/usr/share/rasmol/rasmol.hlp

RasMol 2.7.5 is a molecular graphics program intended for the visualisation 
of proteins, nucleic acids and small molecules, based on Roger Sayles' 
RasMol_2.6. The program is aimed at display, teaching and generation of 
publication quality images. RasMol runs on Microsoft Windows, Apple 
Macintosh, UNIX and VMS systems. The UNIX and VMS systems require an 8, 24 
or 32 bit colour X Windows display (X11R4 or later). The program reads in a 
molecule coordinate file and interactively displays the molecule on the 
screen in a variety of colour schemes and molecule representations. 
Currently available representations include depth-cued wireframes, 
'Dreiding' sticks, spacefilling (CPK) spheres, ball and stick, solid and 
strand biomolecular ribbons, atom labels and dot surfaces. 

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

RasMol Copyright (C) Roger Sayle 1992-1999
Version 2.6x1 Mods Copyright (C) Arne Mueller 1998
Versions 2.5-ucb and 2.6-ucb Mods Copyright (C)
UC Regents/ModularCHEM Consortium 1995, 1996
RasTop 1.3 Copyright (C) Philippe Valadon 2000
Version 2.7.0, 2.7.1, 2.7.1.1, 2.7.2, 2.7.2.1,
2.7.2.1.1, 2.7.3, 2.7.4, 2.7.4.1, 2.7.4.2
2.7.5, 2.7.5.1 Mods
Copyright (C) Herbert J. Bernstein 1998-2009
rasmol@bernstein-plus-sons.com


?notice
?notices


This software has been created from several sources. Much of the code is 
from RasMol 2.6, as created by Roger Sayle. See: 
      http://www.dcs.ed.ac.uk/home/rasmol

The torsion angle code, new POVRAY3 code and other features are derived from 
the RasMol2.6x1 revisions by Arne Mueller. See: 
     ftp://nexus.roko.goe.net/pub/rasmol

The Ramachandran printer plot code was derived from fisipl created by 
Frances C. Bernstein. See the Protein Data Bank program tape. 

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

The CIF modifications make use of a library based in part on CBFlib by Paul 
J. Ellis and Herbert J. Bernstein. See: 
      http://www.bernstein-plus-sons.com/software/CBF

Parts of CBFlib is loosely based on the CIFPARSE software package from the 
NDB at Rutgers university. See: 
      http://www.iucr.org/iucr-top/cif/mmcif/ndb/software/CIFPARSE

Please type the RasMol commands 'help copying', 'help general', 'help IUCR', 
'help CBFlib',  and 'help CIFPARSE' for applicable notices. Please type 
'help copyright' for copyright notices. If you use RasMol V2.6 or an earlier 
version, type the RasMol command 'help oldnotice'. 

?copyright
Copyright
                               RasMol 2.7.5
                     Molecular Graphics Visualisation Tool
                       13 June 2009 (rev. 17 July 2009)

                      Based on RasMol 2.6 by Roger Sayle
       Biomolecular Structures Group,Glaxo Wellcome Research & Development
                         Stevenage, Hertfordshire, UK
             Version 2.6, August 1995, Version 2.6.4, December 1998
                      Copyright (C) Roger Sayle 1992-1999

                            and Based on Mods by

 Author             Version, Date             Copyright

 Arne Mueller       RasMol 2.6x1     May 98   (C) Arne Mueller 1998

 Gary Grossman and  RasMol 2.5-ucb   Nov 95   (C) UC Regents/ModularCHEM
 Marco Molinaro     RasMol 2.5-ucb   Nov 96       Consortium 1995, 1996

 Philippe Valadon   RasTop 1.3       Aug 00   (C) Philippe Valadon 2000

 Herbert J.         RasMol 2.7.0     Mar 99   (C) Herbert J. Bernstein
 Bernstein          RasMol 2.7.1     Jun 99       1998-2001
                    RasMol 2.7.1.1   Jan 01
                    RasMol 2.7.2     Aug 00
                    RasMol 2.7.2.1.1 Jan 04
                    RasMol 2.7.3     Feb 05
                    RasMol 2.7.3.1   Apr 06
                    RasMol 2.7.4     Nov 07
                    RasMol 2.7.4.1   Jan 08
                    RasMol 2.7.4.2   Mar 08
                    RasMol 2.7.5     Jun 09
                    RasMol 2.7.5.1   Jul 09

 RasMol 2.7.5 incorporates changes by T. Ikonen, G. McQuillan, N. Darakev
 and L. Andrews (via the neartree package).  Work on RasMol 2.7.5
 supported in part by grant 1R15GM078077-01 from the National Institute
 of General Medical Sciences (NIGMS), U.S. National Institutes of Health
 and by grant ER63601-1021466-0009501 from the Office of Biological &
 Environmental Research (BER), Office of Science, U. S. Department of
 Energy.  RasMol 2.7.4 incorporated  changes by G. Todorov, Nan Jia,
 N. Darakev, P. Kamburov, G. McQuillan, and J. Jemilawon. Work on RasMol
 2.7.4 supported in part by grant 1R15GM078077-01 from the NIGMS/NIH and
 grant ER63601-1021466-0009501 from BER/DOE.  RasMol 2.7.3 incorporates
 changes by Clarice Chigbo, Ricky Chachra, and Mamoru Yamanishi.  Work
 on RasMol 2.7.3 supported in part by grants DBI-0203064, DBI-0315281
 and EF-0312612 from the U.S. National Science Foundation and grant
 DE-FG02-03ER63601 from BER/DOE. The content is solely the responsibility
 of the authors and does not necessarily represent the official views of
 the funding organizations.

 The code for use of RasMol under GTK in RasMol 2.7.4.2 was written by
 Teemu Ikonen.

                     and Incorporating Translations by

 Author                               Item                     Language

 Isabel Servan Martinez,              2.6 Manual               Spanish
 Jose Miguel Fernandez Fernandez
 Jose Miguel Fernandez Fernandez      2.7.1 Manual             Spanish
 Fernando Gabriel Ranea               2.7.1 menus and messages Spanish

 Jean-Pierre Demailly                 2.7.1 menus and messages French

 Giuseppe Martini, Giovanni Paolella, 2.7.1 menus and messages
 A. Davassi, M. Masullo, C. Liotto    2.7.1 help file          Italian

 G. Pozhvanov                         2.7.3 menus and messages Russian
 G. Todorov                           2.7.3 menus and messages Bulgarian
 Nan Jia, G. Todorov                  2.7.3 menus and messages Chinese
 Mamoru Yamanishi, Katajima Hajime    2.7.3 menus and messages Japanese


                              This Release by
   Herbert J. Bernstein, Bernstein + Sons, P.O. Box 177, Bellport, NY, USA
                        yaya@bernstein-plus-sons.com
                Copyright (C) Herbert J. Bernstein 1998-2009
?copying


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

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

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

or the file GPL or type the command 'help GPL' 

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

?gpl
GPL
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The hypothetical commands `show w' and `show c' should show the appropriate 
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?raslic
RASLIC
If you do not use the GPL, the following license terms apply: 

RasMol License 

Even though the authors of the various documents and software found here 
have made a good faith effort to ensure that the documents are correct and 
that the software performs according to its documentation, and we would 
greatly appreciate hearing of any problems you may encounter, the programs 
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following: 

 4. Please explain in your documentation how what you did differs from this 
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This version of RasMol is _not_ in the public domain, but it is given freely 
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please make them in a responsible manner, and please offer us the 
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?general
?generalnotice
?general notice
General Notice
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?old
?oldnotice
?rasmol v2.6 notice
RasMol V2.6 Notice
The following notice applies to RasMol V 2.6 and older RasMol versions. 

