rasmol(1)
NAME
rasmol - Molecular Graphics Visualisation Tool v2.7.5
SYNOPSIS
rasmol [-nodiplay] [[-format ] filename] [-script scriptfile]
FORMATS
-pdb Protein Data Bank -mdl MDL's MOL File Format -mol2 Tripos' Sybyl MOL2 Format -xyz MSC's XYZ (XMol) Format -mopac MOPAC Input or Output File Format -alchemy Alchemy File Format -charmm CHARMm File Format -cif IUCr CIF or CIF File Format
NOTICES
This software has been created from several sources. Much of the code
is from RasMol 2.6, as created by Roger Sayle. The torsion angle code,
new POVRAY3 code and other features are derived from the RasMol2.6x1
revisions by Arne Mueller. The Ramachandran printer plot code was
derived from fisipl created by Frances C. Bernstein. See the Protein
Data Bank program tape.
The code to display multiple molecules and to allow bond rotation is
derived in large part from the UCB mods by Gary Grossman and Marco
Molinaro, included with permission of Eileen Lewis of the ModularCHEM
Consortium.
The CIF modifications make use of a library based in part on CBFlib by
Paul J. Ellis and Herbert J. Bernstein. Parts of CBFlib is loosely
based on the CIFPARSE software package from the NDB at Rutgers
university. Please type the RasMol commands help copying, help
general, help IUCR, help CBFlib,
and help CIFPARSE for applicable notices. Please type help copyright
for copyright notices. If you use RasMol V2.6 or an earlier version,
type the RasMol command help oldnotice.
COPYING
This version is based directly on RasMol version 2.7.4.2, on RasMol
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
GNU GENERAL PUBLIC LICENSE
Version 2, June 1991
Copyright (C) 1989, 1991 Free Software Foundation, Inc.
59 Temple Place, Suite 330, Boston, MA
02111-1307 USA
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
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<one line to give the program's name and a brief idea of
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Copyright (C) <year> <name of author>
This program is free software; you can redistribute it
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Yoyodyne, Inc., hereby disclaims all copyright interest in the
program
`Gnomovision' (which makes passes at compilers) written by
James Hacker.
<signature of Ty Coon>, 1 April 1989
Ty Coon, President of Vice
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RASLIC If you do not use the GPL, the following license terms apply:
RasMol License
Even though the authors of the various documents and software
found here have made a good faith effort to ensure that the
documents are correct and that the software performs according
to its documentation, and we would greatly appreciate hearing of
any problems you may encounter, the programs and documents any
files created by the programs are provided **AS IS** without any
warranty as to correctness, merchantability or fitness for any
particular or general use.
THE RESPONSIBILITY FOR ANY ADVERSE CONSEQUENCES FROM THE USE OF
PROGRAMS OR DOCUMENTS OR ANY FILE OR FILES CREATED BY USE OF THE
PROGRAMS OR DOCUMENTS LIES SOLELY WITH THE USERS OF THE PROGRAMS
OR DOCUMENTS OR FILE OR FILES AND NOT WITH AUTHORS OF THE
PROGRAMS OR DOCUMENTS.
Subject to your acceptance of the conditions stated above, and
your respect for the terms and conditions stated in the notices
below, if you are not going to make any modifications or create
derived works, you are given permission to freely copy and
distribute this package, provided you do the following:
1. Either include the complete documentation, especially the
file NOTICE, with what you distribute or provide a clear
indication where people can get a copy of the documentation; and
2. Please give credit where credit is due citing the version
and original authors properly; and
3. Please do not give anyone the impression that the original
authors are providing a warranty of any kind.
If you would like to use major pieces of RasMol in some other
program, make modifications to RasMol, or in some other way make
what a lawyer would call a "derived work", you are not only
permitted to do so, you are encouraged to do so. In addition to
the things we discussed above, please do the following:
4. Please explain in your documentation how what you did
differs from this version of RasMol; and
5. Please make your modified source code available.
This version of RasMol is _not_ in the public domain, but it is
given freely to the community in the hopes of advancing science.
If you make changes, please make them in a responsible manner,
and please offer us the opportunity to include those changes in
future versions of RasMol.
General Notice
The following notice applies to this work as a whole and to the
works included within it:
* Creative endeavors depend on the lively exchange of ideas.
There are laws and customs which establish rights and
responsibilities for authors and the users of what authors
create. This notice is not intended to prevent you from using
the software and documents in this package, but to ensure that
there are no misunderstandings about terms and conditions of
such use.
* Please read the following notice carefully. If you do not
understand any portion of this notice, please seek appropriate
professional legal advice before making use of the software and
documents included in this software package. In addition to
whatever other steps you may be obliged to take to respect the
intellectual property rights of the various parties involved, if
you do make use of the software and documents in this package,
please give credit where credit is due by citing this package,
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same authors.
* Some of the software and documents included within this
software package are the intellectual property of various
parties, and placement in this package does not in any way imply
that any such rights have in any way been waived or diminished.
* With respect to any software or documents for which a
copyright exists, ALL RIGHTS ARE RESERVED TO THE OWNERS OF SUCH
COPYRIGHT.
* Even though the authors of the various documents and software
found here have made a good faith effort to ensure that the
documents are correct and that the software performs according
to its documentation, and we would greatly appreciate hearing of
any problems you may encounter, the programs and documents and
any files created by the programs are provided **AS IS** without
any warranty as to correctness, merchantability or fitness for
any particular or general use.
* THE RESPONSIBILITY FOR ANY ADVERSE CONSEQUENCES FROM THE USE
OF PROGRAMS OR DOCUMENTS OR ANY FILE OR FILES CREATED BY USE OF
THE PROGRAMS OR DOCUMENTS LIES SOLELY WITH THE USERS OF THE
PROGRAMS OR DOCUMENTS OR FILE OR FILES AND NOT WITH AUTHORS OF
THE PROGRAMS OR DOCUMENTS.
See the files GPL and RASLIC for two alternate ways to license
this package.
RasMol V2.6 Notice
The following notice applies to RasMol V 2.6 and older RasMol
versions.
Information in this document is subject to change without notice
and does not represent a commitment on the part of the supplier.
This package is sold/distributed subject to the condition that
it shall not, by way of trade or otherwise, be lent, re-sold,
hired out or otherwise circulated without the supplier's prior
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which it was produced. No part of this manual or accompanying
software may be reproduced, stored in a retrieval system on
optical or magnetic disk, tape or any other medium, or
transmitted in any form or by any means, electronic, mechanical,
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This product is not to be used in the planning, construction,
maintenance, operation or use of any nuclear facility nor the
flight, navigation or communication of aircraft or ground
support equipment. The author shall not be liable, in whole or
in part, for any claims or damages arising from such use,
including death, bankruptcy or outbreak of war.
IUCR Policy
The IUCr Policy for the Protection and the Promotion of the STAR
File and CIF Standards for Exchanging and Archiving Electronic
Data.
Overview
The Crystallographic Information File (CIF)[1] is a standard for
information interchange promulgated by the International Union
of Crystallography (IUCr). CIF (Hall, Allen & Brown, 1991) is
the recommended method for submitting publications to Acta
Crystallographica Section C and reports of crystal structure
determinations to other sections of Acta Crystallographica and
many other journals. The syntax of a CIF is a subset of the more
general STAR File[2] format. The CIF and STAR File approaches
are used increasingly in the structural sciences for data
exchange and archiving, and are having a significant influence
on these activities in other fields.
Statement of intent
The IUCr's interest in the STAR File is as a general data
interchange standard for science, and its interest in the CIF, a
conformant derivative of the STAR File, is as a concise data
exchange and archival standard for crystallography and
structural science.
Protection of the standards
To protect the STAR File and the CIF as standards for
interchanging and archiving electronic data, the IUCr, on behalf
of the scientific community,
* holds the copyrights on the standards themselves,
* owns the associated trademarks and service marks, and
* holds a patent on the STAR File.
These intellectual property rights relate solely to the
interchange formats, not to the data contained therein, nor to
the software used in the generation, access or manipulation of
the data.
Promotion of the standards
The sole requirement that the IUCr, in its protective role,
imposes on software purporting to process STAR File or CIF data
is that the following conditions be met prior to sale or
distribution.
* Software claiming to read files written to either the STAR
File or the CIF standard must be able to extract the pertinent
data from a file conformant to the STAR File syntax, or the CIF
syntax, respectively.
* Software claiming to write files in either the STAR File,
or the CIF, standard must produce files that are conformant to
the STAR File syntax, or the CIF syntax, respectively.
* Software claiming to read definitions from a specific data
dictionary approved by the IUCr must be able to extract any
pertinent definition which is conformant to the dictionary
definition language (DDL)[3] associated with that dictionary.
The IUCr, through its Committee on CIF Standards, will assist
any developer to verify that software meets these conformance
conditions.
Glossary of terms
[1] CIF:
is a data file conformant to the file syntax defined at
http://www.iucr.org/iucr-top/cif/spec/index.html
[2] STAR File:
is a data file conformant to the file syntax defined at
http://www.iucr.org/iucr-top/cif/spec/star/index.html
[3] DDL:
is a language used in a data dictionary to define data items in
terms of "attributes". Dictionaries currently approved by the
IUCr, and the DDL versions used to construct these dictionaries,
are listed at http://www.iucr.org/iucr-
top/cif/spec/ddl/index.html
Last modified: 30 September 2000
IUCr Policy Copyright (C) 2000 International Union of
Crystallography
CBFLIB The following Disclaimer Notice applies to CBFlib V0.1, from
which this code in part is derived.
* The items furnished herewith were developed under the
sponsorship of the U.S. Government. Neither the U.S., nor the
U.S. D.O.E., nor the Leland Stanford Junior University, nor
their employees, makes any warranty, express or implied, or
assumes any liability or responsibility for accuracy,
completeness or usefulness of any information, apparatus,
product or process disclosed, or represents that its use will
not infringe privately-owned rights. Mention of any product, its
manufacturer, or suppliers shall not, nor is it intended to,
imply approval, disapproval, or fitness for any particular use.
The U.S. and the University at all times retain the right to use
and disseminate the furnished items for any purpose whatsoever.
Notice 91 02 01
CIFPARSE
Portions of this software are loosely based on the CIFPARSE
software package from the NDB at Rutgers University. See
http://ndbserver.rutgers.edu/NDB/mmcif/software
CIFPARSE is part of the NDBQUERY application, a program
component of the Nucleic Acid Database Project [ H. M. Berman,
W. K. Olson, D. L. Beveridge, J. K. Westbrook, A. Gelbin, T.
Demeny, S. H. Shieh, A. R. Srinivasan, and B. Schneider.
(1992). The Nucleic Acid Database: A Comprehensive Relational
Database of Three-Dimensional Structures of Nucleic Acids.
Biophys J., 63, 751-759.], whose cooperation is gratefully
acknowledged, especially in the form of design concepts created
by J. Westbrook.
Please be aware of the following notice in the CIFPARSE API:
This software is provided WITHOUT WARRANTY OF MERCHANTABILITY OR
FITNESS FOR A PARTICULAR PURPOSE OR ANY OTHER WARRANTY, EXPRESS
OR IMPLIED. RUTGERS MAKE NO REPRESENTATION OR WARRANTY THAT THE
SOFTWARE WILL NOT INFRINGE ANY PATENT, COPYRIGHT OR OTHER
PROPRIETARY RIGHT.
DESCRIPTION
RasMol is a molecular graphics program intended for the visualisation
of proteins, nucleic acids and small molecules. The program is aimed
at display, teaching and generation of publication quality images.
RasMol runs on wide range of architectures and operating systems
including Microsoft Windows, Apple Macintosh, UNIX and VMS systems.
UNIX and VMS versions require an 8, 24 or 32 bit colour X Windows
display (X11R4 or later). The X Windows version of RasMol provides
optional support for a hardware dials box and accelerated shared memory
communication (via the XInput and MIT-SHM extensions) if available on
the current X Server.
The program reads in a molecule coordinate file and interactively
displays the molecule on the screen in a variety of colour schemes and
molecule representations. Currently available representations include
depth-cued wireframes, 'Dreiding' sticks, spacefilling (CPK) spheres,
ball and stick, solid and strand biomolecular ribbons, atom labels and
dot surfaces.
Up to 5 molecules may be loaded and displayed at once. Any one or all
of
the molecules may be rotated and translated.
The RasMol help facility can be accessed by typing "help <topic>" or
"help <topic> <subtopic>" from the command line. A complete list of
RasMol commands may be displayed by typing "help commands". A single
question mark may also be used to abbreviate the keyword "help".
Please type "help notices" for important notices.
COMMANDS
RasMol allows the execution of interactive commands typed at the
RasMol> prompt in the terminal window. Each command must be given on a
separate line. Keywords are case insensitive and may be entered in
either upper or lower case letters. All whitespace characters are
ignored except to separate keywords and their arguments.
All commands may be prefixed by a parenthesized atom expression to
temporarily select certain atoms just for the execution of that one
command. After execution of the command, the previous selection is
restored except for the commands select , restrict and script.
The commands/keywords currently recognised by RasMol are given below.
