules",  Journal  of  Molecular  Graphics,  Vol.5,  No.2,
       pp.103-106, June 1987.

       [12]  Mike  Carson  and  Charles E. Bugg, "Algorithm for Ribbon Models of Proteins", Journal of Molecular
       Graphics, Vol.4, No.2, pp.121-122, June 1986.

       [13] H. Iijima, J. B. Dunbar Jr. and G. Marshall, "Calibration of Effective van der Waals Atomic  Contact
       Radii for Proteins and Peptides", Proteins: Structure, Functions and Genetics, Vol.2, pp.330-339,1987.

       Graphics Algorithms

       [14]  J.  Foley,  A.  van Dam, S. Feiner and J. Hughes, "Computer Graphics: Principles and Practice", 2nd
       Edition, Addison Wesley Publishers, 1990.

       [15] J. Cleary and G. Wyvill, "Analysis of  an  Algorithm  for  Fast  Ray  Tracing  using  Uniform  Space
       Subdivision", The Visual Computer, Vol.4, pp.65-83, 1988.

       [16] Thomas Porter,"Spherical Shading", Computer Graphics Vol.12, ACM SIGGRAPH, pp.282-285, 1978.

       [17]  Jean-Michel  Cense,  "Exact  Visibility Calculation for Space-Filling Molecular Models", Journal of
       Molecular Graphics, Vol.9, No.3, pp.191-193, September 1991.

       [18] Chris Schafmeister, "Fast Algorithm for Generating CPK Images on Graphics Workstations", Journal  of
       Molecular Graphics, Vol.8, No.4, pp.201-206, December 1990.

       [19] Bruce A. Johnson, "MSURF: A Rapid and General Program for the Representation of Molecular Surfaces",
       Journal of Molecular Graphics, Vol.5, No.3, pp.167-169, September 1987.

       File Formats

       [20] Frances  C.  Bernstein  et  al.,  "The  Protein  Data  Bank:  A  Computer-Based  Archival  File  for
       Macromolecular Structures", Journal of Molecular Biology, Vol.112, pp.535-542, 1977.

       [21]  Arthur Dalby, James G. Nourse, W. Douglas Hounshell, Ann K. I.  Gushurst, David L. Grier, Burton A.
       Leland and John Laufer, "Description of Several Chemical File Formats Used by Computer Programs Developed
       at  Molecular  Design  Limited",  Journal  of  Chemical  Information and Computer Sciences, Vol.32, No.3,
       pp.244-255, 1992.

       [22] Adobe Systems Inc., "PostScript Language  Reference  Manual",  Addison-Wesley  Publishers,  Reading,
       Mass., 1985.

       [23]  Philip  E.  Bourne  et  al.,  "The Macromolecular Crystallographic Information File (mmCIF)", Meth.
       Enzymol. (1997) 277, 571-590.

       [24] Sydney R. Hall, "The STAR File: a New Format for Electronic Data Transfer and Archiving", Journal of
       Chemical Information and Computer Sciences, Vol. 31, 326-333, 1991.

SEE ALSO

       The RasMol User Manual!

AUTHOR

       1992-1998 by Roger Sayle (rasmol@ggr.co.uk)

                                                    July 2009                                          RASMOL(1)