Information in this document is subject to change without notice and does 
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?iucrpolicy
?iucr policy
?iucr policy
IUCR Policy
The IUCr Policy for the Protection and the Promotion of the STAR File and 
CIF Standards for Exchanging and Archiving Electronic Data. 

Overview 

The Crystallographic Information File (CIF)[1] is a standard for information 
interchange promulgated by the International Union of Crystallography 
(IUCr). CIF (Hall, Allen & Brown, 1991) is the recommended method for 
submitting publications to Acta Crystallographica Section C and reports of 
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significant influence on these activities in other fields. 

Statement of intent 

The IUCr's interest in the STAR File is as a general data interchange 
standard for science, and its interest in the CIF, a conformant derivative 
of the STAR File, is as a concise data exchange and archival standard for 
crystallography and structural science. 

Protection of the standards 

To protect the STAR File and the CIF as standards for interchanging and 
archiving electronic data, the IUCr, on behalf of the scientific community, 

 * holds the copyrights on the standards themselves, 

 * owns the associated trademarks and service marks, and 

 * holds a patent on the STAR File. 

These intellectual property rights relate solely to the interchange formats, 
not to the data contained therein, nor to the software used in the 
generation, access or manipulation of the data. 

Promotion of the standards 

The sole requirement that the IUCr, in its protective role, imposes on 
software purporting to process STAR File or CIF data is that the following 
conditions be met prior to sale or distribution. 

 * Software claiming to read files written to either the STAR File or the 
CIF standard must be able to extract the pertinent data from a file 
conformant to the STAR File syntax, or the CIF syntax, respectively. 

 * Software claiming to write files in either the STAR File, or the CIF, 
standard must produce files that are conformant to the STAR File syntax, or 
the CIF syntax, respectively. 

 * Software claiming to read definitions from a specific data dictionary 
approved by the IUCr must be able to extract any pertinent definition which 
is conformant to the dictionary definition language (DDL)[3] associated with 
that dictionary. 

The IUCr, through its Committee on CIF Standards, will assist any developer 
to verify that software meets these conformance conditions. 

Glossary of terms 

[1] CIF: 

is a data file conformant to the file syntax defined at 
http://www.iucr.org/iucr-top/cif/spec/index.html 

[2] STAR File: 

is a data file conformant to the file syntax defined at 
http://www.iucr.org/iucr-top/cif/spec/star/index.html 

[3] DDL: 

is a language used in a data dictionary to define data items in terms of 
"attributes". Dictionaries currently approved by the IUCr, and the DDL 
versions used to construct these dictionaries, are listed at 
http://www.iucr.org/iucr-top/cif/spec/ddl/index.html 

Last modified: 30 September 2000 

IUCr Policy Copyright (C) 2000 International Union of Crystallography 

?cbflib
CBFLIB
The following Disclaimer Notice applies to CBFlib V0.1, from which this code 
in part is derived. 

* The items furnished herewith were developed under the sponsorship of the 
U.S. Government. Neither the U.S., nor the U.S. D.O.E., nor the Leland 
Stanford Junior University, nor their employees, makes any warranty, express 
or implied, or assumes any liability or responsibility for accuracy, 
completeness or usefulness of any information, apparatus, product or process 
disclosed, or represents that its use will not infringe privately-owned 
rights. Mention of any product, its manufacturer, or suppliers shall not, 
nor is it intended to, imply approval, disapproval, or fitness for any 
particular use. The U.S. and the University at all times retain the right to 
use and disseminate the furnished items for any purpose whatsoever. 

Notice 91 02 01 

?cifparse
CIFPARSE
Portions of this software are loosely based on the CIFPARSE software package 
from the NDB at Rutgers University. See 

 http://ndbserver.rutgers.edu/NDB/mmcif/software 

CIFPARSE is part of the NDBQUERY application, a program component of the 
Nucleic Acid Database Project [ H. M. Berman, W. K. Olson, D. L. Beveridge, 
J. K. Westbrook, A. Gelbin, T. Demeny, S. H. Shieh, A. R. Srinivasan, and B. 
Schneider. (1992). The Nucleic Acid Database: A Comprehensive Relational 
Database of Three-Dimensional Structures of Nucleic Acids. Biophys J., 63, 
751-759.], whose cooperation is gratefully acknowledged, especially in the 
form of design concepts created by J. Westbrook. 

Please be aware of the following notice in the CIFPARSE API: 

This software is provided WITHOUT WARRANTY OF MERCHANTABILITY OR FITNESS FOR 
A PARTICULAR PURPOSE OR ANY OTHER WARRANTY, EXPRESS OR IMPLIED. RUTGERS MAKE 
NO REPRESENTATION OR WARRANTY THAT THE SOFTWARE WILL NOT INFRINGE ANY 
PATENT, COPYRIGHT OR OTHER PROPRIETARY RIGHT. 

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

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

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

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

RasMol Copyright (C) Roger Sayle 1992-1999
Version 2.6x1 Mods Copyright (C) Arne Mueller 1998
Version 2.5-ucb, 2.6-ucb Mods
  Copyright (C) UC Regents/ModularCHEM Consortium 1995, 1996
RasTop 1.3 Copyright (C) Philippe Valadon 2000
Version 2.7.0, 2.7.1, 2.7.1.1, 2.7.2, 2.7.2.1, 2.7.2.1.1,
        2.7.3, 2.7.3.1, 2.7.4, 2.7.4.1, 2.7.4.2,
        2.7.5, 2.7.5.1 Mods
  Copyright (C) Herbert J. Bernstein 1998-2009
  (yaya@bernstein-plus-sons.com)


?commands
?keywords
RasMol allows the execution of interactive commands typed at the 'RasMol>' 
prompt in the terminal window. Each command must be given on a separate 
line. Keywords are case insensitive and may be entered in either upper or 
lower case letters. All whitespace characters are ignored except to separate 
keywords and their arguments. 

All commands may be prefixed by a parenthesized 'atom expression' to 
temporarily select certain atoms just for the execution of that one command. 
After execution of the command, the previous selection is restored except 
for the commands 'select' , 'restrict' and 'script'. 