Backbone
The RasMol backbone command permits the representation of a
polypeptide backbone as a series of bonds connecting the
adjacent alpha carbons of each amino acid in a chain. The
display of these backbone 'bonds' is turned on and off by the
command parameter in the same way as with the wireframe command.
The command backbone off turns off the selected 'bonds', and
backbone on or with a number turns them on. The number can be
used to specify the cylinder radius of the representation in
either Angstrom or RasMol units. A parameter value of 500 (2.0
Angstroms) or above results in a "Parameter value too large"
error. Backbone objects may be coloured using the RasMol colour
backbone command.
The reserved word backbone is also used as a predefined set
("help sets") and as a parameter to the set hbond and set ssbond
commands. The RasMol command trace renders a smoothed backbone,
in contrast to backbone which connects alpha carbons with
straight lines.
The backbone may be displayed with dashed lines by use of the
backbone dash command.
Background
The RasMol background command is used to set the colour of the
"canvas" background. The colour may be given as either a colour
name or a comma separated triple of Red, Green and Blue (RGB)
components enclosed in square brackets. Typing the command help
colours will give a list of the predefined colour names
recognised by RasMol. When running under X Windows, RasMol also
recognises colours in the X server's colour name database.
The background command is synonymous with the RasMol set
background command.
Bond The RasMol command bond <number> <number> + adds the designated
bond to the drawing, increasing the bond order if the bond
already exists. The command bond <number> <number> pick selects
the two atoms specified by the atom serial numbers as the two
ends of a bond around which the rotate bond <angle> command will
be applied. If no bond exists, it is created.
Rotation around a previously picked bond may be specified by the
rotate bond <angle> command, or may also be controlled with the
mouse, using the bond rotate on/off or the equivalent rotate
bond on/off commands.
Bulgarian
The RasMol Bulgarian command sets the menus and messages to the
Bulgarian versions.
This command may not work correctly unless appropriate fonts
have been installed. The commands Bulgarian, Chinese, English,
French, Italian, Russian and Spanish may be used to select
Bulgarian, Chinese, English, French, Italian, Japanese, Russian
and Spanish menus and messages if the appropriate fonts have
been installed.
Cartoon
The RasMol cartoon command does a display of a molecule ribbons
as Richardson (MolScript) style protein cartoons, implemented as
thick (deep) ribbons. The easiest way to obtain a cartoon
representation of a protein is to use the Cartoons option on the
Display menu. The cartoon command represents the currently
selected residues as a deep ribbon with width specified by the
command's argument. Using the command without a parameter
results in the ribbon's width being taken from the protein's
secondary structure, as described in the ribbons command. By
default, the C-termini of beta-sheets are displayed as arrow
heads. This may be enabled and disabled using the set cartoons
command. The depth of the cartoon may be adjusted using the set
cartoons <number> command. The set cartoons command without any
parameters returns these two options to their default values.
Centre The RasMol centre command defines the point about which the
rotate command and the scroll bars rotate the current molecule.
Without a parameter the centre command resets the centre of
rotation to be the centre of gravity of the molecule. If an atom
expression is specified, RasMol rotates the molecule about the
centre of gravity of the set of atoms specified by the
expression. Hence, if a single atom is specified by the
expression, that atom will remain 'stationary' during rotations.
Type help expression for more information on RasMol atom
expressions.
Alternatively the centring may be given as a comma separated
triple of [CenX, CenY, CenZ] offsets in RasMol units (1/250 of
an Angstrom) from the centre of gravity. The triple must be
enclosed in square brackets.
The optional forms centre ... translate and centre ... center
may be used to specify use of a translated centre of rotation
(not necessarily in the centre of the canvas) or a centre of
rotation which is placed at the centre of the canvas. Starting
with RasMol 2.7.2, the default is to center the new axis on the
canvas.
Chinese
The RasMol Chinese command sets the menus and messages to the
Chinese versions.
This command may not work correctly unless appropriate fonts
have been installed. The commands Bulgarian, Chinese, English,
French, Italian, Russian and Spanish may be used to select
Bulgarian, Chinese, English, French, Italian, Japanese, Russian
and Spanish menus and messages if the appropriate fonts have
been installed.
Clipboard
The RasMol clipboard command places a copy of the currently
displayed image on the local graphics 'clipboard'. Note: this
command is not yet supported on UNIX or VMS machines. It is
intended to make transferring images between applications easier
under Microsoft Windows or on an Apple Macintosh.
When using RasMol on a UNIX or VMS system this functionality may
be achieved by generating a raster image in a format that can be
read by the receiving program using the RasMol write command.
Colour Colour the atoms (or other objects) of the selected region. The
colour may be given as either a colour name or a comma separated
triple of Red, Green and Blue (RGB) components enclosed in
square brackets. Typing the command help colours will give a
list of all the predefined colour names recognised by RasMol.
Allowed objects are atoms, bonds, backbone, ribbons, labels,
dots, hbonds, map, and ssbonds. If no object is specified, the
default keyword atom is assumed. Some colour schemes are
defined for certain object types. The colour scheme none can be
applied to all objects except atoms and dots, stating that the
selected objects have no colour of their own, but use the colour
of their associated atoms (i.e. the atoms they connect). Atom
objects can also be coloured by alt, amino, chain, charge, cpk,
group, model, shapely, structure, temperature or user. Hydrogen
bonds can also be coloured by type and dot surfaces can also be
coloured by electrostatic potential. For more information type
help colour <colour>. Map objects may be coloured by specific
color of by nearest atom.
ColourMode
ColourMode allows the user to switch between using the new
colour method. At present, the new coloring technique is the
same as the old one, but to preserve compatibility for older
scripts it may be wise to add a "colormode on" near the top of
your script somewhere, if the script was designed for version
2.7.3 of RasMol or earlier. The new color method, when
completed, aims to fix a few bugs in the coloring routines.
Connect
The RasMol connect command is used to force RasMol to
(re)calculate the connectivity of the current molecule. If the
original input file contained connectivity information, this is
discarded. The command connect false uses a fast heuristic
algorithm that is suitable for determining bonding in large bio-
molecules such as proteins and nucleic acids. The command
connect true uses a slower more accurate algorithm based upon
covalent radii that is more suitable to small molecules
containing inorganic elements or strained rings. If no
parameters are given, RasMol determines which algorithm to use
based on the number of atoms in the input file. Greater than 255
atoms causes RasMol to use the faster implementation. This is
the method used to determine bonding, if necessary, when a
molecule is first read in using the load command.
Defer The RasMol defer command adds the command given to the macro
with given name, if no name is given, the command is added to
the macro with a blank name. The command zap is a special case.
In that case the macro is erased. If no name is given the
command must begin with a selection, e.g. defer
(selection).spacefill
The deferred commands accumulated under the given name can be
executed using the execute command
Define The RasMol define command allows the user to associate an
arbitrary set of atoms with a unique identifier. This allows the
definition of user-defined sets. These sets are declared
statically, i.e. once defined the contents of the set do not
change, even if the expression defining them depends on the
current transformation and representation of the molecule.
Depth The RasMol depth command enables, disables or positions the
back-clipping plane of the molecule. The program only draws
those portions of the molecule that are closer to the viewer
than the clipping plane. Integer values range from zero at the
very back of the molecule to 100 which is completely in front of
the molecule. Intermediate values determine the percentage of
the molecule to be drawn.
This command interacts with the slab <value> command, which
clips to the front of a given z-clipping plane.
Dots The RasMol dots command is used to generate a van der Waals' dot
surface around the currently selected atoms. Dot surfaces
display regularly spaced points on a sphere of van der Waals'
radius about each selected atom. Dots that would are 'buried'
within the van der Waals' radius of any other atom (selected or
not) are not displayed. The command dots on deletes any
existing dot surface and generates a dots surface around the
currently selected atom set with a default dot density of 100.
The command dots off deletes any existing dot surface. The dot
density may be specified by providing a numeric parameter
between 1 and 1000. This value approximately corresponds to the
number of dots on the surface of a medium sized atom.
By default, the colour of each point on a dot surface is the
colour of its closest atom at the time the surface is generated.
The colour of the whole dot surface may be changed using the
colour dots command.
Echo The RasMol echo command is used to display a message in the
RasMol command/terminal window. The string parameter may
optionally be delimited in double quote characters. If no
parameter is specified, the echo command displays a blank line.
This command is particularly useful for displaying text from
within a RasMol script file.
English
The RasMol English command sets the menus and messages to the
English versions.
This command may not work correctly unless appropriate fonts
have been installed. The commands Bulgarian, Chinese, English,
French, Italian, Russian and Spanish may be used to select
Bulgarian, Chinese, English, French, Italian, Japanese, Russian
and Spanish menus and messages if the appropriate fonts have
been installed.
Execute
The RasMol execute command:
1. saves the old poise of the molecule (translation, rotation
and zoom)
2. executes the specified macro suppressing both screen updates
and recording
3. animates motion of the newly rendered molecule linearly from
the old poise to the new poise
The macro must have been previously defined by calls to the
defer command.
The animation of the motion depends on the prior settings of the
record command.
French The RasMol French command sets the menus and messages to the
French versions.
This command may not work correctly unless appropriate fonts
have been installed. The commands Bulgarian, Chinese, English,
French, Italian, Russian and Spanish may be used to select
Bulgarian, Chinese, English, French, Italian, Japanese, Russian
and Spanish menus and messages if the appropriate fonts have
been installed.
HBonds The RasMol hbond command is used to represent the hydrogen
bonding of the protein molecule's backbone. This information is
useful in assessing the protein's secondary structure. Hydrogen
bonds are represented as either dotted lines or cylinders
between the donor and acceptor residues. The first time the
hbond command is used, the program searches the structure of the
molecule to find hydrogen bonded residues and reports the number
of bonds to the user. The command hbonds on displays the
selected 'bonds' as dotted lines, and the hbonds off turns off
their display. The colour of hbond objects may be changed by the
colour hbond command. Initially, each hydrogen bond has the
colours of its connected atoms.
By default the dotted lines are drawn between the accepting
oxygen and the donating nitrogen. By using the set hbonds
command the alpha carbon positions of the appropriate residues
may be used instead. This is especially useful when examining
proteins in backbone representation.
Help The RasMol help command provides on-line help on the given
topic.
Italian
The RasMol Italian command sets the menus and messages to the
Italian versions.
This command may not work correctly unless appropriate fonts
have been installed. The commands Bulgarian, Chinese, English,
French, Italian, Russian and Spanish may be used to select
Bulgarian, Chinese, English, French, Italian, Japanese, Russian
and Spanish menus and messages if the appropriate fonts have
been installed.
Japanese
The RasMol Japanese command sets the menus and messages to the
Japanese versions.
This command may not work correctly unless appropriate fonts
have been installed. The commands Bulgarian, Chinese, English,
French, Italian, Russian and Spanish may be used to select
Bulgarian, Chinese, English, French, Italian, Japanese, Russian
and Spanish menus and messages if the appropriate fonts have
been installed.
Label The RasMol label command allows an arbitrary formatted text
string to be associated with each currently selected atom. This
string may contain embedded 'expansion specifiers' which display
properties of the atom being labelled. An expansion specifier
consists of a '%' character followed by a single alphabetic
character specifying the property to be displayed. An actual
'%' character may be displayed by using the expansion specifier
'%%'.
Atom labelling for the currently selected atoms may be turned
off with the command label off. By default, if no string is
given as a parameter, RasMol uses labels appropriate for the
current molecule.
The colour of each label may be changed using the colour label
command. By default, each label is drawn in the same colour as
the atom to which it is attached. The size and spacing of the
displayed text may be changed using the set fontsize command.
The width of the strokes in the displayed text may be changed
using the set fontstroke
command.
Load Load a molecule coordinate file into RasMol. Valid molecule file
formats are pdb (Protein Data Bank format), mdl (Molecular
Design Limited's MOL file format), alchemy (Tripos' Alchemy file
format), mol2 (Tripos' Sybyl Mol2 file format), charmm (CHARMm
file format), xyz (MSC's XMol XYZ file format), mopac (J. P.
Stewart's MOPAC file format) or cif (IUCr CIF or mmCIF file
format). If no file format is specified, PDB, CIF, or mmCIF is
assumed by default. Up to 20 molecules may be loaded at a time.
If CHEM_COMP ligand models are included in an mmCIF file, they
will be loaded as NMR models, first giving the all the NMR
models for model coordinates if specified and then giving all
the NMR models for ideal model coordinates.
To delete a molecule prior to loading another use the RasMol zap
command. To select a molecule for manipulation use the RasMol
molecule <n> command.
The load command selects all the atoms in the molecule, centres
it on the screen and renders it as a CPK coloured wireframe
model. If the molecule contains no bonds (i.e. contains only
alpha carbons), it is drawn as an alpha carbon backbone. If the
file specifies fewer bonds than atoms, RasMol determines
connectivity using the connect command.
The load inline command also allows the storing of atom
coordinates in scripts to allow better integration with WWW
browsers. A load command executed inside a script file may
specify the keyword inline instead of a conventional filename.
This option specifies that the coordinates of the molecule to
load are stored in the same file as the currently executing
commands.
