Provided by: rasmol_2.7.6.0-3_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
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              using  it.   (Some  other  Free  Software Foundation software is covered by the GNU
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                                  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
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              You may charge a fee for the physical act of transferring a copy, and  you  may  at
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              These requirements apply to the modified work as a whole.  If identifiable sections
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                                          NO WARRANTY

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                                   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
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                  <one line to give the program's name and a brief idea of what it does.>
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                  This program is free software; you can redistribute it and/or modify
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              Also add information on how to contact you by electronic and paper mail.

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              The  hypothetical  commands `show w' and `show c' should show the appropriate parts
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                <signature of Ty Coon>, 1 April 1989
                Ty Coon, President of Vice

              This General Public  License  does  not  permit  incorporating  your  program  into
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       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
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              programs  are  provided  **AS  IS**  without  any  warranty  as   to   correctness,
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              THE  RESPONSIBILITY  FOR  ANY  ADVERSE  CONSEQUENCES  FROM  THE  USE OF PROGRAMS OR
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              Subject to your acceptance of the conditions stated above, and your respect for the
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              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
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                3.  Please do not give anyone  the  impression  that  the  original  authors  are
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              If  you  would  like  to  use  major  pieces  of RasMol in some other program, make
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              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
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                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
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       General Notice
              The following notice applies to this work as a whole  and  to  the  works  included
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              *  Creative  endeavors  depend  on the lively exchange of ideas. There are laws and
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              *  Please read the following notice carefully. If you do not understand any portion
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              * Some of the software and documents included within this software package are  the
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              * With respect to any software or documents  for  which  a  copyright  exists,  ALL
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              *  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
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              * 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
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              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
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              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)