The commands/keywords currently recognised by RasMol are given below. 
Type "help <command>" for more information on each RasMol function.


    backbone     background   bond         bulgarian    cartoon
    centre       chinese      clipboard    colour       colourmode
    connect      cpk          cpknew       define       depth
    dots         echo         english      exit         french
    hbonds       help         italian      japanese     label
    load         map          molecule     monitor      notoggle
    pause        print        quit         refresh      renumber
    reset        restrict     ribbons      rotate       save
    script       select       set          show         slab
    source       spacefill    spanish      ssbonds      star
    stereo       strands      structure    surface      trace
    translate    unbond       wireframe    write        zap
    zoom


?backbone
Backbone
Syntax:  backbone {<boolean>}
         backbone <value>
         backbone dash

The RasMol 'backbone' command permits the representation of a polypeptide 
backbone as a series of bonds connecting the adjacent alpha carbons of each 
amino acid in a chain. The display of these backbone 'bonds' is turned on 
and off by the command parameter in the same way as with the 'wireframe' 
command. The command 'backbone off' turns off the selected 'bonds', and 
'backbone on' or with a number turns them on. The number can be used to 
specify the cylinder radius of the representation in either Angstrom or 
RasMol units. A parameter value of 500 (2.0 Angstroms) or above results in a 
"Parameter value too large" error. Backbone objects may be coloured using 
the RasMol 'colour backbone' command. 

The reserved word backbone is also used as a predefined set ("help sets") 
and as a parameter to the 'set hbond' and 'set ssbond' commands. The RasMol 
command 'trace' renders a smoothed backbone, in contrast to 'backbone' which 
connects alpha carbons with straight lines. 

The backbone may be displayed with dashed lines by use of the 'backbone 
dash' command. 

?background
Background
Syntax:  background <colour>

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

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

?bond
Bond
Syntax:  bond <number> <number> +
         bond <number> <number> pick
         bond rotate {<boolean>}

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
Bulgarian
Syntax:  Bulgarian

The RasMol 'Bulgarian' command sets the menus and messages to the Bulgarian 
versions. 

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

?cartoon
Cartoon
Syntax:  cartoon {<number>}

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. 

?center
?centre
Centre
Syntax:  centre {<expression>} {translate|center}
         center {<expression>} {translate|center}

The RasMol 'centre' command defines the point about which the 'rotate' 
command and the scroll bars rotate the current molecule. Without a parameter 
the centre command resets the centre of rotation to be the centre of gravity 
of the molecule. If an atom expression is specified, RasMol rotates the 
molecule about the centre of gravity of the set of atoms specified by the 
expression. Hence, if a single atom is specified by the expression, that 
atom will remain 'stationary' during rotations. 

Type 'help expression' for more information on RasMol atom expressions. 

Alternatively the centring may be given as a comma separated triple of 
[CenX, CenY, CenZ] offsets in RasMol units (1/250 of an Angstrom) from the 
centre of gravity. The triple must be enclosed in square brackets. 

The optional forms 'centre ... translate' and 'centre ... center' may be 
used to specify use of a translated centre of rotation (not necessarily in 
the centre of the canvas) or a centre of rotation which is placed at the 
centre of the canvas. Starting with RasMol 2.7.2, the default is to center 
the new axis on the canvas. 

?chinese
Chinese
Syntax:  Chinese

The RasMol 'Chinese' command sets the menus and messages to the Chinese 
versions. 

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

?clipboard
Clipboard
Syntax:  clipboard

The RasMol 'clipboard' command places a copy of the currently displayed 
image on the local graphics 'clipboard'. Note: this command is not yet 
supported on UNIX or VMS machines. It is intended to make transfering images 
between applications easier under Microsoft Windows or on an Apple 
Macintosh. 

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

?color
?colour
Colour
Syntax:  colour {<object>} <colour>
         color {<object>} <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
ColourMode
Syntax:  colourmode {<boolean>}
         colormode {<boolean>}

ColourMode allows the user to switch between using the new 'colour' method. 
At present, the new coloring technique is the same as the old one, but to 
preserve compatibility for older scripts it may be wise to add a "colormode 
on" near the top of your script somewhere, if the script was designed for 
version 2.7.3 of RasMol or earlier. The new color method, when completed, 
aims to fix a few bugs in the coloring routines. 

?connect
Connect
Syntax:  connect {<boolean>}

The RasMol 'connect' command is used to force RasMol to (re)calculate the 
connectivity of the current molecule. If the original input file contained 
connectivity information, this is discarded. The command 'connect false' 
uses a fast heuristic algorithm that is suitable for determining bonding in 
large bio-molecules such as proteins and nucleic acids. The command 'connect 
true' uses a slower more accurate algorithm based upon covalent radii that 
is more suitable to small molecules containing inorganic elements or 
strained rings. If no parameters are given, RasMol determines which 
algorithm to use based on the number of atoms in the input file. Greater 
than 255 atoms causes RasMol to use the faster implementation. This is the 
method used to determine bonding, if necessary, when a molecule is first 
read in using the 'load' command. 

?defer
Defer
Syntax:  defer <name> <command to defer>

The RasMol 'defer' command adds the command given to the macro with given 
name, if no name is given, the command is added to the macro with a blank 
name. The command 'zap' is a special case. In that case the macro is erased. 
If no name is given the command must begin with a selection, e.g. 'defer 
(selection).spacefill' 

The deferred commands accumulated under the given name can be executed using 
the 'execute' command 

?define
Define
Syntax:  define <identifier> <expression>

The RasMol 'define' command allows the user to associate an arbitrary set of 
atoms with a unique identifier. This allows the definition of user-defined 
sets. These sets are declared statically, i.e. once defined the contents of 
the set do not change, even if the expression defining them depends on the 
current transformation and representation of the molecule. 

?depth
Depth
Syntax:  depth {<boolean>}
         depth <value>

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. 

?dot surface
?surface
?dots
Dots
Syntax:  dots {<boolean>}
         dots <value>

The RasMol 'dots' command is used to generate a van der Waals' dot surface 
around the currently selected atoms. Dot surfaces display regularly spaced 
points on a sphere of van der Waals' radius about each selected atom. Dots 
that would are 'buried' within the van der Waals' radius of any other atom 
(selected or not) are not displayed. The command 'dots on' deletes any 
existing dot surface and generates a dots surface around the currently 
selected atom set with a default dot density of 100. The command 'dots off' 
deletes any existing dot surface. The dot density may be specified by 
providing a numeric parameter between 1 and 1000. This value approximately 
corresponds to the number of dots on the surface of a medium sized atom. 

By default, the colour of each point on a dot surface is the colour of its 
closest atom at the time the surface is generated. The colour of the whole 
dot surface may be changed using the 'colour dots' command. 

?echo
Echo
Syntax:  echo {<string>}

The RasMol 'echo' command is used to display a message in the RasMol 
command/terminal window. The string parameter may optionally be delimited in 
double quote characters. If no parameter is specified, the 'echo' command 
displays a blank line. This command is particularly useful for displaying 
text from within a RasMol 'script' file. 

?english
English
Syntax:  English

The RasMol 'English' command sets the menus and messages to the English 
versions. 