Map The RasMol map commands manipulate electron density maps in
coordination with the display of molecules. These commands are
very memory intensive and may not work on machines with limited
memory. Each molecule may have as many maps as available memory
permits. Maps may be read from files or generated from Gaussian
density distributions around atoms.
map colour, to colour a map according to a given colour scheme,
map generate, to generate a map from selected atoms based on
pseudo-Gaussians, map level, to set the contouring level for
selected maps, map load, to load a map from a file, map mask to
designate a mask for the selected maps, map resolution, to set
the resolution for contouring selected maps, map restrict, to
select one or more maps and to disable all others, map save, to
save map information to a file, map scale, control the scaling
of pseudo-Gaussians when generating maps, map select, to select
one or more maps, map show, to display information about one or
more maps or about the parameters to be used in generating or
loading the next map, map spacing, to set the spacing 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.
Map colour
The RasMol map colour command colours the selected maps
according to the specified colour scheme. The colour scheme may
be a colour name or and RBG triple in brackets, or the keyword
atom to cause the map points to be coloured by the color of the
nearest atom.
Map generate
The RasMol map generate command generates a map from whatever
atoms are currently selected, by summing electron densities
approximated by Gaussian distributions. The height of each
Gaussian is determined by the setting of the map scale command.
In the default of map scale true, each Gaussian has a height
proportional element type of the atom. If the optional 'LRSurf'
parameter is given or if map scale false has been executed, each
Gaussian is scaled so that the Gaussian contour level 1 is at
the van der Waals radius. In either case a standard deviation
determined by the most recently specified spread or resolution
is used. If a non-zero spread has been given the radius of the
atom is multiplied by the spread to find the standard deviation.
The default is 2/3rds. If a resolution has been given, the
spread is inferred as 2/3rds of the resolution.
For example, if the resolution is given as 1., and the atom in
question is a Carbon with a van der Waals radius of 468 RasMol
units (1.87 Angstroms), the inferred spead is .6667, and the
standard deviation of the Gaussian is taken as 1.25 Angstroms.
If the spread has been set to zero, the spread for each atom is
determined from the van der Waals radius and the probe atom
radius to simulate the effect of a Lee-Richards surface.
If no specific map was given by the map selector, the new map is
given the next available map number.
If a specific map was given by the map selector, the new map
replaces that map. If more than one map was given by the map
selector, the new map replaces the lowest numbered of the
selected maps. In any case the new map becomes the currently
selected map.
The map is displayed as dots, mesh or a surface, depending on
the last map rendering mode selected or the mode selected on the
command itself.
Map level
The RasMol map level command sets the contour level to be used
in creating subsequent representations of generated or loaded
maps. If the keyword MEAN in used the level is relative to the
mean of the map data. Otherwise the level is absolute.
In general, a lower level results in a map containing more of
the displayed volume, while a higher level results in a map
containing less of the displayed volume.
Map load
The RasMol map load command loads a map file into RasMol. The
valid formats are CCP4 map format and imgCIF format.
If no specific map was given by the map selector, the new map is
given the next available map number.
If a specific map was given by the map selector, the new map
replaces that map. If more than one map was given by the map
selector, the new map replaces the lowest numbered of the
selected maps. In any case the new map becomes the currently
selected map.
The map is displayed as dots, mesh or a surface depending on the
last map rendering mode selected.
Map mask
The RasMol map mask command specifies a mask to be used to limit
the display space to be used for making representations of other
maps or removes an earlier mask specification.
The 'selected' option indicates that the mask is to be created
from the currently selected atoms. The '<number>' option
indicates that the mask is to be copied from the map of the
number specified. The 'none' option removes the previously
specified mask, if any.
The map selector specifies the map or maps to which the
specified mask will the applied. For example, 'map next mask
selected' specifies that the currently selected atoms are to be
used to generate a mask to be applied to any maps created by
subsequent 'map load' or 'map generate' commands.
Any map may be used as a mask. The portions of the mask map
greater than than or equal to the average value of the mask map
allow the values of the map being masked to be used as given.
The portions of the mask map lower than the average value of the
mask map cause the values of the map being masked to be treated
as if they were equal to the lowest data value of the map being
masked.
Map resolution
The RasMol map resolution command specifies the resolution in
RasMol units or, if a number containing a decimal point is
given, the resolution in Angstroms to be used in generating and
in representing maps.
The resolution is used at the map spacing for representations of
maps, indicating the separation between contour levels (see the
map spacing command) and to infer the map spread to be used in
generated maps from selected atoms (see the map spread command).
The map spread is set to two thirds of the specified resolution.
Map restrict
The RasMol map restrict command selects particular maps to make
them active for subsequent map commands. This is similar to the
map select command, but does disables the display of the maps
that were not selected.
Map save
The RasMol map save command saves an imgCIF map file.
If no specific map was given by the map selector, the currently
selected maps and their masks are written to the file, one map
and mask pair per data block.
Map scale
The RasMol map scale command selects the scaling of pseudo-
Gaussians in the map generate commands. In the default of map
scale true, each Gaussian has a height proportional element type
of the atom. If map scale false has been executed, each
Gaussian is scaled so that the Gaussian contour level 1 is at
the van der Waals radius. In either case a standard deviation
determined by the most recently specified spread or resolution
is used.
Map select
The RasMol map select command selects particular maps to make
them active for subsequent map commands. This is similar to the
map restrict command, but does not disable the display of the
maps that were not selected.
If the optional atom parameter is given, the command selects the
atoms with centres closest to the map points. The radius of the
search may be specified by the parameter search_radius. The
default is to look for atoms within 4 Angstroms plus the probe
radius. If the optional within parameter is given, the new
selection is taken from within the currently selected atoms. If
the options add parameter is given, the new selection is added
to the currently selected atoms. The default is to search
within all atoms.
Map show
The RasMol map show command causes information about the maps
specified by the map selector to be written to the command
window.
Map spacing
The RasMol map spacing command specifies the spacing to be used
between contour lines in creating representations of maps. The
spacing is typically
given in Angstroms with a decimal point, but may also be
specified in RasMol units (250ths of an Angstom) as an integer.
For maps loaded in grid coordinates that spacing is parallel to
the cell edges. The default spacing is one half Angstrom.
Map spread
The RasMol map spread command specifies the reciprocal of the
number of standard deviations per radius to be used in
generating maps as sums of Gaussians centered on atomic
positions. The default spread is one two thirds (i.e. each
radius covers 1.5 standard deviations).
If the spread has been set to zero, the spread for each atom is
determined from the van der Waals radius and the probe atom
radius to simulate the effect of a Lee-Richards surface.
Map zap
The RasMol map zap command removes the data and representations
of the maps specified by the map selector. The map numbers of
maps that have not been removed are not changed.
Molecule
The RasMol molecule command selects one of up to 5 previously
loaded molecules for active manipulation. While all the
molcules are displayed and may be rotated collectively (see the
rotate all command), only one molecule at a time time is active
for manipulation by the commands which control the details of
rendering.
Monitor
The RasMol monitor command allows the display of distance
monitors. A distance monitor is a dashed (dotted) line between
an arbitrary pair of atoms, optionally labelled by the distance
between them. The RasMol command monitor <number> <number> adds
such a distance monitor between the two atoms specified by the
atom serial numbers given as parameters
Distance monitors are turned off with the command monitors off.
By default, monitors display the distance between its two end
points as a label at the centre of the monitor. These distance
labels may be turned off with the command set monitors off, and
re-enabled with the command set monitors on. Like most other
representations, the colour of a monitor is taken from the
colour of its end points unless specified by the colour monitors
command.
Distance monitors may also be added to a molecule interactively
with the mouse, using the set picking monitor command. Clicking
on an atom results in its being identified on the rasmol command
line. In addition every atom picked increments a modulo counter
such that, in monitor mode, every second atom displays the
distance between this atom and the previous one. The shift key
may be used to form distance monitors between a fixed atom and
several consecutive positions. A distance monitor may also be
removed (toggled) by selecting the appropriate pair of atom end
points a second time.
Notoggle
The RasMol NoToggle command enables or disables the use of the
toggle ability that is used by some of the other RasMol
commands. When no boolean value is specified, NoToggle mode is
ENABLED. When NoToggle mode is ENABLED, all toggle
functionality is DISABLED. To turn it off, one must explicitly
set notoggle off.
Some commands which use the toggle feature are: ColourMode.
More functions that utilize this capability may be added at a
later date.
Pause The RasMol pause command is used in script files to stop the
script file for local manipulation by a mouse, until any key is
pushed to restart the script file. Wait is synonymous with
pause. This command may be executed in RasMol script files to
suspend the sequential execution of commands and allow the user
to examine the current image. When RasMol executes a pause
command in a script file, it suspends execution of the rest of
the file, refreshes the image on the screen and allows the
manipulation of the image using the mouse and scroll bars, or
resizing of the graphics window. Once a key is pressed, control
returns to the script file at the line following the pause
command. While a script is suspended the molecule may be
rotated, translated, scaled, slabbed and picked as usual, but
all menu commands are disabled.
Play The RasMol play command specifies the recording medium from
which to play back a movie. The playback frame start time is
given in seconds to millisecond precision. Since we are working
on computers, the medium is specified as a set of files, each
marked with the playback frame start time in milliseconds as
part of the name. The place in the name at which to look for the
playback frame start time in milliseconds is marked by the
characters "ssssss" with an appropriate number of digits.
RasMol accepts either upper or lower case s's or decimal digits
to mark the place for the time. The play off and play eject
commands effectively remove the specified medium from use. If no
medium is specified, play off suspends playing and play on
resumes playing. Normally play starts immediately and runs to
the end of the medium. However, if play off and/or or some
combination of play from and play until is entered before play
type medium, those settings will be used.
As of release 2.7.5, RasMol support play from scripts and data
files.
Print The RasMol print command sends the currently displayed image to
the local default printer using the operating system's native
printer driver. Note: this command is not yet supported under
UNIX or VMS. It is intended to take advantage of Microsoft
Windows and Apple Macintosh printer drivers. For example, this
allows images to be printed directly on a dot matrix printer.
When using RasMol on a UNIX or VMS system this functionality may
be achieved by either generating a PostScript file using the
RasMol write ps or write vectps commands and printing that or
generating a raster image file and using a utility to dump that
to the local printer.
Quit Exit from the RasMol program. The RasMol commands exit and quit
are synonymous, except within nested scripts. In that case,
exit terminates only the current level, while quit terminates
all nested levels of scripts.
Record The RasMol record command specifies the recording medium to hold
the movie. Since we are working on computers, the medium is
specified as a template for a set of files, each marked with the
playback frame start time in milliseconds (rather than as
seconds to avoid embedding a decimal point) as part of the name.
The place in the name to be replaced with the playback frame
start time in milliseconds is marked by the characters "ssssss"
with an appropriate number of digits. RasMol accepts either
upper or lower case s's or decimal digits to mark the place for
the time. The record off commands remove the specified medium
from use. If no medium is specified, record off suspends
recording and record on resumes recording with the next
available time on the same medium. The screen is the default
medium and is, by default, on. Writing to disk must be
explicitly specified so that the disk does not get filled up
unintentionally. The type of a recording medium may be an image
type such as gif, pict or png to record the actual screen images
or script to record the RasMol commands used to generate the
frames.
Normally recording starts at playback frame start time 0
seconds. A non-zero starting time in seconds can be specified
with the record from command as in record from 25 or record from
37.25 to help in organizing scenes of movies to be assembled
later in an appropriate order. The record until command allows
an upper limit to be set on recording time in seconds. The
default is to have no limit. Issuing the commands
record from 600
record until 1800
would result in a 20 minute movie segment intended to start 10
minutes into a longer movie. These commands allow control over
rewriting selected time segments.
Refresh
The RasMol refresh command redraws the current image. This is
useful in scripts to ensure application of a complex list of
parameter changes.
Renumber
The RasMol renumber command sequentially numbers the residues in
a macromolecular chain. The optional parameter specifies the
value of the first residue in the sequence. By default, this
value is one. For proteins, each amino acid is numbered
consecutively from the N terminus to the C terminus. For nucleic
acids, each base is numbered from the 5' terminus to the 3'
terminus. All chains in the current database are renumbered and
gaps in the original sequence are ignored. The starting value
for numbering may be negative.
Reset The RasMol reset command restores the original viewing
transformation and centre of rotation. The scale is set to its
default value, zoom 100, the centre of rotation is set to the
geometric centre of the currently loaded molecule, centre all,
this centre is translated to the middle of the screen and the
viewpoint set to the default orientation.
This command should not be mistaken for the RasMol zap command
which deletes the currently stored molecule, returning the
program to its initial state.
Restrict
The RasMol restrict command both defines the currently selected
region of the molecule and disables the representation of (most
of) those parts of the molecule no longer selected. All
subsequent RasMol commands that modify a molecule's colour or
representation affect only the currently selected region. The
parameter of a restrict command is a RasMol atom expression that
is evaluated for every atom of the current molecule. This
command is very similar to the RasMol select command, except
restrict disables the wireframe, spacefill and backbone
representations in the non-selected region.
Type "help expression" for more information on RasMol atom
expressions or see section Atom Expressions.