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

?execute
Execute
Syntax:  execute <name>

The RasMol 'execute' command: 

1. saves the old poise of the molecule (translation, rotation and zoom) 

2. executes the specified macro suppressing both screen updates and 
recording 

3. animates motion of the newly rendered molecule linearly from the old 
poise to the new poise 

The macro must have been previously defined by calls to the 'defer' command. 

The animation of the motion depends on the prior settings of the 'record' 
command. 

?french
French
Syntax:  French

The RasMol 'French' command sets the menus and messages to the French 
versions. 

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

?hbond
?hbonds
HBonds
Syntax:  hbonds {<boolean>}
         hbonds <value>

The RasMol 'hbond' command is used to represent the hydrogen bonding of the 
protein molecule's backbone. This information is useful in assessing the 
protein's secondary structure. Hydrogen bonds are represented as either 
dotted lines or cylinders between the donor and acceptor residues. The first 
time the 'hbond' command is used, the program searches the structure of the 
molecule to find hydrogen bonded residues and reports the number of bonds to 
the user. The command 'hbonds on' displays the selected 'bonds' as dotted 
lines, and the 'hbonds off' turns off their display. The colour of hbond 
objects may be changed by the 'colour hbond' command. Initially, each 
hydrogen bond has the colours of its connected atoms. 

By default the dotted lines are drawn between the accepting oxygen and the 
donating nitrogen. By using the 'set hbonds' command the alpha carbon 
positions of the appropriate residues may be used instead. This is 
especially useful when examining proteins in backbone representation. 

?help
Help
Syntax:  help {<topic> {<subtopic>}}
         ? {<topic> {<subtopic>}

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

?italian
Italian
Syntax:  Italian

The RasMol 'Italian' command sets the menus and messages to the Italian 
versions. 

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

?japanese
Japanese
Syntax:  Japanese

The RasMol 'Japanese' command sets the menus and messages to the Japanese 
versions. 

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

?labels
?label
Label
Syntax:  label {<string>}
         label <boolean>

The RasMol 'label' command allows an arbitrary formatted text string to be 
associated with each currently selected atom. This string may contain 
embedded 'expansion specifiers' which display properties of the atom being 
labelled. An expansion specifier consists of a '%' character followed by a 
single alphabetic character specifying the property to be displayed. An 
actual '%' character may be displayed by using the expansion specifier '%%'. 

Atom labelling for the currently selected atoms may be turned off with the 
command 'label off'. By default, if no string is given as a parameter, 
RasMol uses labels appropriate for the current molecule. 

The colour of each label may be changed using the 'colour label' command. By 
default, each label is drawn in the same colour as the atom to which it is 
attached. The size and spacing of the displayed text may be changed using 
the 'set fontsize' command. The width of the strokes in the displayed text 
may be changed  using the 'set fontstroke'  command. 

For a list of expansion specifiers, type "help specifiers". 

?expansion
?specifiers
?expansion specifiers
?label specifiers
Label Specifiers
Label specifiers are characters sequences that are embedded in the string 
parameter passed to the RasMol 'label' command. These specifiers are then 
expanded as the labels are drawn to display properties associated with the 
atom being labelled. The following table lists the current expansion 
specifiers. The specifier '%%' is treated as an exception and is displayed 
as a single '%' character. 

    %a      Atom Name
    %b %t   B-factor/Temperature
    %c %s   Chain Identifier
    %e      Element Atomic Symbol
    %i      Atom Serial Number
    %n      Residue Name
    %r      Residue Number
    %M      NMR Model Number (with leading "/")
    %A      Alternate Conformation Identifier (with leading ";")


?load
Load
Syntax:  load {<format>} <filename>

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
Map
Syntax:  map {<map_selector>} {<map_subcommand> <parameters>}

The RasMol 'map' commands manipulate electron density maps in coordination 
with the display of molecules. These commands are very memory intensive and 
may not work on machines with limited memory. Each molecule may have as many 
maps as available memory permits. Maps may be read from files or generated 
from Gaussian density distributions around atoms. 

'map colour', to colour a map according to a given colour scheme, 'map 
generate', to generate a map from selected atoms based on pseudo-Gaussians, 
'map level', to set the contouring level for selected maps, 'map load', to 
load a map from a file, 'map mask' to designate a mask for the selected 
maps, 'map resolution', to set the resolution for contouring selected maps, 
'map restrict', to select one or more maps and to disable all others, 'map 
save', to save map information to a file, 'map scale', 'control the scaling 
of pseudo-Gaussians when generating maps', 'map select', to select one or 
more maps, 'map show', to display information about one or more maps or 
about the parameters to be used in generating or loading the next map, 'map 
spacing', to set the spacing betwen contour lines of selected maps, 'map 
spread', to set the variance of the Gaussians for map generation as a 
fraction of the atomic radius, and 'map zap' to delete previously generated 
or loaded maps. 

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

?mapcolour
?map colour
Map colour
Syntax:  map {<map_selector>} colour <colour_scheme>

The RasMol 'map colour' command colours the selected maps according to the 
specified colour scheme. The colour scheme may be a colour name or and RBG 
triple in brackets, or the keyword 'atom' to cause the map points to be 
coloured by the color of the nearest atom. 

?mapgenerate
?map generate
Map generate
Syntax:  map {<map_selector>} generate {LRsurf} dots
         map {<map_selector>} generate {LRsurf} mesh
         map {<map_selector>} generate {LRsurf} surface

The RasMol 'map generate' command generates a map from whatever atoms are 
currently selected, by summing electron densities approximated by Gaussian 
distributions. The height of each Gaussian is determined by the setting of 
the ' map scale' command. In the default of map scale true, each Gaussian 
has a height proportional element type of the atom. If the optional 'LRSurf' 
parameter is given or if map scale false has been executed, each Gaussian is 
scaled so that the Gaussian contour level 1 is at the van der Waals radius. 
In either case a standard deviation determined by the most recently 
specified spread or resolution is used. If a non-zero spread has been given 
the radius of the atom is multiplied by the spread to find the standard 
deviation. The default is 2/3rds. If a resolution has been given, the spread 
is inferred as 2/3rds of the resolution. 

For example, if the resolution is given as 1., and the atom in question is a 
Carbon with a van der Waals radius of 468 RasMol units (1.87 Angstroms), the 
inferred spead is .6667, and the standard deviation of the Gaussian is taken 
as 1.25 Angstroms. 

If the spread has been set to zero, the spread for each atom is determined 
from the van der Waals radius and the probe atom radius to simulate the 
effect of a Lee-Richards surface. 

If no specific map was given by the map selector, the new map is given the 
next available map number. 

If a specific map was given by the map selector, the new map replaces that 
map. If more than one map was given by the map selector, the new map 
replaces the lowest numbered of the selected maps. In any case the new map 
becomes the currently selected map. 

The map is displayed as dots, mesh or a surface, depending on the last map 
rendering mode selected or the mode selected on the command itself. 