Ribbons
The RasMol ribbons command displays the currently loaded protein
or nucleic acid as a smooth solid "ribbon" surface passing along
the backbone of the protein. The ribbon is drawn between each
amino acid whose alpha carbon is currently selected. The colour
of the ribbon is changed by the RasMol colour ribbon command. If
the current ribbon colour is none (the default), the colour is
taken from the alpha carbon at each position along its length.
The width of the ribbon at each position is determined by the
optional parameter in the usual RasMol units. By default the
width of the ribbon is taken from the secondary structure of the
protein or a constant value of 720 (2.88 Angstroms) for nucleic
acids. The default width of protein alpha helices and beta
sheets is 380 (1.52 Angstroms) and 100 (0.4 Angstroms) for turns
and random coil. The secondary structure assignment is either
from the PDB file or calculated using the DSSP algorithm as used
by the structure command. This command is similar to the RasMol
command strands which renders the biomolecular ribbon as
parallel depth-cued curves.
Rotate Rotate the molecule about the specified axis. Permitted values
for the axis parameter are "x", "y", "z" and "bond". The
integer parameter states the angle in degrees for the structure
to be rotated. For the X and Y axes, positive values move the
closest point up and right, and negative values move it down and
left, respectively. For the Z axis, a positive rotation acts
clockwise and a negative angle anti-clockwise.
Alternatively, this command may be used to specify which
rotations the mouse or dials will control. If rotate bond true
is selected, the horizontal scroll bar will control rotation
around the axis selected by the bond src dst pick command. If
rotate all true is selected, and multiple molecules have been
loaded, then all molecules will rotate together. In all other
cases, the mouseand dials control the the rotation of the
molecule selected by the molecule n command.
Russian
The RasMol Russian command sets the menus and messages to the
Russian versions.
This command may not work correctly unless appropriate fonts
have been installed. The commands Bulgarian, Chinese, English,
French, Italian, Russian and Spanish may be used to select
Bulgarian, Chinese, English, French, Italian, Japanese, Russian
and Spanish menus and messages if the appropriate fonts have
been installed.
Save Save the currently selected set of atoms in a Protein Data Bank
(PDB), 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.
Script The RasMol script command reads a set of RasMol commands
sequentially from a text file and executes them. This allows
sequences of commonly used commands to be stored and performed
by single command. A RasMol script file may contain a further
script command up to a maximum "depth" of 10, allowing
complicated sequences of actions to be executed. RasMol ignores
all characters after the first '#' character on each line
allowing the scripts to be annotated. Script files are often
also annotated using the RasMol echo command.
The most common way to generate a RasMol script file is to use
the write script or write rasmol commands to output the sequence
of commands that are needed to regenerate the current view,
representation and colouring of the currently displayed
molecule.
The RasMol command source is synonymous with the script command.
Select Define the currently selected region of the molecule. All
subsequent RasMol commands that manipulate a molecule or modify
its colour or representation only affect the currently selected
region. The parameter of a select command is a RasMol expression
that is evaluated for every atom of the current molecule. The
currently selected (active) region of the molecule are those
atoms that cause the expression to evaluate true. To select the
whole molecule use the RasMol command select all. The behaviour
of the select command without any parameters is determined by
the RasMol hetero and hydrogen parameters.
Type "help expression" for more information on RasMol atom
expressions or see section Atom Expressions.
Set The RasMol set command allows the user to alter various internal
program parameters such as those controlling rendering options.
Each parameter has its own set or permissible parameter options.
Typically, omitting the parameter option resets that parameter
to its default value. A list of valid parameter names is given
below.
Show The RasMol show command display details of the status of the
currently loaded molecule. The command show information lists
the molecule's name, classification, PDB code and the number of
atoms, chains, groups it contains. If hydrogen bonding,
disulphide bridges or secondary structure have been determined,
the number of hbonds, ssbonds, helices, ladders and turns are
also displayed, respectively. The command show centre shows any
non-zero centering values selected by the centre [CenX, CenY,
CenZ] command. The command show phipsi shows the phi and psi
angles of the currently selected residues and the omega angles
of cis peptide bonds. The command show RamPrint (or 'show RPP'
or 'show RamachandranPrinterPlot') shows a simple Ramachandran
printer plot in the style of Frances Bernstein's fisipl program.
The command show rotation (or 'show rot' or 'show 'rotate')
shows the currently selected values of z, y, x and bond
rotations, if any. The command show selected (or 'show selected
group' or 'show selected chain' or 'show selected atom' ) shows
the groups (default), chains or atoms of the current selection.
The command show sequence lists the residues that comprise each
chain of the molecule. The command show symmetry shows the
space group and unit cell of the molecule. The command show
translation shows any non-zero translation values selected by
the translate <axis> <value> command. The command show zoom
shows any non-zero zoom value selected by the zoom <value>
command.
Slab The RasMol slab command enables, disables or positions the z-
clipping plane of the molecule. The program only draws those
portions of the molecule that are further from the viewer than
the slabbing plane. Integer values range from zero at the very
back of the molecule to 100 which is completely in front of the
molecule. Intermediate values determine the percentage of the
molecule to be drawn.
This command interacts with the depth <value> command, which
clips to the rear of a given z-clipping plane.
Spacefill
The RasMol spacefill command is used to represent all of the
currently selected atoms as solid spheres. This command is used
to produce both union-of-spheres and ball-and-stick models of a
molecule. The command, spacefill true, the default, represents
each atom as a sphere of van der Waals radius. The command
spacefill off turns off the representation of the selected atom
as spheres. A sphere radius may be specified as an integer in
RasMol units (1/250th Angstrom) or a value containing a decimal
point. A value of 500 (2.0 Angstroms) or greater results in a
"Parameter value too large" error.
The temperature option sets the radius of each sphere to the
value stored in its temperature field. Zero or negative values
have no effect and values greater than 2.0 are truncated to 2.0.
The user option allows the radius of each sphere to be specified
by additional lines in the molecule's PDB file using Raster 3D's
COLOUR record extension.
The RasMol command cpk is synonymous with the spacefill command.
The RasMol command cpknew is synonymous with the spacefill
command, except that a slightly different set of colours is
used.
Spanish
The RasMol Spanish command sets the menus and messages to the
Spanish versions.
This command may not work correctly unless appropriate fonts
have been installed. The commands Bulgarian, Chinese, English,
French, Italian, Russian and Spanish may be used to select
Bulgarian, Chinese, English, French, Italian, Japanese, Russian
and Spanish menus and messages if the appropriate fonts have
been installed.
SSBonds
The RasMol ssbonds command is used to represent the disulphide
bridges of the protein molecule as either dotted lines or
cylinders between the connected cysteines. The first time that
the ssbonds command is used, the program searches the structure
of the protein to find half-cysteine pairs (cysteines whose
sulphurs are within 3 Angstroms of each other) and reports the
number of bridges to the user. The command ssbonds on displays
the selected "bonds" as dotted lines, and the command ssbonds
off disables the display of ssbonds in the currently selected
area. Selection of disulphide bridges is identical to normal
bonds, and may be adjusted using the RasMol set bondmode
command. The colour of disulphide bonds may be changed using the
colour ssbonds command. By default, each disulphide bond has the
colours of its connected atoms.
By default disulphide bonds are drawn between the sulphur atoms
within the cysteine groups. By using the set ssbonds command the
position of the cysteine's alpha carbons may be used instead.
Star The RasMol star command is used to represent all of the
currently selected atoms as stars (six strokes, one each in the
x, -x, y, -y, z and -z directions). The commands select not
bonded followed by star 75 are useful to mark unbonded atoms in
a wireframe display with less overhead than provided by
spacefill 75. This can be done automatically for all subsequent
wireframe displays with the command set bondmode not bonded.
The command star true, the default, represents each atom as a
star with strokes length equal to van der Waals radius. The
command star off turns off the representation of the selected
atom as stars. A star stroke length may be specified as an
integer in RasMol units (1/250th Angstrom) or a value containing
a decimal point. A value of 500 (2.0 Angstroms) or greater
results in a "Parameter value too large" error.
The temperature option sets the stroke length of each star to
the value stored in its temperature field. Zero or negative
values have no effect and values greater than 2.0 are truncated
to 2.0. The user option allows the stroke length of each star
to be specified by additional lines in the molecule's PDB file
using Raster 3D's COLOUR record extension.
The RasMol spacefill command can be used for more artistic
rendering of atoms as spheres.
Stereo The RasMol stereo command provides side-by-side stereo display
of images. Stereo viewing of a molecule may be turned on (and
off) either by selecting Stereo from the Options menu, or by
typing the commands stereo on or stereo off.
Starting with RasMol version 2.7.2.1, the Stereo menu selection
and the command stereo without arguments cycle from the initial
state of stereo off to stereo on in cross-eyed mode to stereo on
in wall-eyed mode and then back to stereo off.
The separation angle between the two views may be adjusted with
the set stereo [-] <number> command, where positive values
result in crossed eye viewing and negative values in relaxed
(wall-eyed) viewing. The inclusion of [-] <number> in the
stereo command, as for example in stereo 3 or stereo -5, also
controls angle and direction.
The stereo command is only partially implemented. When stereo is
turned on, the image is not properly recentred. (This can be
done with a translate x -<number>
command.) It is not supported in vector PostScript output
files, is not saved by the write script command, and in general
is not yet properly interfaced with several other features of
the program.
Strands
The RasMol strands command displays the currently loaded protein
or nucleic acid as a smooth "ribbon" of depth-cued curves
passing along the backbone of the protein. The ribbon is
composed of a number of strands that run parallel to one another
along the peptide plane of each residue. The ribbon is drawn
between each amino acid whose alpha carbon is currently
selected. The colour of the ribbon is changed by the RasMol
colour ribbon command. If the current ribbon colour is none (the
default), the colour is taken from the alpha carbon at each
position along its length. The central and outermost strands may
be coloured independently using the colour ribbon1 and colour
ribbon2 commands, respectively. The number of strands in the
ribbon may be altered using the RasMol set strands command.
The width of the ribbon at each position is determined by the
optional parameter in the usual RasMol units. By default the
width of the ribbon is taken from the secondary structure of the
protein or a constant value of 720 for nucleic acids (which
produces a ribbon 2.88 Angstroms wide). The default width of
protein alpha helices and beta sheets is 380 (1.52 Angstroms)
and 100 (0.4 Angstroms) for turns and random coil. The secondary
structure assignment is either from the PDB file or calculated
using the DSSP algorithm as used by the structure command. This
command is similar to the RasMol command ribbons which renders
the biomolecular ribbon as a smooth shaded surface.
Structure
The RasMol structure command calculates secondary structure
assignments for the currently loaded protein. If the original
PDB file contained structural assignment records (HELIX, SHEET
and TURN) these are discarded. Initially, the hydrogen bonds of
the current molecule are found, if this hasn't been done
already. The secondary structure is then determined using Kabsch
and Sander's DSSP algorithm. Once finished the program reports
the number of helices, strands and turns found.
Surface
The RasMol surface command renders a Lee-Richards molecular
surface resulting from rolling a probe atom on the selected
atoms. The value given specifies the radius of the probe. If
given in the first form, the evolute of the surface of the probe
is shown (the solvent excluded surface). If given in the second
form, the envelope of the positions of the center of the probe
is shown (the solvent accessible surface).
Trace The RasMol trace command displays a smooth spline between
consecutive alpha carbon positions. This spline does not pass
exactly through the alpha carbon position of each residue, but
follows the same path as ribbons, strands and cartoons. Note
that residues may be displayed as ribbons, strands, cartoons or
as a trace. Enabling one of these representations disables the
others. However, a residue may be displayed simultaneously as
backbone and as one of the above representations. This may
change in future versions of RasMol. Prior to version 2.6,
trace was synonymous with backbone.
Trace temperature displays the backbone as a wider cylinder at
high temperature factors and thinner at lower. This
representation is useful to X-ray crystallographers and NMR
spectroscopists.
Translate
The RasMol translate command moves the position of the centre of
the molecule on the screen. The axis parameter specifies along
which axis the molecule is to be moved and the integer parameter
specifies the absolute position of the molecule centre from the
middle of the screen. Permitted values for the axis parameter
are "x", "y" and "z". Displacement values must be between -100
and 100 which correspond to moving the current molecule just off
the screen. A positive "x" displacement moves the molecule to
the right, and a positive "y" displacement moves the molecule
down the screen. The pair of commands translate x 0 and
translate y 0 centres the molecule on the screen.
UnBond The RasMol command unbond <number> <number> removes the
designated bond from the drawing.
The command unbond without arguments removes a bond previously
picked by the bond <number> <number> pick command.
Wireframe
The RasMol wireframe command represents each bond within the
selected region of the molecule as a cylinder, a line or a
depth-cued vector. The display of bonds as depth-cued vectors
(drawn darker the further away from the viewer) is turned on by
the command wireframe or wireframe on. The selected bonds are
displayed as cylinders by specifying a radius either as an
integer in RasMol units or containing a decimal point as a value
in Angstroms. A parameter value of 500 (2.0 Angstroms) or above
results in an "Parameter value too large" error. Bonds may be
coloured using the colour bonds command.
If the selected bonds involved atoms of alternate conformers
then the bonds are narrowed in the middle to a radius of .8 of
the specified radius (or to the radius specified as the optional
second parameter).