?maplevel
?map level
Map level
Syntax:  map {<map_selector>} level {MEAN} <number>

The RasMol 'map level' command sets the contour level to be used in creating 
subsequent representations of generated or loaded maps. If the keyword MEAN 
in used the level is relative to the mean of the map data. Otherwise the 
level is absolute. 

In general, a lower level results in a map containing more of the displayed 
volume, while a higher level results in a map containing less of the 
displayed volume. 

?mapload
?map load
Map load
Syntax:  map {<map_selector>} load <filename>

The RasMol 'map load' command loads a map file into RasMol. The valid 
formats are CCP4 map format and imgCIF format. 

If no specific map was given by the map selector, the new map is given the 
next available map number. 

If a specific map was given by the map selector, the new map replaces that 
map. If more than one map was given by the map selector, the new map 
replaces the lowest numbered of the selected maps. In any case the new map 
becomes the currently selected map. 

The map is displayed as dots, mesh or a surface depending on the last map 
rendering mode selected. 

?mapmask
?map mask
Map mask
Syntax:  map {<map_selector>} mask selected
         map {<map_selector>} mask <number>
         map {<map_selector>} mask none

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

The 'selected' option indicates that the mask is to be created from the 
currently selected atoms. The '<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. 

?mapresolution
?map resolution
Map resolution
Syntax:  map {<map_selector>} resolution <number>

The RasMol 'map resolution' command specifies the resolution in RasMol units 
or, if a number containing a decimal point is given, the resolution in 
Angstroms to be used in generating and in representing maps. 

The resolution is used at the map spacing for representations of maps, 
indicating the separation between contour levels (see the 'map spacing' 
command) and to infer the map spread to be used in generated maps from 
selected atoms (see the 'map spread' command). The map spread is set to two 
thirds of the specified resolution. 

?maprestrict
?map restrict
Map restrict
Syntax:  map {<map_selector>} restrict

The RasMol 'map restrict' command selects particular maps to make them 
active for subsequent map commands. This is similar to the 'map select' 
command, but does disables the display of the maps that were not selected. 

?mapsave
?map save
Map save
Syntax:  map {<map_selector>} save <filename>

The RasMol 'map save' command saves an imgCIF map file. 

If no specific map was given by the map selector, the currently selected 
maps and their masks are written to the file, one map and mask pair per data 
block. 

?mapscale
?map scale
Map scale
Syntax:  map {<map_selector>} scale <boolean>

The RasMol 'map scale' command selects the scaling of pseudo-Gaussians in 
the 'map generate' commands. In the default of map scale true, each Gaussian 
has a height proportional element type of the atom. If map scale false has 
been executed, each Gaussian is scaled so that the Gaussian contour level 1 
is at the van der Waals radius. In either case a standard deviation 
determined by the most recently specified spread or resolution is used. 

?mapselect
?map select
Map select
Syntax:  map {<map_selector>} select {atom {within} {add} {<search_radius>}}

The RasMol 'map select' command selects particular maps to make them active 
for subsequent map commands. This is similar to the 'map restrict' command, 
but does not disable the display of the maps that were not selected. 

If the optional 'atom' parameter is given, the command selects the atoms 
with centres closest to the map points. The radius of the search may be 
specified by the parameter 'search_radius'. The default is to look for atoms 
within 4 Angstroms plus the probe radius. If the optional 'within' parameter 
is given, the new selection is taken from within the currently selected 
atoms. If the options 'add' parameter is given, the new selection is added 
to the currently selected atoms. The default is to search within all atoms. 

?mapshow
?map show
Map show
Syntax:  map {<map_selector>} show

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

?mapspacing
?map spacing
Map spacing
Syntax:  map {<map_selector>} spacing <number>

The RasMol 'map spacing' command specifies the spacing to be used between 
contour lines in creating representations of maps. The spacing is typically  
given in Angstroms with a decimal point, but may also be specified in RasMol 
units (250ths of an Angstom) as an integer. For maps loaded in grid 
coordinates that spacing is parallel to the cell edges. The default spacing 
is one half Angstrom. 

?mapspread
?map spread
Map spread
Syntax:  map {<map_selector>} spread <number>

The RasMol 'map spread' command specifies the reciprocal of the number of 
standard deviations per radius to be used in generating maps as sums of 
Gaussians centered on atomic positions. The default spread is one two thirds 
(i.e. each radius covers 1.5 standard deviations). 

If the spread has been set to zero, the spread for each atom is determined 
from the van der Waals radius and the probe atom radius to simulate the 
effect of a Lee-Richards surface. 

?mapzap
?map zap
Map zap
Syntax:  map {<map_selector>} zap

The RasMol 'map zap' command removes the data and representations of the 
maps specified by the map selector. The map numbers of maps that have not 
been removed are not changed. 

?molecule
Molecule
Syntax:  molecule <number>

The RasMol 'molecule' command selects one of up to 5 previously loaded 
molecules for active manipulation. While all the molcules are displayed and 
may be rotated collectively (see the 'rotate all' command), only one 
molecule at a time time is active for manipulation by the commands which 
control the details of rendering. 

?monitor
Monitor
Syntax:  monitor <number> <number>
         monitor {<boolean>}

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
Notoggle
Syntax:  notoggle {<boolean>}

The RasMol 'NoToggle' command enables or disables the use of the toggle 
ability that is used by some of the other RasMol commands. When no boolean 
value is specified, NoToggle mode is ENABLED. When NoToggle mode is ENABLED, 
all toggle functionality is DISABLED. To turn it off, one must explicitly 
set 'notoggle off'. 

Some commands which use the toggle feature are: 'ColourMode'. More functions 
that utilize this capability may be added at a later date. 

?pause
Pause
Syntax:  pause
         wait

The RasMol 'pause' command is used in script files to stop the script file 
for local manipulation by a mouse, until any key is pushed to restart the 
script file. 'Wait' is synonymous with 'pause'. This command may be executed 
in RasMol script files to suspend the sequential execution of commands and 
allow the user to examine the current image. When RasMol executes a 'pause' 
command in a script file, it suspends execution of the rest of the file, 
refreshes the image on the screen and allows the manipulation of the image 
using the mouse and scroll bars, or resizing of the graphics window. Once a 
key is pressed, control returns to the script file at the line following the 
'pause' command. While a script is suspended the molecule may be rotated, 
translated, scaled, slabbed and picked as usual, but all menu commands are 
disabled. 

?play
Play
Syntax:  play {from <time>} {until <time>} {{on|off|eject} {<type>} <medium>}

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
Print
Syntax:  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. 

?exit
?quit
Quit
Syntax:  quit
         exit

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
Record
Syntax:  record {from <time>} {until <time>} {{on|off} {<type>} <medium>}
         record {mouse|motion|appearance} {on|off}

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
Refresh
Syntax:  refresh

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

?renum
?renumber
Renumber
Syntax:  renumber {{-} <value>}

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
Reset
Syntax:  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
Restrict
Syntax:  restrict {<expression>}

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'. 

?ribbon
?ribbons
Ribbons
Syntax:  ribbons {<boolean>}
         ribbons <value>

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
Syntax:  rotate <axis> {-} <value>
         rotate bond {<boolean>}
         rotate molecule {<boolean>}
         rotate all {<boolean>}

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
Russian
Syntax:  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
Syntax:  save {pdb} <filename>
         save mdl <filename>
         save alchemy <filename>
         save xyz <filename>

Save the currently selected set of atoms in a Protein Data Bank (PDB), MDL, 
Alchemy(tm) or XYZ format file. 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. 

?source
?scripts
?script
Script
Syntax:  script <filename>

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
Select
Syntax:  select {<expression>}

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
Set
Syntax:  set <parameter> {<option>}

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 
paramter option resets that parameter to its default value. A list of valid 
parameter names is given below. For more information on each internal 
parameter type "help set parameter". 

    ambient         axes            background      backfade
    bondmode        bonds           boundbox        cartoon
    cisangle        display         fontsize        fontstroke
    hbond           hetero          hourglass       hydrogen
    kinemage        menus           monitor         mouse
    picking         radius          shadepower      shadow
    slabmode        solvent         specular        specpower
    stereo          ssbonds         strands         transparent
    unitcell        vectps          write


?show
Show
Syntax:  show information
         show centre
         show phipsi
         show RamPrint
         show rotation
         show selected { group | chain |atom }
         show sequence
         show symmetry
         show translation
         show zoom

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
Slab
Syntax:  slab {<boolean>}
         slab <value>

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. 

?cpk
?cpknew
?spacefill
Spacefill
Syntax:  spacefill {<boolean>}
         spacefill temperature
         spacefill user
         spacefill <value>

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
Spanish
Syntax:  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. 

?ssbond
?bridges
?disulphide bridges
?ssbonds
SSBonds
Syntax:  ssbonds {<boolean>}
         ssbonds <value>

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
Star
Syntax:  star {<boolean>}
         star temperature
         star user
         star <value>

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
Stereo
Syntax:  stereo on
         stereo [-] <number>
         stereo off

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
Strands
Syntax:  strands {<boolean>}
         strands <value>

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
Structure
Syntax:  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
Surface
Syntax:  surface molecule <value>
Syntax:  surface solvent  <value>

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
Trace
Syntax:  trace {<boolean>}
         trace <value>
         trace temperature

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
Translate
Syntax:  translate <axis> {-} <value>

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
UnBond
Syntax:  unbond <number> <number>
         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
Wireframe
Syntax:  wireframe {<boolean>}
         wireframe <value> {<value>}

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 specifed 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
Syntax:  write {<format>} <filename>

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
Zap
Syntax:  zap

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

?zoom
Zoom
Syntax:  zoom {<boolean>}
         zoom <value>

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. 

?parameters
?set parameters
?internal parameters
Internal 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. 

A complete list of internal parameter names is given below. Type "help set 
<parametername>" for more information on each option. 

    ambient         axes            background      backfade
    bondmode        bonds           boundbox        cartoon
    cisangle        display         fontsize        fontstroke
    hbond           hetero          hourglass       hydrogen
    kinemage        menus           monitor         mouse
    record.dwell    record.fps      shadow          slabmode
    solvent         specular        specpower       stereo
    ssbonds         strands         transparent     unitcell
    vectps          write


?ambient
?set ambient
Set Ambient
Syntax:  set ambient {<value>}

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. 

?axis
?axes
?set axis
?set axes
Set Axes
Syntax:  set axes <boolean>

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
Set Backfade
Syntax:  set backfade <boolean>

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
Set Background
Syntax:  set background <colour>

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'. 

?bondmode
?set bondmode
Set BondMode
Syntax:  set bondmode and
         set bondmode or
         set bondmode all
         set bondmode none
         set bondmode not bonded

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. 

?setbond
?set bonds
Set Bonds
Syntax:  set bond <boolean>

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. 

?boundbox
?boundingbox
?bounding box
?set boundbox
Set BoundBox
Syntax:  set boundbox <boolean>

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
Set Cartoon
Syntax:  set cartoon {<boolean>}
         set cartoon {<number>}

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. 

?cisangle
?cis
?cis angle
?set cisangle
Set CisAngle
Syntax:  set cisangle {<value>}

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. 

?display
?set display
Set Display
Syntax:  set display selected
         set display normal

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). 

?fontsize
?set fontsize
Set FontSize
Syntax:  set fontsize {<value>} { FS | PS }


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. 

?fontstroke
?set fontstroke
Set FontStroke
Syntax:  set fontstroke {<value>}


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
Set HBonds
Syntax:  set hbonds backbone
         set hbonds sidechain

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. 

?hetero
?set hetero
Set Hetero
Syntax:  set hetero <boolean>

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'. 

?hourglass
?set hourglass
Set HourGlass
Syntax:  set hourglass <boolean>

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. 

?hydrogen
?set hydrogen
Set Hydrogen
Syntax:  set hydrogen <boolean>

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'. 

?mage
?kinemage
?set kinemage
Set Kinemage
Syntax:  set kinemage <boolean>

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
Set Menus
Syntax:  set menus <boolean>

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
Set Monitor
Syntax:  set monitor <boolean>

?setmonitors
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'. 

?mouse
?set mouse
Set Mouse
Syntax:  set mouse rasmol
         set mouse insight
         set mouse quanta

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. 

?pick
?picking
?setpick
?set picking
Set Picking
Syntax:  set picking <boolean>
         set picking off
         set picking none
         set picking ident
         set picking distance
         set picking monitor
         set picking angle
         set picking torsion
         set picking label
         set picking centre
         set picking center
         set picking coord
         set picking bond
         set picking atom
         set picking group
         set picking chain

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 futher 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. 

?setplay
?set play
Set Play
Syntax:  set play.fps {<value>}

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. 

?radius
?set radius
Set Radius
Syntax:  set radius {<value>}

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. 

?setrecord
?set record
Set Record
Syntax:  set record.aps {<value>}
         set record.fps {<value>}
         set record.dwell {<value>}

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). 

?shadepower
?set shadepower
Set ShadePower
Syntax:  set shadepower {<value>}

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). 

?shadow
?shadows
?set shadow
Set Shadow
Syntax:  set shadow <boolean>

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 appropiate viewpoint is 
selected, to provide a greater impression of depth. 

?slabmode
?set slab
?set slabmode
Set SlabMode
Syntax:  set slabmode <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". 

?solvent
?set solvent
Set Solvent
Syntax:  set solvent <boolean>

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). 

?specular
?set specular
Set Specular
Syntax:  set specular <boolean>

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. 

?specpower
?set specpower
Set SpecPower
Syntax:  set specpower {<value>}

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
Set SSBonds
Syntax:  set ssbonds backbone
         set ssbonds sidechain

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
Set Stereo
Syntax:  set stereo <boolean>
         set stereo [-] <number>

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
Set Strands
Syntax:  set strands {<value>}

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
Set Transparent
Syntax:  set transparent <boolean>

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. 