Non-bonded atoms, which could become invisible in an ordinary
wireframe display can be marked by a preceding set bondmode not
bonded command. If nearly co-linear bonds to atoms cause them
to be difficult to see in a wireframe display, the set bondmode
all command will add markers for all atoms in subsequent
wireframe command executions.
Write Write the current image to a file in a standard format.
Currently supported image file formats include bmp (Microsoft
bitmap) and gif (Compuserve GIF), iris (IRIS RGB), ppm (Portable
Pixmap), ras (Sun rasterfile), ps and epsf (Encapsulated
PostScript), monops (Monochrome Encapsulated PostScript), pict
(Apple PICT), vectps (Vector Postscript). The write command may
also be used to generate command scripts for other graphics
programs. The format script writes out a file containing the
RasMol script commands to reproduce the current image. The
format molscript writes out the commands required to render the
current view of the molecule as ribbons in Per Kraulis'
Molscript program and the format kinemage the commands for David
Richardson's program Mage. The following formats are useful for
further processing: povray (POVRay 2), povray3 (POVRay 3 --
under development), vrml (VRML file). Finally, several formats
are provided to provide phi-psi data for listing or for phipsi
(phi-psi data as an annotated list with cis omegas), ramachan
and RDF and RamachandranDataFile (phi-psi data as columns of
numbers for gnuplot), RPP and RamachandranPrinterPlot (phi-psi
data as a printer plot).
The distinction between this command and the RasMol save command
has been dropped. The only difference is that without a format
specifier the save command generates a PDB file and the write
command generates a GIF image.
Zap Deletes the contents of the current database and resets
parameter variables to their initial default state.
Zoom Change the magnification of the currently displayed image.
Boolean parameters either magnify or reset the scale of current
molecule. An integer parameter specifies the desired
magnification as a percentage of the default scale. The minimum
parameter value is 10; the maximum parameter value is dependent
upon the size of the molecule being displayed. For medium sized
proteins this is about 500.
SET PARAMETERS
RasMol has a number of internal parameters that may be modified using
the set command. These parameters control a number of program options
such as rendering options and mouse button mappings.
picking play.fps radius record.aps
Set Ambient
The RasMol ambient parameter is used to control the amount of
ambient (or surrounding) light in the scene. The ambient value
must be between 0 and 100. It controls the percentage intensity
of the darkest shade of an object. For a solid object, this is
the intensity of surfaces facing away from the light source or
in shadow. For depth-cued objects this is the intensity of
objects furthest from the viewer.
This parameter is commonly used to correct for monitors with
different "gamma values" (brightness), to change how light or
dark a hardcopy image appears when printed or to alter the
feeling of depth for wireframe or ribbon representations.
Set Axes
The RasMol axes parameter controls the display of orthogonal
coordinate axes on the current display. The coordinate axes are
those used in the molecule data file, and the origin is the
centre of the molecule's bounding box. The set axes command is
similar to the commands set boundbox and set unitcell that
display the bounding box and the crystallographic unit cell,
respectively.
Set Backfade
The RasMol backfade parameter is used to control backfade to the
specified background colour, rather than black. This is
controlled by the commands set backfade on and set backfade off.
For example, this may be used to generate depth-cued images that
fade to white, rather than black.
Set Background
The RasMol background parameter is used to set the colour of the
"canvas" background. The colour may be given as either a colour
name or a comma separated triple of Red, Green, Blue (RGB)
components enclosed in square brackets. Typing the command help
colours will give a list of the predefined colour names
recognised by RasMol. When running under X Windows, RasMol also
recognises colours in the X server's colour name database.
The command set background is synonymous with the RasMol command
background.
Set BondMode
The RasMol set bondmode command controls the mechanism used to
select individual bonds and modifies the display of bonded and
non-bonded atoms by subsequent wireframe commands.
When using the select and restrict commands, a given bond will
be selected if i) the bondmode is or and either of the connected
atoms is selected, or ii) the bondmode is and and both atoms
connected by the bond are selected. Hence an individual bond may
be uniquely identified by using the command set bondmode and and
then uniquely selecting the atoms at both ends.
The bondmode [all | none | not bonded] commands add star 75 or
spacefill 75 markers for the designated atoms to wireframe
displays. Stars are used when the specified wireframe radius is
zero.
Set Bonds
The RasMol bonds parameter is used to control display of double
and triple bonds as multiple lines or cylinders. Currently
bond orders are only read from MDL Mol files, Sybyl Mol2 format
files, Tripos Alchemy format files, CIF and mmCIF, and suitable
PDB files. Double (and triple) bonds are specified in some
PDB files by specifying a given bond twice (and three times) in
CONECT records. The command set bonds on enables the display
of bond orders, and the command set bonds off disables them.
Set BoundBox
The RasMol boundbox parameter controls the display of the
current molecule's bounding box on the display. The bounding box
is orthogonal to the data file's original coordinate axes. The
set boundbox command is similar to the commands set axes and set
unitcell that display orthogonal coordinate axes and the
bounding box, respectively.
Set Cartoon
The RasMol cartoon parameter is used to control display of the
cartoon version of the ribbons display. By default, the C-
termini of beta-sheets are displayed as arrow heads. This may be
enabled and disabled using the set cartoons <boolean> command.
The depth of the cartoon may be adjusted using the cartoons
<number> command. The set cartoons command without any
parameters returns these two options to
their default values.
Set CisAngle
The RasMol cisangle parameter controls the cutoff angle for
identifying cis peptide
bonds. If no value is given, the cutoff is set to 90 degrees.
Set Display
This command controls the display mode within RasMol. By
default, set display normal, RasMol displays the molecule in the
representation specified by the user. The command set display
selected changes the display mode such that the molecule is
temporarily drawn so as to indicate currently selected portion
of the molecule. The user specified colour scheme and
representation remains unchanged. In this representation all
selected atoms are shown in yellow and all non selected atoms
are shown in blue. The colour of the background is also changed
to a dark grey to indicate the change of display mode. This
command is typically only used by external Graphical User
Interfaces (GUIs).
Set FontSize
The RasMol set fontsize command is used to control the size of
the characters that form atom labels. This value corresponds to
the height of the displayed character in pixels. The maximum
value of fontsize is 48 pixels, and the default value is 8
pixels high. Fixed or proportional spacing may be selected by
appending the "FS" or "PS" modifiers, respectively. The default
is "FS". To display atom labels on the screen use the RasMol
label command and to change the colour of displayed labels, use
the colour labels command.
Set FontStroke
The RasMol set fontstroke command is used to control the size of
the stroke width of the characters that form atom labels. This
value is the radius in pixels of cylinders used to form the
strokes. The special value of "0" is the default used for the
normal single pixel stroke width, which allows for rapid drawing
and rotation of the image. Non-zero values are provided to
allow for more artistic atom labels for publication at the
expense of extra time in rendering the image.
When wider strokes are used, a larger font size is recommend,
e.g. by using the RasMol set fontsize 24 PS command, followed
by set fontstroke 2
To display atom labels on the screen use the RasMol label
command, and to change the colour of displayed labels use the
colour labels command.
Set HBonds
The RasMol hbonds parameter determines whether hydrogen bonds
are drawn between the donor and acceptor atoms of the hydrogen
bond, set hbonds sidechain or between the alpha carbon atoms of
the protein backbone and between the phosphorous atoms of the
nucleic acid backbone, set hbonds backbone. The actual display
of hydrogen bonds is controlled by the hbonds command. Drawing
hydrogen bonds between protein alpha carbons or nucleic acid
phosphorous atoms is useful when the rest of the molecule is
shown in only a schematic representation such as backbone,
ribbons or strands. This parameter is similar to the RasMol
ssbonds parameter.
Set Hetero
The RasMol hetero parameter is used to modify the 'default'
behaviour of the RasMol select command, i.e. the behaviour of
select without any parameters. When this value is false, the
default select region does not include any heterogeneous atoms
(refer to the predefined set hetero ). When this value is true,
the default select region may contain hetero atoms. This
parameter is similar to the RasMol hydrogen parameter which
determines whether hydrogen atoms should be included in the
default set. If both hetero and hydrogen are true, select
without any parameters is equivalent to select all.
Set HourGlass
The RasMol hourglass parameter allows the user to enable and
disable the use of the 'hour glass' cursor used by RasMol to
indicate that the program is currently busy drawing the next
frame. The command set hourglass on enables the indicator,
whilst set hourglass off prevents RasMol from changing the
cursor. This is useful when spinning the molecule, running a
sequence of commands from a script file or using interprocess
communication to execute complex sequences of commands. In these
cases a 'flashing' cursor may be distracting.
Set Hydrogen
The RasMol hydrogen parameter is used to modify the "default"
behaviour of the RasMol select command, i.e. the behaviour of
select without any parameters. When this value is false, the
default select region does not include any hydrogen, deuterium
or tritium atoms (refer to the predefined set hydrogen ). When
this value is true, the default select region may contain
hydrogen atoms. This parameter is similar to the RasMol hetero
parameter which determines whether heterogeneous atoms should be
included in the default set. If both hydrogen and hetero are
true, select without any parameters is equivalent to select all.
Set Kinemage
The RasMol set kinemage command controls the amount of detail
stored in a Kinemage output file generated by the RasMol write
kinemage command. The output kinemage files are intended to be
displayed by David Richardson's Mage program. set kinemage
false, the default, only stores the currently displayed
representation in the generated output file. The command set
kinemage true, generates a more complex Kinemage that contains
both the wireframe and backbone representations as well as the
coordinate axes, bounding box and crystal unit cell.
Set Menus
The RasMol set menus command enables the canvas window's menu
buttons or menu bar. This command is typically only used by
graphical user interfaces or to create as large an image as
possible when using Microsoft Windows.
Set Monitor
The RasMol set monitor command enables monitors. The distance
monitor labels may be turned off with the command set monitor
off, and re-enabled with the command set monitor on.
Set Mouse
The RasMol set mouse command sets the rotation, translation,
scaling and zooming mouse bindings. The default value is rasmol
which is suitable for two button mice (for three button mice the
second and third buttons are synonymous); X-Y rotation is
controlled by the first button, and X-Y translation by the
second. Additional functions are controlled by holding a
modifier key on the keyboard. [Shift] and the first button
performs scaling, [shift] and the second button performs Z-
rotation, and [control] and the first mouse button controls the
clipping plane. The insight and quanta options provide the same
mouse bindings as other packages for experienced users.
Set Picking
The RasMol set picking series of commands affects how a user may
interact with a molecule displayed on the screen in RasMol.
Enabling/Disabling Atom Identification Picking: Clicking on an
atom with the mouse results in identification and the display of
its residue name, residue number, atom name, atom serial number
and chain in the command window. This behavior may be disabled
with the command set picking none and restored with the command
set picking ident. The command set picking coord adds the
atomic coordinates of the atom to the display.
Disabling picking, by using set picking off is useful when
executing the pause command in RasMol scripts as it prevents the
display of spurious message on the command line while the script
is suspended.
Measuring Distances, Angles and Torsions: Interactive
measurement of distances, angles and torsions is achieved using
the commands: set picking distance, set picking monitor, set
picking angle and set picking torsion, respectively. In these
modes, clicking on an atom results in it being identified on the
rasmol command line. In addition every atom picked increments a
modulo counter such that in distance mode, every second atom
displays the distance (or distance monitor) between this atom
and the previous one. In angle mode, every third atom displays
the angle between the previous three atoms and in torsion mode
every fourth atom displays the torsion between the last four
atoms. By holding down the shift key while picking an atom, this
modulo counter is not incremented and allows, for example, the
distances of consecutive atoms from a fixed atom to be
displayed. See the monitor command for how to control the
display of distance monitor lines and labels.
Labelling Atoms with the Mouse: The mouse may also be used to
toggle the display of an atom label on a given atom. The RasMol
command set picking label removes a label from a picked atom if
it already has one or displays a concise label at that atom
position otherwise.
Centring Rotation with the Mouse: A molecule may be centred on a
specified atom position using the RasMol commands set picking
centre or set picking center. In this mode, picking an atom
causes all 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.
Set Play
The RasMol set play.fps command gives the number of frames per
second for playback by the play command (default 24 frames per
second).
In the current release of RasMol, the play timing is not
controlled by this parameter.
Set Radius
The RasMol set radius command is used to alter the behaviour of
the RasMol dots command depending upon the value of the solvent
parameter. When solvent is true, the radius parameter controls
whether a true van der Waals' surface is generated by the dots
command. If the value of radius is anything other than zero,
that value is used as the radius of each atom instead of its
true vdW value. When the value of solvent is true, this
parameter determines the 'probe sphere' (solvent) radius. The
parameter may be given as an integer in rasmol units or
containing a decimal point in Angstroms. The default value of
this parameter is determined by the value of solvent and
changing solvent resets radius to its new default value.
Set Record
The RasMol set record.aps gives the maximum on-screen velocity
in Angstroms per second in animating translations, rotations and
zooms (default 10 A/second).
The RasMol set record.aps command gives number of frames per
second for recording by the record command (default 24 frames
per second).
The RasMol set record.dwell command sets the time in seconds to
dwell on a change in appearance (default .5 sec).
Set ShadePower
The shadepower parameter (adopted from RasTop) determines the
shade repartition (the contrast) used in rendering solid
objects. This value between 0 and 100 adjusts shading on an
object surface oriented along the direction to the light source.
Changing the shadepower parameter does not change the maximum or
the minimum values of this shading, as does changing the ambient
parameter. A value of 100 concentrates the light on the top of
spheres, giving a highly specular, glassy rendering (see the
specpower parameter). A value of 0 distributes the light on the
entire object.
This implementation of shadepower differs from the one in RasTop
only in the choice of range (0 to 100 versus -20 to 20 in
RasTop).
Set Shadow
The RasMol set shadow command enables and disables ray-tracing
of the currently rendered image. Currently only the
spacefilling representation is shadowed or can cast shadows.
Enabling shadowing will automatically disable the Z-clipping
(slabbing) plane using the command slab off. Ray-tracing
typically takes about several seconds for a moderately sized
protein. It is recommended that shadowing be normally disabled
whilst the molecule is being transformed or manipulated, and
only enabled once an appropriate viewpoint is selected, to
provide a greater impression of depth.
Set SlabMode
The RasMol slabmode parameter controls the rendering method of
objects cut by the slabbing (z-clipping) plane. Valid slabmode
parameters are "reject", "half", "hollow", "solid" and
"section".
Set Solvent
The RasMol set solvent command is used to control the behaviour
of the RasMol dots command. Depending upon the value of the
solvent parameter, the dots command either generates a van der
Waals' or a solvent accessible surface around the currently
selected set of atoms. Changing this parameter automatically
resets the value of the RasMol radius parameter. The command
set solvent false, the default value, indicates that a van der
Waals' surface should be generated and resets the value of
radius to zero. The command set solvent true indicates that a
'Connolly' or 'Richards' solvent accessible surface should be
drawn and sets the radius parameter, the solvent radius, to 1.2
Angstroms (or 300 RasMol units).
Set Specular
The RasMol set specular command enables and disables the display
of specular highlights on solid objects drawn by RasMol.
Specular highlights appear as white reflections of the light
source on the surface of the object. The current RasMol
implementation uses an approximation function to generate this
highlight.
The specular highlights on the surfaces of solid objects may be
altered by using the specular reflection coefficient, which is
altered using the RasMol set specpower command.
Set SpecPower
The specpower parameter determines the shininess of solid
objects rendered by RasMol. This value between 0 and 100 adjusts
the reflection coefficient used in specular highlight
calculations. The specular highlights are enabled and disabled
by the RasMol set specular command. Values around 20 or 30
produce plastic looking surfaces. High values represent more
shiny surfaces such as metals, while lower values produce more
diffuse/dull surfaces.
Set SSBonds
The RasMol ssbonds parameter determines whether disulphide
bridges are drawn between the sulphur atoms in the sidechain
(the default) or between the alpha carbon atoms in the backbone
of the cysteines residues. The actual display of disulphide
bridges is controlled by the ssbonds command. Drawing disulphide
bridges between alpha carbons is useful when the rest of the
protein is shown in only a schematic representation such as
backbone, ribbons or strands. This parameter is similar to the
RasMol hbonds parameter.
Set Stereo
The RasMol set stereo parameter controls the separation between
the left and right images. Turning stereo on and off doesn't
reposition the centre of the molecule.
Stereo viewing of a molecule may be turned on (and off) either
by selecting Stereo from the Options menu, or by typing the
commands stereo on or stereo off.
The separation angle between the two views may be adjusted with
the set stereo [-] <number> command, where positive values
result in crossed eye viewing and negative values in relaxed
(wall-eyed) viewing. Currently, stereo viewing is not supported
in vector PostScript output files.
Set Strands
The RasMol strands parameter controls the number of parallel
strands that are displayed in the ribbon representations of
proteins. The permissible values for this parameter are 1, 2, 3,
4, 5 and 9. The default value is 5. The number of strands is
constant for all ribbons being displayed. However, the ribbon
width (the separation between strands) may be controlled on a
residue by residue basis using the RasMol ribbons command.
Set Transparent
The RasMol transparent parameter controls the writing of
transparent GIFs by the write gif <filename> command. This may
be controlled by the set transparent on and set transparent off
commands.
Set UnitCell
The RasMol unitcell parameter controls the display of the
crystallographic unit cell on the current display. The crystal
cell is only enabled if the appropriate crystal symmetry
information is contained in the PDB, CIF or mmCIF data file. The
RasMol command show symmetry display details of the crystal's
space group and unit cell axes. The set unitcell command is
similar to the commands set axes and set boundbox that display
orthogonal coordinate axes and the bounding box, respectively.
Set VectPS
The RasMol vectps parameter is use to control the way in which
the RasMol write command generates vector PostScript output
files. The command set vectps on enables the use of black
outlines around spheres and cylinder bonds producing "cartoon-
like" high resolution output. However, the current
implementation of RasMol incorrectly cartoons spheres that are
intersected by more than one other sphere. Hence "ball and
stick" models are rendered correctly but not large spacefilling
spheres models. Cartoon outlines can be disabled, the default,
by the command set vectps off.
Set Write
The RasMol write parameter controls the use of the save and
write commands within scripts, but it may only be executed from
the command line. By default, this value is false, prohibiting
the generation of files in any scripts executed at start-up
(such as those launched from a WWW browser). However, animators
may start up RasMol interactively: type set write on and then
execute a script to generate each frame using the source
command.
ATOM EXPRESSIONS
RasMol atom expressions uniquely identify an arbitrary group of atoms
within a molecule. Atom expressions are composed of either primitive
expressions, predefined sets, comparison operators, within expressions,
or logical (boolean) combinations of the above expression types.
The logical operators allow complex queries to be constructed out of
simpler ones using the standard boolean connectives and, or and not.
These may be abbreviated by the symbols "&", "|" and "!", respectively.
Parentheses (brackets) may be used to alter the precedence of the
operators. For convenience, a comma may also be used for boolean
disjunction.
The atom expression is evaluated for each atom, hence protein and
backbone selects protein backbone atoms, not the protein and [nucleic]
acid backbone atoms!
Primitive Expressions
RasMol primitive expressions are the fundamental building blocks
of atom expressions. There are two types of primitive
expression. The first type is used to identify a given residue
number or range of residue numbers. A single residue is
identified by its number (position in the sequence), and a range
is specified by lower and upper bounds separated by a hyphen
character. For example select 5,6,7,8 is also select 5-8. Note
that this selects the given residue numbers in all macromolecule
chains.
The second type of primitive expression specifies a sequence of
fields that must match for a given atom. The first part
specifies a residue (or group of residues) and an optional
second part specifies the atoms within those residues. The first
part consists of a residue name, optionally followed by a
residue number and/or chain identifier.
The second part consists of a period character followed by an
atom name. An atom name may be up to four alphabetic or numeric
characters. An optional semicolon followed by an alternate
conformation identifier may be appended. An optional slash
followed by a model number may also be appended.
An asterisk may be used as a wild card for a whole field and a
question mark as a single character wildcard.
Comparison Operators
Parts of a molecule may also be distinguished using equality,
inequality and ordering operators on their properties. The
format of such comparison expression is a property name,
followed by a comparison operator and then an integer value.
The atom properties that may be used in RasMol are atomno for
the atom serial number, elemno for the atom's atomic number
(element), resno for the residue number, radius for the
spacefill radius in RasMol units (or zero if not represented as
a sphere) and temperature for the PDB isotropic temperature
value.
The equality operator is denoted either "=" or "==". The
inequality operator as either "<>", "!=" or "/=". The ordering
operators are "<" for less than, "<=" for less than or equal to,
">" for greater than, and ">" for greater than or equal to.
Within Expressions
A RasMol within expression allows atoms to be selected on their
proximity to another set of atoms. A within expression takes two
parameters separated by a comma and surrounded by parentheses.
The first argument is an integer value called the "cut-off"
distance of the within expression and the second argument is any
valid atom expression. The cut-off distance is expressed in
either integer RasMol units or Angstroms containing a decimal
point. An atom is selected if it is within the cut-off distance
of any of the atoms defined by the second argument. This allows
complex expressions to be constructed containing nested within
expressions.
For example, the command select within(3.2,backbone) selects any
atom within a 3.2 Angstrom radius of any atom in a protein or
nucleic acid backbone. Within expressions are particularly
useful for selecting the atoms around an active site.
Predefined Sets
RasMol atom expressions may contain predefined sets. These sets
are single keywords that represent portions of a molecule of
interest. Predefined sets are often abbreviations of primitive
atom expressions. In some cases the use of predefined sets
allows selection of areas of a molecule that could not otherwise
be distinguished. A list of the currently predefined sets is
given below. In addition to the sets listed here, RasMol also
treats element names (and their plurals) as predefined sets
containing all atoms of that element type, i.e. the command
select oxygen is equivalent to the command select elemno=8.
Predefined Sets
AT Set This set contains the atoms in the complementary nucleotides
adenosine and thymidine (A and T, respectively). All nucleotides
are classified as either the set at or the set cg This set is
equivalent to the RasMol atom expressions a,t, and nucleic and
not cg.
Acidic Set
The set of acidic amino acids. These are the residue types Asp
and Glu. All amino acids are classified as either acidic, basic
or neutral. This set is equivalent to the RasMol atom
expressions asp, glu and amino and not (basic or neutral).
Acyclic Set
The set of atoms in amino acids not containing a cycle or ring.
All amino acids are classified as either cyclic or acyclic.
This set is equivalent to the RasMol atom expression amino and
not cyclic.
Aliphatic Set
This set contains the aliphatic amino acids. These are the
amino acids Ala, Gly, Ile, Leu and Val. This set is equivalent
to the RasMol atom expression ala, gly, ile, leu, val.
Alpha Set
The set of alpha carbons in the protein molecule. This set is
approximately equivalent to the RasMol atom expression *.CA.
This command should not be confused with the predefined set
helix which contains the atoms in the amino acids of the
protein's alpha helices.
Amino Set
This set contains all the atoms contained in amino acid
residues. This is useful for distinguishing the protein from
the nucleic acid and heterogeneous atoms in the current molecule
database.
Aromatic Set
The set of atoms in amino acids containing aromatic rings.
These are the amino acids His, Phe, Trp and Tyr. Because they
contain aromatic rings all members of this set are member of the
predefined set cyclic. This set is equivalent to the RasMol
atom expressions his, phe, trp, tyr and cyclic and not pro.
Backbone Set
This set contains the four atoms of each amino acid that form
the polypeptide N-C-C-O backbone of proteins, and the atoms of
the sugar phosphate backbone of nucleic acids. Use the RasMol
predefined sets protein and nucleic to distinguish between the
two forms of backbone. Atoms in nucleic acids and proteins are
either backbone or sidechain. This set is equivalent to the
RasMol expression (protein or nucleic) and not sidechain.
The predefined set mainchain is synonymous with the set
backbone.
Basic Set
The set of basic amino acids. These are the residue types Arg,
His and Lys. All amino acids are classified as either acidic,
basic or neutral. This set is equivalent to the RasMol atom
expressions arg, his, lys and amino and not (acidic or neutral).
Bonded Set
This set contain all the atoms in the current molecule database
that are bonded to at least one other atom.
Buried Set
This set contains the atoms in those amino acids that tend
(prefer) to be buried inside protein, away from contact with
solvent molecules. This set refers to the amino acids preference
and not the actual solvent accessibility for the current
protein. All amino acids are classified as either surface or
buried. This set is equivalent to the RasMol atom expression
amino and not surface.
CG Set This set contains the atoms in the complementary nucleotides
cytidine and guanosine (C and G, respectively). All nucleotides
are classified as either the set at or the set cg This set is
equivalent to the RasMol atom expressions c,g and nucleic and
not at.
Charged Set
This set contains the charged amino acids. These are the amino
acids that are either acidic or basic. Amino acids are
classified as being either charged or neutral. This set is
equivalent to the RasMol atom expressions acidic or basic and
amino and not neutral.
Cyclic Set
The set of atoms in amino acids containing a cycle or rings.
All amino acids are classified as either cyclic or acyclic.
This set consists of the amino acids His, Phe, Pro, Trp and Tyr.
The members of the predefined set aromatic are members of this
set. The only cyclic but non-aromatic amino acid is proline.
This set is equivalent to the RasMol atom expressions his, phe,
pro, trp, tyr and aromatic or pro and amino and not acyclic.
Cystine Set
This set contains the atoms of cysteine residues that form part
of a disulphide bridge, i.e. half cystines. RasMol automatically
determines disulphide bridges, if neither the predefined set
cystine nor the RasMol ssbonds command have been used since the
molecule was loaded. The set of free cysteines may be determined
using the RasMol atom expression cys and not cystine.
Helix Set
This set contains all atoms that form part of a protein alpha
helix as determined by either the PDB file author or Kabsch and
Sander's DSSP algorithm. By default, RasMol uses the secondary
structure determination given in the PDB file if it exists.
Otherwise, it uses the DSSP algorithm as used by the RasMol
structure command.
This predefined set should not be confused with the predefined
set alpha which contains the alpha carbon atoms of a protein.