?unitcell
?unit cell
?set unitcell
Set UnitCell
Syntax:  set unitcell <boolean>

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. 

?vectps
?set vectps
Set VectPS
Syntax:  set vectps <boolean>

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
Set Write
Syntax:  set write <boolean>

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. 

?expression
?expressions
?atom expressions
Atom Expressions
RasMol atom expressions uniquely identify an arbitrary group of atoms within 
a molecule. Atom expressions are composed of either primitive expressions, 
(for more details type "help primitives"), predefined sets, (type "help 
sets"), comparison operators, ("help comparisons"), 'within' expressions, 
("help within") 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! 

Examples:    backbone and not helix
             within( 8.0, ser70 )
             not (hydrogen or hetero)
             not *.FE and hetero
             8, 12, 16, 20-28
             arg, his, lys


?examples
?example expressions
Example Expressions
The following table gives some useful examples of RasMol atom expressions. 
For examples of the precise syntax, type "help expressions". 

    Expression      Interpretation

    *               All atoms
    cys             Atoms in cysteines
    hoh             Atoms in heterogeneous water molecules
    as?             Atoms in either asparagine or aspartic acid
    *120            Atoms at residue 120 of all chains
    *p              Atoms in chain P
    *.n?            Nitrogen atoms
    cys.sg          Sulphur atoms in cysteine residues
    ser70.c?        Carbon atoms in serine-70
    hem*p.fe        Iron atoms in the Heme groups of chain P
    *.*;A           All atoms in alternate conformation A
    */4             All atoms in model 4


?primitive
?primitives
?primitive expression
?primitive expressions
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. 

For examples of RasMol expressions type "help examples". 

?comparison
?comparisons
?comparison expressions
?comparison operators
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. 

Examples:    resno < 23
             temperature >= 900
             atomno == 487


?within expressions
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. 

?sets
?predefined
?predefined sets
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'. Type "help sets setname" for more information about a given set. 

    at              acidic          acyclic         aliphatic
    alpha           amino           aromatic        backbone
    basic           bonded          buried          cg
    charged         cyclic          cystine         helix
    hetero          hydrogen        hydrophobic     ions
    large           ligand          medium          neutral
    nucleic         polar           protein         purine
    pyrimidine      selected        sheet           sidechain
    small           solvent         surface         turn
    water


?at
?sets at
?at set
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
?sets acidic
?acidic set
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
?sets acyclic
?acyclic set
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
?sets aliphatic
?aliphatic set
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
?alpha carbon
?alpha carbons
?sets alpha
?alpha set
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
?sets amino
?amino set
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
?sets aromatic
?aromatic set
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". 

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

?buried
?sets buried
?buried set
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
?sets cg
?cg set
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
?sets charged
?charged set
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
?sets cyclic
?cyclic set
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
?sets cystine
?cystine set
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
?helices
?alpha helix
?alpha helices
?sets helix
?sets helices
?helix set
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
?sets hetero
?hetero set
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
?sets hydrogen
?hydrogen set
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
?sets hydrophobic
?hydrophobic set
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
?sets ions
?ions set
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
?sets large
?large set
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
?sets ligand
?ligand set
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
?sets medium
?medium set
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
?sets neutral
?neutral set
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
?sets nucleic
?nucleic set
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
?sets polar
?polar 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
?sets protein
?protein set
Protein Set
The set of all atoms in proteins. This consists of the RasMol predefined set 
'amino' and common post-translation modifications. 

?purine
?sets purine
?purine set
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
?sets pyrimidine
?pyrimidine set
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
?sets selected
?selected set
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
?sheets
?beta sheet
?beta sheets
?sets sheet
?sets sheets
?sheet set
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
?sets sidechain
?sidechain set
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
?sets small
?small set
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
?sets solvent
?solvent set
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
?sets surface
?surface set
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
?turns
?sets turn
?sets turns
?turn set
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
?waters
?sets water
?sets waters
?water set
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
Set Summary
The table below summarises RasMol's classification of the common amino 
acids. 

 Residues  ALA ASN CYS GLN HIS LEU MET PRO THR TYR
             ARG ASP GLU GLY ILE LYS PHE SER TRP VAL
            A R N D C E Q G H I L K M F P S T W Y V
====================================================
Predefined
Set:
acidic            *   *
acyclic     * * * * * * * *   * * * *     * *     *
aliphatic   *             *   * *                 *
aromatic                    *         *       * *
basic         *             *     *
buried      *       *         * *   * *       *   *
charged       *   *   *     *     *
cyclic                      *         * *     * *
hydrophobic *             *   * *   * * *     * * *
large         *       * *   * * * * * *       * *
medium          * * *                   *   *     *
negative          *   *
neutral     *   *   *   * * * * *   * * * * * * * *
polar         * * * * * *   *     *       * *
positive      *             *     *
small       *             *               *
surface       * * *   * * * *     *     * * *   *


?colors
?colours
?color schemes
?colour schemes
?color names
?colour names
?predefined colors
?predefined colours
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 listed below with their corresponding RGB triplet. 

    Black        [0,0,0]            Orange       [255,165,0]
    Blue         [0,0,255]          Pink         [255,101,117]
    BlueTint     [175,214,255]      PinkTint     [255,171,187]
    Brown        [175,117,89]       Purple       [160,32,240]
    Cyan         [0,255,255]        Red          [255,0,0]
    Gold         [255,156,0]        RedOrange    [255,69,0]
    Grey         [125,125,125]      SeaGreen     [0,250,109]
    Green        [0,255,0]          SkyBlue      [58,144,255]
    GreenBlue    [46,139,87]        Violet       [238,130,238]
    GreenTint    [152,255,179]      White        [255,255,255]
    HotPink      [255,0,101]        Yellow       [255,255,0]
    Magenta      [255,0,255]        YellowTint   [246,246,117]


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
?color alt
?colour alt
?alt colours
?alternate
?alternate conformer
?alt colours
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. 

?color amino
?colour amino
?amino colours
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. 

   ASP,GLU Bright Red [230,10,10]     CYS,MET     Yellow [230,230,0]
   LYS,ARG Blue       [20,90,255]     SER,THR     Orange [250,150,0]
   PHE,TYR Mid Blue   [50,50,170]     ASN,GLN     Cyan   [0,220,220]
   GLY     Light Grey [235,235,235]   LEU,VAL,ILE Green  [15,130,15]
   ALA     Dark Grey  [200,200,200]   TRP         Purple [180,90,180]
   HIS     Pale Blue  [130,130,210]   PRO         Flesh  [220,150,130]
   Others  Tan        [190,160,110]


?chain
?color chain
?colour chain
?chain colours
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
?color charge
?colour temperature
?charge colours
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. 

?color cpk
?colour cpk
?cpk colours
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. 

    Carbon       light grey       Chlorine         green
    Oxygen       red              Bromine, Zinc    brown
    Hydogen      white            Sodium           blue
    Nitrogen     light blue       Iron             orange
    Sulphur      yellow           Magnesium        forest green
    Phosphorous  orange           Calcium          dark grey
                                  Unknown          deep pink


?group
?color group
?colour group
?group colours
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. 

?model
?color model
?colour model
?modelcolours
?modelcolors
?model colors
?NMR
?NMR model
?nmr model colours
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
?shapely colors
?shapely colours
?shapely colours
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. 

ALA      Medium Green  [140,255,140]   GLY      White         [255,255,255]
LEU      Olive Green   [ 69, 94, 69]   SER      Medium Orange [255,112, 66]
VAL      Light Purple  [255,140,255]   THR      Dark Orange   [184, 76,  0]
LYS      Royal Blue    [ 71, 71,184]   ASP      Dark Rose     [160,  0, 66]
ILE      Dark Green    [ 0,  76,  0]   ASN      Light Salmon  [255,124,112]
GLU      Dark Brown    [102,  0,  0]   PRO      Dark Grey     [ 82, 82, 82]
ARG      Dark Blue     [  0,  0,124]   PHE      Olive Grey    [ 83, 76, 66]
GLN      Dark Salmon   [255, 76, 76]   TYR      Medium Brown  [140,112, 76]
HIS      Medium Blue   [112,112,255]   CYS      Medium Yellow [255,255,112]
MET      Light Brown   [184,160, 66]   TRP      Olive Brown   [ 79, 70,  0]
ASX,GLX,PCA,HYP
         Medium Purple [255,  0,255]

A        Light Blue    [160,160,255]   C        Light Orange  [255,140, 75]
G        Medium Salmon [255,112,112]   T        Light Green   [160,255,160]

Backbone Light Grey    [184,184,184]   Special  Dark Purple   [ 94, 0, 94]
Default  Medium Purple [255,  0,255]


?color structure
?colour structure
?structure colours
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
?color temperature
?colour temperature
?temperature colours
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
?color user
?colour user
?user colours
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. 

?type
?color type
?colour type
?hbond type colours
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). 

      Offset    Colour    Triple
        +2      white     [255,255,255]
        +3      magenta   [255,0,255]
        +4      red       [255,0,0]
        +5      orange    [255,165,0]
        -3      cyan      [0,255,255]
        -4      green     [0,255,0]
      default   yellow    [255,255,0]


?potential
?electrostatic
?electrostatic potential
?potential colours
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 assocated 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. The table below shows the static assignment of colours using 
a dielectric constant value of 10. 

     25 < V          red       [255,0,0]
     10 < V <  25    orange    [255,165,0]
      3 < V <  10    yellow    [255,255,0]
      0 < V <   3    green     [0,255,0]
     -3 < V <   0    cyan      [0,255,255]
    -10 < V <   3    blue      [0,0,255]
    -25 < V < -10    purple    [160,32,240]
          V < -25    white     [255,255,255]


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

    Alanine         A  ALA         Arginine        R  ARG
    Asparagine      N  ASN         Aspartic acid   D  ASP
    Cysteine        C  CYS         Glutamic acid   E  GLU
    Glutamine       Q  GLN         Glycine         G  GLY
    Histidine       H  HIS         Isoleucine      I  ILE
    Leucine         L  LEU         Lysine          K  LYS
    Methionine      M  MET         Phenylalanine   F  PHE
    Proline         P  PRO         Serine          S  SER
    Threonine       T  THR         Tryptophan      W  TRP
    Tyrosine        Y  TYR         Valine          V  VAL


?boolean expression
?boolean expressions
?booleans
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
?chfile
?fileformats
?file formats
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. 

FORMAT(6A1,I5,1X,A4,A1,A3,1X,A1,I4,A1,3X,3F8.3,2F6.2,1X,I3,2X,A4,2A2)

   Column   Content                                              fmt
    1-6     'ATOM' or 'HETATM'                                   all
    7-11    Atom serial number (may have gaps)                   all
   13-16    Atom name, in IUPAC standard format                  all
    17      Alternate location indicator indicated by A, B or C  all
   18-20    Residue name, in IUPAC standard format               all
   23-26    Residue sequence number                              all
    27      Code for insertions of residues (i.e. 66A & 66B)     all
   31-38    X coordinate                                         all
   39-46    Y coordinate                                         all
   47-54    Z coordinate                                         all
   55-60    Occupancy                                            all
   61-66    Temperature factor                                   all
   68-70    Footnote number                                      92
   73-76    Segment Identifier (left-justified)                  96
   77-78    Element Symbol (right-justified)                     96
   79-80    Charge on the Atom                                   96



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
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
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. 

   Column   Content
    1-6     'COLOR' or 'COLOUR'
    7-30    Mask (described below)
   31-38    Red component
   39-46    Green component
   47-54    Blue component
   55-60    Sphere radius in Angstroms
   61-70    Comments



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
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 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: 
   mmCIF tag                   CIF tag               Used for

   _struct_biol.details                              Info.classification
   _database_2.database_code                         Info.identcode
   _entry.id
   _struct_biol.id
   _struct.title                                     Info.moleculename
   _chemical_name_common
   _chemical_name_systematic
   _chemical_name_mineral

   _symmetry.space_group_name_H-M
                               _symmetry_space_group_name_H-M
                                                      Info.spacegroup
   _cell.length_a              _cell_length_a         Info.cell
   _cell.length_b              _cell_length_b
   _cell.length_c              _cell_length_c
   _cell.angle_alpha           _cell_angle_alpha
   _cell.angle_alpha           _cell_angle_alpha
   _cell.angle_beta            _cell_angle_beta
   _cell.angle_gamma           _cell_angle_gamma

   _atom_sites.fract_transf_matrix[1][1]
                               _atom_sites_fract_tran_matrix_11
                                                      Used to compute
                                                      orthogonal coords
   ...                         ...
   _atom_sites.fract_transf_vector[1]
                               _atom_sites_fract_tran_vector_1
   ...                         ...
   _atom_sites.cartn_transf_matrix[1][1]
                               _atom_sites_cartn_tran_matrix_11
                                                      Alternative to
                                                      compute orth. coords
   ...                         ...
   _atom_sites.cartn_transf_vector[1]
                               _atom_sites_cartn_tran_vector_1
   ...                         ...
   _atom_site.cartn_x          _atom_site_cartn_x
                                                      atomic coordinates
   ...                         ...
   or
   _atom_site.fract_x          _atom_site_fract_x
   ...                         ...

   _struct_conn.id                                    bonds
   ...
   _geom_bond.atom_site_id_1
                               _geom_bond_atom_site_label_1
   ...                         ...

   _struct_conf.id                                    helices, sheets, turns
   _struct_sheet_range.id
   ...                         ...

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
?chmacspec
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
?monochrome x-windows support
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. 

?tcltk
?tcl/tk ipc support
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). 

?sockets
?ipc
?unix sockets based ipc
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'. 

?borland
?metrowerks
?compiling raswin with borland and metrowerks
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
?chbib
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.
rasmol 2.7.5.2-2 / usr / share / rasmol / rasmol.hlp