Hetero Set
This set contains all the heterogeneous atoms in the molecule.
These are the atoms described by HETATM entries in the PDB file.
These typically contain water, cofactors and other solvents and
ligands. All hetero atoms are classified as either ligand or
solvent atoms. These heterogeneous solvent atoms are further
classified as either water or ions.
Hydrogen Set
This predefined set contains all the hydrogen, deuterium and
tritium atoms of the current molecule. This predefined set is
equivalent to the RasMol atom expression elemno=1.
Hydrophobic Set
This set contains all the hydrophobic amino acids. These are
the amino acids Ala, Leu, Val, Ile, Pro, Phe, Met and Trp. All
amino acids are classified as either hydrophobic or polar. This
set is equivalent to the RasMol atom expressions ala, leu, val,
ile, pro, phe, met, trp and amino and not polar.
Ions Set
This set contains all the heterogeneous phosphate and sulphate
ions in the current molecule data file. A large number of these
ions are sometimes associated with protein and nucleic acid
structures determined by X-ray crystallography. These atoms tend
to clutter an image. All hetero atoms are classified as either
ligand or solvent atoms. All solvent atoms are classified as
either water or ions.
Large Set
All amino acids are classified as either small, medium or large.
This set is equivalent to the RasMol atom expression amino and
not (small or medium).
Ligand Set
This set contains all the heterogeneous cofactor and ligand
moieties that are contained in the current molecule data file.
This set is defined to be all hetero atoms that are not solvent
atoms. Hence this set is equivalent to the RasMol atom
expression hetero and not solvent.
Medium Set
All amino acids are classified as either small, medium or large.
This set is equivalent to the RasMol atom expression amino and
not (large or small).
Neutral Set
The set of neutral amino acids. All amino acids are classified
as either acidic, basic or neutral. This set is equivalent to
the RasMol atom expression amino and not (acidic or basic).
Nucleic Set
The set of all atoms in nucleic acids, which consists of the
four nucleotide bases adenosine, cytidine, guanosine and
thymidine (A, C, G and T, respectively). All neucleotides are
classified as either purine or pyrimidine. This set is
equivalent to the RasMol atom expressions a,c,g,t and purine or
pyrimidine. The symbols for RNA nucleotides (U, +U, I, 1MA,
5MC, OMC, 1MG, 2MG, M2G, 7MG, OMG, YG, H2U, 5MU, and PSU) are
also recognized as members of this set.
Polar Set
This set contains the polar amino acids. All amino acids are
classified as either hydrophobic or polar. This set is
equivalent to the RasMol atom expression amino and not
hydrophobic.
Protein Set
The set of all atoms in proteins. This consists of the RasMol
predefined set amino and common post-translation modifications.
Purine Set
The set of purine nucleotides. These are the bases adenosine
and guanosine (A and G, respectively). All nucleotides are
either purines or pyrimidines. This set is equivalent to the
RasMol atom expressions a,g and nucleic and not pyrimidine.
Pyrimidine Set
The set of pyrimidine nucleotides. These are the bases cytidine
and thymidine (C and T, respectively). All nucleotides are
either purines or pyrimidines. This set is equivalent to the
RasMol atom expressions c,t and nucleic and not purine.
Selected Set
This set contains the set of atoms in the currently selected
region. The currently selected region is defined by the
preceding select or restrict command and not the atom expression
containing the selected keyword.
Sheet Set
This set contains all atoms that form part of a protein beta
sheet as determined by either the PDB file author or Kabsch and
Sander's DSSP algorithm. By default, RasMol uses the secondary
structure determination given in the PDB file if it exists.
Otherwise, it uses the DSSP algorithm as used by the RasMol
structure command.
Sidechain Set
This set contains the functional sidechains of any amino acids
and the base of each nucleotide. These are the atoms not part of
the polypeptide N-C-C-O backbone of proteins or the sugar
phosphate backbone of nucleic acids. Use the RasMol predefined
sets protein and nucleic to distinguish between the two forms of
sidechain. Atoms in nucleic acids and proteins are either
backbone or sidechain. This set is equivalent to the RasMol
expression (protein or nucleic) and not backbone.
Small Set
All amino acids are classified as either small, medium or large.
This set is equivalent to the RasMol atom expression amino and
not (medium or large).
Solvent Set
This set contains the solvent atoms in the molecule coordinate
file. These are the heterogeneous water molecules, phosphate
and sulphate ions. All hetero atoms are classified as either
ligand or solvent atoms. All solvent atoms are classified as
either water or ions. This set is equivalent to the RasMol atom
expressions hetero and not ligand and water or ions.
Surface Set
This set contains the atoms in those amino acids that tend
(prefer) to be on the surface of proteins, in contact with
solvent molecules. This set refers to the amino acids preference
and not the actual solvent accessibility for the current
protein. All amino acids are classified as either surface or
buried. This set is equivalent to the RasMol atom expression
amino and not buried.
Turn Set
This set contains all atoms that form part of a protein turns as
determined by either the PDB file author or Kabsch and Sander's
DSSP algorithm. By default, RasMol uses the secondary structure
determination given in the PDB file if it exists. Otherwise, it
uses the DSSP algorithm as used by the RasMol structure command.
Water Set
This set contains all the heterogeneous water molecules in the
current database. A large number of water molecules are
sometimes associated with protein and nucleic acid structures
determined by X-ray crystallography. These atoms tend to clutter
an image. All hetero atoms are classified as either ligand or
solvent atoms. The solvent atoms are further classified as
either water or ions.
Set Summary
The table below summarises RasMol's classification of the common
amino acids.
COLOUR SCHEMES
The RasMol colour command allows different objects (such as atoms,
bonds and ribbon segments) to be given a specified colour. Typically
this colour is either a RasMol predefined colour name or an RGB triple.
Additionally RasMol also supports alt, amino, chain, charge, cpk,
group, model, shapely, structure, temperature or user colour schemes
for atoms, and hbond type colour scheme for hydrogen bonds and
electrostatic potential colour scheme for dot surfaces. The 24
currently predefined colour names are Black, Blue, BlueTint, Brown,
Cyan, Gold, Grey, Green, GreenBlue, GreenTint, HotPink, Magenta,
Orange, Pink, PinkTint, Purple, Red, RedOrange, SeaGreen, SkyBlue,
Violet, White, Yellow and YellowTint
If you frequently wish to use a colour not predefined, you can write a
one-line script. For example, if you make the file grey.col containing
the line, colour [180,180,180] #grey, then the command script grey.col
colours the currently selected atom set grey.
Alt Colours
The RasMol alt (Alternate Conformer) colour scheme codes the
base structure with one colour and applies a limited number of
colours to each alternate conformer. In a RasMol built for
8-bit colour systems, 4 colours are allowed for alternate
conformers. Otherwise, 8 colours are available.
Amino Colours
The RasMol amino colour scheme colours amino acids according to
traditional amino acid properties. The purpose of colouring is
to identify amino acids in an unusual or surprising environment.
The outer parts of a protein that are polar are visible (bright)
colours and non-polar residues darker. Most colours are hallowed
by tradition. This colour scheme is similar to the shapely
scheme.
Chain Colours
The RasMol chain colour scheme assigns each macromolecular chain
a unique colour. This colour scheme is particularly useful for
distinguishing the parts of multimeric structure or the
individual 'strands' of a DNA chain. Chain can be selected from
the RasMol Colours menu.
Charge Colours
The RasMol charge colour scheme colour codes each atom according
to the charge value stored in the input file (or beta factor
field of PDB files). High values are coloured in blue (positive)
and lower values coloured in red (negative). Rather than use a
fixed scale this scheme determines the maximum and minimum
values of the charge/temperature field and interpolates from red
to blue appropriately. Hence, green cannot be assumed to be 'no
net charge' charge.
The difference between the charge and temperature colour schemes
is that increasing temperature values proceed from blue to red,
whereas increasing charge values go from red to blue.
If the charge/temperature field stores reasonable values it is
possible to use the RasMol colour dots potential command to
colour code a dot surface (generated by the dots command) by
electrostatic potential.
CPK Colours
The RasMol cpk colour scheme is based upon the colours of the
popular plastic spacefilling models which were developed by
Corey, Pauling and later improved by Kultun. This colour scheme
colours 'atom' objects by the atom (element) type. This is the
scheme conventionally used by chemists. The assignment of the
most commonly used element types to colours is given below.
Group Colours
The RasMol group colour scheme colour codes residues by their
position in a macromolecular chain. Each chain is drawn as a
smooth spectrum from blue through green, yellow and orange to
red. Hence the N terminus of proteins and 5' terminus of nucleic
acids are coloured red and the C terminus of proteins and 3'
terminus of nucleic acids are drawn in blue. If a chain has a
large number of heterogeneous molecules associated with it, the
macromolecule may not be drawn in the full 'range' of the
spectrum. Group can be selected from the RasMol Colours menu.
If a chain has a large number of heterogeneous molecules
associated with it, the macromolecule may not be drawn in the
full range of the spectrum. When RasMol performs group colouring
it decides the range of colours it uses from the residue
numbering given in the PDB file. Hence the lowest residue number
is displayed in blue and the highest residue number is displayed
as red. Unfortunately, if a PDB file contains a large number of
heteroatoms, such as water molecules, that occupy the high
residue numbers, the protein is displayed in the blue-green end
of the spectrum and the waters in the yellow-red end of the
spectrum. This is aggravated by there typically being many more
water molecules than amino acid residues. The solution to this
problem is to use the command set hetero off before applying the
group colour scheme. This can also be achieved by toggling
Hetero Atoms on the Options menu before selecting Group on the
Colour menu. This command instructs RasMol to only use non-
hetero residues in the group colour scaling.
NMR Model Colours
The RasMol model colour scheme codes each NMR model with a
distinct colour. The NMR model number is taken as a numeric
value. High values are coloured in blue and lower values
coloured in red. Rather than use a fixed scale this scheme
determines the maximum value of the NMR model number and
interpolates from red to blue appropriately.
Shapely Colours
The RasMol shapely colour scheme colour codes residues by amino
acid property. This scheme is based upon Bob Fletterick's
"Shapely Models". Each amino acid and nucleic acid residue is
given a unique colour. The shapely colour scheme is used by
David Bacon's Raster3D program. This colour scheme is similar to
the amino colour scheme.
Structure Colours
The RasMol structure colour scheme colours the molecule by
protein secondary structure. Alpha helices are coloured
magenta, [240,0,128], beta sheets are coloured yellow,
[255,255,0], turns are coloured pale blue, [96,128,255] and all
other residues are coloured white. The secondary structure is
either read from the PDB file (HELIX, SHEET and TURN records),
if available, or determined using Kabsch and Sander's DSSP
algorithm. The RasMol structure command may be used to force
DSSP's structure assignment to be used.
Temperature Colours
The RasMol temperature colour scheme colour codes each atom
according to the anisotropic temperature (beta) value stored in
the PDB file. Typically this gives a measure of the
mobility/uncertainty of a given atom's position. High values are
coloured in warmer (red) colours and lower values in colder
(blue) colours. This feature is often used to associate a
"scale" value [such as amino acid variability in viral mutants]
with each atom in a PDB file, and colour the molecule
appropriately.
The difference between the temperature and charge colour schemes
is that increasing temperature values proceed from blue to red,
whereas increasing charge values go from red to blue.
User Colours
The RasMol user colour scheme allows RasMol to use the colour
scheme stored in the PDB file. The colours for each atom are
stored in COLO records placed in the PDB data file. This
convention was introduced by David Bacon's Raster3D program.
HBond Type Colours
The RasMol type colour scheme applies only to hydrogen bonds,
hence is used in the command colour hbonds type. This scheme
colour codes each hydrogen bond according to the distance along
a protein chain between hydrogen bond donor and acceptor. This
schematic representation was introduced by Belhadj-Mostefa and
Milner-White. This representation gives a good insight into
protein secondary structure (hbonds forming alpha helices appear
red, those forming sheets appear yellow and those forming turns
appear magenta).
Potential Colours
The RasMol potential colour scheme applies only to dot surfaces,
hence is used in the command colour dots potential. This scheme
colours each currently displayed dot by the electrostatic
potential at that point in space. This potential is calculated
using Coulomb's law taking the temperature/charge field of the
input file to be the charge 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.
Amino Acid Codes
The following table lists the names, single letter and three
letter codes of each of the amino acids.
Booleans
A boolean parameter is a truth value. Valid boolean values are
'true' and 'false', and their synonyms 'on' and 'off'. Boolean
parameters are commonly used by RasMol to either enable or
disable a representation or option.
FILE FORMATS
Protein Data Bank Files
If you do not have the PDB documentation, you may find the following
summary of the PDB file format useful. The Protein Data Bank is a
computer-based archival database for macromolecular structures. The
database was established in 1971 by Brookhaven National Laboratory,
Upton, New York, as a public domain repository for resolved
crystallographic structures. The Bank uses a uniform format to store
atomic coordinates and partial bond connectivities as derived from
crystallographic studies. In 1999 the Protein Data Bank moved to the
Research Collaboratory for Structural Biology.
PDB file entries consist of records of 80 characters each. Using the
punched card analogy, columns 1 to 6 contain a record-type identifier,
the columns 7 to 70 contain data. In older entries, columns 71 to 80
are normally blank, but may contain sequence information added by
library management programs. In new entries conforming to the 1996 PDB
format, there is other information in those columns. The first four
characters of the record identifier are sufficient to identify the type
of record uniquely, and the syntax of each record is independent of the
order of records within any entry for a particular macromolecule.
The only record types that are of major interest to the RasMol program
are the ATOM and HETATM records which describe the position of each
atom. ATOM/HETATM records contain standard atom names and residue
abbreviations, along with sequence identifiers, coordinates in Angstrom
units, occupancies and thermal motion factors. The exact details are
given below as a FORTRAN format statement. The "fmt" column indicates
use of the field in all PDB formats, in the 1992 and earlier formats or
in the 1996 and later formats.
Residues occur in order starting from the N-terminal residue for
proteins and 5'-terminus for nucleic acids. If the residue sequence is
known, certain atom serial numbers may be omitted to allow for future
insertion of any missing atoms. Within each residue, atoms are ordered
in a standard manner, starting with the backbone (N-C-C-O for proteins)
and proceeding in increasing remoteness from the alpha carbon, along
the side chain.
HETATM records are used to define post-translational modifications and
cofactors associated with the main molecule. TER records are
interpreted as breaks in the main molecule's backbone.
If present, RasMol also inspects HEADER, COMPND, HELIX, SHEET, TURN,
CONECT, CRYST1, SCALE, MODEL, ENDMDL, EXPDTA and END records.
Information such as the name, database code, revision date and
classification of the molecule are extracted from HEADER and COMPND
records, initial secondary structure assignments are taken from HELIX,
SHEET and TURN records, and the end of the file may be indicated by an
END record.
RasMol Interpretation of PDB fields
Atoms located at 9999.000, 9999.000, 9999.000 are assumed to be
Insight pseudo atoms and are ignored by RasMol. Atom names
beginning ' Q' are also assumed to be pseudo atoms or position
markers.
When a data file contains an NMR structure, multiple
conformations may be placed in a single PDB file delimited by
pairs of MODEL and ENDMDL records. RasMol displays all the NMR
models contained in the file.
Residue names "CSH", "CYH" and "CSM" are considered pseudonyms
for cysteine "CYS". Residue names "WAT", "H20", "SOL" and "TIP"
are considered pseudonyms for water "HOH". The residue name
"D20" is consider heavy water "DOD". The residue name "SUL" is
considered a sulphate ion "SO4". The residue name "CPR" is
considered to be cis-proline and is translated as "PRO". The
residue name "TRY" is considered a pseudonym for tryptophan
"TRP".
RasMol uses the HETATM fields to define the sets hetero, water,
solvent and ligand. Any group with the name "HOH", "DOD", "SO4"
or "PO4" (or aliased to one of these names by the preceding
rules) is considered a solvent and is considered to be defined
by a HETATM field.
RasMol only respects CONECT connectivity records in PDB files
containing fewer than 256 atoms. This is explained in more
detail in the section on determining molecule connectivity.
CONECT records that define a bond more than once are interpreted
as specifying the bond order of that bond, i.e. a bond specified
twice is a double bond and a bond specified three (or more)
times is a triple bond. This is not a standard PDB feature.
PDB Colour Scheme Specification
RasMol also accepts the supplementary COLO record type in the
PDB files. This record format was introduced by David Bacon's
Raster3D program for specifying the colour scheme to be used
when rendering the molecule. This extension is not currently
supported by the PDB. The COLO record has the same basic record
type as the ATOM and HETATM records described above.
Colours are assigned to atoms using a matching process. The Mask
field is used in the matching process as follows. First RasMol
reads in and remembers all the ATOM, HETATM and COLO records in
input order. When the user-defined ('User') colour scheme is
selected, RasMol goes through each remembered ATOM/HETATM record
in turn, and searches for a COLO record that matches in all of
columns 7 through 30. The first such COLO record to be found
determines the colour and radius of the atom.
Note that the Red, Green and Blue components are in the same
positions as the X, Y, and Z components of an ATOM or HETA
record, and the van der Waals radius goes in the place of the
Occupancy. The Red, Green and Blue components must all be in the
range 0 to 1.
In order that one COLO record can provide colour and radius
specifications for more than one atom (e.g. based on residue,
atom type, or any other criterion for which labels can be given
somewhere in columns 7 through 30), a 'don't-care' character,
the hash mark "#" (number or sharp sign) is used. This
character, when found in a COLO record, matches any character in
the corresponding column in a ATOM/HETATM record. All other
characters must match identically to count as a match. As an
extension to the specification, any atom that fails to match a
COLO record is displayed in white.
Multiple NMR Models
RasMol loads all of the NMR models from a PDB file no matter
which command is used: load pdb <filename> or load nmrpdb
<filename>
Once multiple NMR conformations have been loaded they may be
manipulated with the atom expression extensions described in
Primitive Expressions. In particular, the command restrict */1
will restrict the display to the first model only.
CIF and mmCIF Format Files
CIF is the IUCr standard for presentation of small molecules and
mmCIF is intended as the replacement for the fixed-field PDB
format for presentation of macromolecular structures. RasMol can
accept data sets in either format.
There are many useful sites on the World Wide Web where
information tools and software related to CIF, mmCIF and the PDB
can be found. The following are good starting points for
exploration:
The International Union of Crystallography (IUCr) provides
access to software, dictionaries, policy statements and
documentation relating to CIF and mmCIF at: IUCr, Chester,
England (www.iucr.org/iucr-top/cif/) with many mirror sites.
The Nucleic Acid Database Project provides access to its
entries, software and documentation, with an mmCIF page giving
access to the dictionary and mmCIF software tools at Rutgers
University, New Jersey, USA
(http://ndbserver.rutgers.edu/NDB/mmcif) with many mirror sites.
This version of RasMol restricts CIF or mmCIF tag values to
essentially the same conventions as are used for the fixed-field
PDB format. Thus chain identifiers and alternate conformation
identifiers are limited to a single character, atom names are
limited to 4 characters, etc. RasMol interprets the following
CIF and mmCIF tags: A search is made through multiple data
blocks for the desired tags, so a single dataset may be composed
from multiple data blocks, but multiple data sets may not be
stacked in the same file.
MACHINE-SPECIFIC SUPPORT
In the following sections, support for Monochrome X-Windows, Tcl/Tk
IPC, UNIX sockets based IPC, Compiling RasWin with Borland and
MetroWerks are described.
Monochrome X-Windows Support
RasMol supports the many monochrome UNIX workstations typically
found in academia, such as low-end SUN workstations and NCD X-
terminals. The X11 version of RasMol (when compiled in 8 bit
mode) now detects black and white X-Windows displays and enables
dithering automatically. The use of run-time error diffusion
dithering means that all display modes of RasMol are available
when in monochrome mode. For best results, users should
experiment with the set ambient command to ensure the maximum
contrast in resulting images.
Tcl/Tk IPC support
Version 4 of Tk graphics library changed the protocol used to
communicate between Tk applications. RasMol version 2.6 was
modified such that it could communicate with both this new
protocol and the previous version 3 protocol supported by RasMol
v2.5. Although Tcl/Tk 3.x applications may only communicate with
other 3.x applications and Tcl/Tk 4.x applications with other
4.x applications, these changes allow RasMol to communicate
between processes with both protocols (potentially
concurrently).
UNIX sockets based IPC
The UNIX implementation of RasMol supports BSD-style socket
communication. An identical socket mechanism is also being
developed for VMS, Apple Macintosh and Microsoft Windows
systems. This should allow RasMol to interactively display
results of a computation on a remote host. The current protocol
acts as a TCP/IP server on port 21069 that executes command
lines until either the command exit or the command quit is
typed. The command exit from the RasMol server, the command quit
both disconnects the current session and terminates RasMol. This
functionality may be tested using the UNIX command telnet
<hostname> 21069.
Compiling RasWin with Borland and MetroWerks
A number of changes were made to the source code in the
transition from version 2.5 to 2.6 to allow the Microsoft
Windows version of RasMol to compile using the Borland C/C++
compiler. These fixes include name changes for the standard
library and special code to avoid a bug in _fmemset. Additional
changes were made in the transition from 2.6 to 2.7 to allow
compilation with the MetroWerks compilers.
BIBLIOGRAPHY
Molecular Graphics [1] Nelson Max, "Computer Representation of Molecular Surfaces", IEEE Computer Graphics and Applications, pp.21-29, August 1983. [2] Arthur M. Lesk, "Protein Architecture: A Practical Approach", IRL Press Publishers, 1991. Molecular Graphics Programs [3] Per J. Kraulis, "MOLSCRIPT: A Program to Produce both Detailed and Schematic Plots of Protein Structures", Journal of Applied Crystallography, Vol.24, pp.946-950, 1991. [4] David Bacon and Wayne F. Anderson, "A Fast Algorithm for Rendering Space-Filling Molecule Pictures", Journal of Molecular Graphics, Vol.6, No.4, pp.219-220, December 1988. [5] David C. Richardson and Jane S. Richardson, "The Kinemage: A tool for Scientific Communication", Protein Science, Vol.1, No.1,pp.3-9, January 1992. [6] Mike Carson, "RIBBONS 2.0", Journal of Applied Crystallography, Vol.24, pp.958-961, 1991. [7] Conrad C. Huang, Eric F. Pettersen, Teri E. Klein, Thomas E. Ferrin and Robert Langridge, "Conic: A Fast Renderer for Space-Filling Molecules with Shadows", Journal of Molecular Graphics, Vol.9, No.4, pp.230-236, December 1991. Molecular Biology Algorithms [8] Wolfgang Kabsch and Christian Sander, "Dictionary of Protein Secondary Structure: Pattern Recognition of Hydrogen-Bonded and Geometrical Features", Biopolymers, Vol.22, pp.2577-2637, 1983. [9] Michael L. Connolly, "Solvent-Accessible Surfaces of Proteins and Nucleic Acids", Science, Vol.221, No.4612, pp.709-713, August 1983. [10] Khaled Belhadj-Mostefa, Ron Poet and E. James Milner-White, "Displaying Inter-Main Chain Hydrogen Bond Patterns in Proteins", Journal of Molecular Graphics, Vol.9, No.3, pp.194-197, September 1991. [11] Mike Carson, "Ribbon Models of Macromolecules", Journal of Molecular Graphics, Vol.5, No.2, pp.103-106, June 1987. [12] Mike Carson and Charles E. Bugg, "Algorithm for Ribbon Models of Proteins", Journal of Molecular Graphics, Vol.4, No.2, pp.121-122, June 1986. [13] H. Iijima, J. B. Dunbar Jr. and G. Marshall, "Calibration of Effective van der Waals Atomic Contact Radii for Proteins and Peptides", Proteins: Structure, Functions and Genetics, Vol.2, pp.330-339,1987. Graphics Algorithms [14] J. Foley, A. van Dam, S. Feiner and J. Hughes, "Computer Graphics: Principles and Practice", 2nd Edition, Addison Wesley Publishers, 1990. [15] J. Cleary and G. Wyvill, "Analysis of an Algorithm for Fast Ray Tracing using Uniform Space Subdivision", The Visual Computer, Vol.4, pp.65-83, 1988. [16] Thomas Porter,"Spherical Shading", Computer Graphics Vol.12, ACM SIGGRAPH, pp.282-285, 1978. [17] Jean-Michel Cense, "Exact Visibility Calculation for Space-Filling Molecular Models", Journal of Molecular Graphics, Vol.9, No.3, pp.191-193, September 1991. [18] Chris Schafmeister, "Fast Algorithm for Generating CPK Images on Graphics Workstations", Journal of Molecular Graphics, Vol.8, No.4, pp.201-206, December 1990. [19] Bruce A. Johnson, "MSURF: A Rapid and General Program for the Representation of Molecular Surfaces", Journal of Molecular Graphics, Vol.5, No.3, pp.167-169, September 1987. File Formats [20] Frances C. Bernstein et al., "The Protein Data Bank: A Computer- Based Archival File for Macromolecular Structures", Journal of Molecular Biology, Vol.112, pp.535-542, 1977. [21] Arthur Dalby, James G. Nourse, W. Douglas Hounshell, Ann K. I. Gushurst, David L. Grier, Burton A. Leland and John Laufer, "Description of Several Chemical File Formats Used by Computer Programs Developed at Molecular Design Limited", Journal of Chemical Information and Computer Sciences, Vol.32, No.3, pp.244-255, 1992. [22] Adobe Systems Inc., "PostScript Language Reference Manual", Addison-Wesley Publishers, Reading, Mass., 1985. [23] Philip E. Bourne et al., "The Macromolecular Crystallographic Information File (mmCIF)", Meth. Enzymol. (1997) 277, 571-590. [24] Sydney R. Hall, "The STAR File: a New Format for Electronic Data Transfer and Archiving", Journal of Chemical Information and Computer Sciences, Vol. 31, 326-333, 1991.
SEE ALSO
The RasMol User Manual!
AUTHOR
1992-1998 by Roger Sayle (rasmol@ggr.co.uk)
July 2009 RASMOL(1)
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