Table of Contents|
rasmol - Molecular Graphics Visualisation Tool v2.7.1
[-nodiplay] [[-format] filename] [-script scriptfile]
- MDL's MOL File Format
- Tripos' Sybyl MOL2 Format
XYZ (XMol) Format
- MOPAC Input or Output File Format
- CHARMm File Format
- IUCr CIF or CIF File Format
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 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,
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
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.
- Copying RasMol
- This version is based on RasMol version
2.6_CIF.2, RasMol 2.6x1 and RasMol_2.6.4. If you are not going to make changes
to RasMol, you are not only permitted to freely make copies and distribute
them, you are encouraged to do so, provided you do the following:
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:
explain in your documentation how what you did differs
from this version of RasMol; and
5. Please make your modified source
This version of RasMol is _not_ in the public domain, but it is given
freely to the community in the hopes of advancing science. If you make
changes, please make them in a responsible manner, and please offer us
the opportunity to include those changes in future versions of RasMol.
- General Notice
- The following notice applies to this work as a whole and
to the works included within it:
* Creative endeavors depend on the lively
exchange of ideas. There are laws and customs which establish rights and
responsibilities for authors and the users of what authors create. This
notice is not intended to prevent you from using the software and documents
in this package, but to ensure that there are no misunderstandings about
terms and conditions of such use.
* Please read the following notice carefully.
If you do not understand any portion of this notice, please seek appropriate
professional legal advice before making use of the software and documents
included in this software package. In addition to whatever other steps you
may be obliged to take to respect the intellectual property rights of the
various parties involved, if you do make use of the software and documents
in this package, please give credit where credit is due by citing this
package, its authors and the URL or other source from which you obtained
it, or equivalent primary references in the literature with the same authors.
* Some of the software and documents included within this software package
are the intellectual property of various parties, and placement in this
package does not in any way imply that any such rights have in any way
been waived or diminished.
* With respect to any software or documents
for which a copyright exists, ALL RIGHTS ARE RESERVED TO THE OWNERS OF
* 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.
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
credit where credit is due citing the version and original authors properly;
3. Do not give anyone the impression that the original authors are
providing a warranty of any kind.
In addition, you may also modify this
package and create derived works provided you do the following:
in your documentation how what you did differs from this version of RasMol;
5. Make your modified source code available.
- RasMol V2.6 Notice
following notice applies to RasMol V 2.6 and older RasMol versions.
in this document is subject to change without notice and does not represent
a commitment on the part of the supplier. This package is sold/distributed
subject to the condition that it shall not, by way of trade or otherwise,
be lent, re-sold, hired out or otherwise circulated without the supplier's
prior consent, in any form of packaging or cover other than that in which
it was produced. No part of this manual or accompanying software may be
reproduced, stored in a retrieval system on optical or magnetic disk, tape
or any other medium, or transmitted in any form or by any means, electronic,
mechanical, photocopying, recording or otherwise for any purpose other
than the purchaser's personal use.
This product is not to be used in the
planning, construction, maintenance, operation or use of any nuclear facility
nor the flight, navigation or communication of aircraft or ground support
equipment. The author shall not be liable, in whole or in part, for any
claims or damages arising from such use, including death, bankruptcy or
outbreak of war.
- IUCR Policy
- The IUCr Policy on the Use of the Crystallographic
Information File (CIF)
The Crystallographic Information File (Hall, Allen
& Brown, 1991) is, as of January 1992, the recommended method for submitting
publications to Acta Crystallographica Section C. The International Union
of Crystallography holds the Copyright on the CIF, and has applied for
Patents on the STAR File syntax which is the basis for the CIF format.
It is a principal objective of the IUCr to promote the use of CIF for the
exchange and storage of scientific data. The IUCr's sponsorship of the CIF
development was motivated by its responsibility to its scientific journals,
which set the standards in crystallographic publishing. The IUCr intends
that CIFs will be used increasingly for electronic submission of manuscripts
to these journals in future. The IUCr recognises that, if the CIF and the
STAR File are to be adopted as a means for universal data exchange, the
syntax of these files must be strictly and uniformly adhered to. Even small
deviations from the syntax would ultimately cause the demise of the universal
file concept. Through its Copyrights and Patents the IUCr has taken the
steps needed to ensure strict conformance with this syntax.
The IUCr policy
on the use of the CIF and STAR File processes is as follows:
1. CIFs and
STAR Files may be generated, stored or transmitted, without permission
or charge, provided their purpose is not specifically for profit or commercial
gain, and provided that the published syntax is strictly adhered to.
Computer software may be developed for use with CIFs or STAR files, without
permission or charge, provided it is distributed in the public domain. This
condition also applies to software for which a charge is made, provided
that its primary function is for use with files that satisfy condition
1 and that it is distributed as a minor component of a larger package of
3. Permission will be granted for the use of CIFs and STAR Files
for specific commercial purposes (such as databases or network exchange
processes), and for the distribution of commercial CIF/STAR software, on
written application to the IUCr Executive Secretary, 2 Abbey Square, Chester
CH1 2HU, England. The nature, terms and duration of the licenses granted
will be determined by the IUCr Executive and Finance Committees.
the IUCr wishes to promote the use of the STAR File concepts as a standard
universal data file. It will insist on strict compliance with the published
syntax for all applications. To assist with this compliance, the IUCr provides
public domain software for checking the logical integrity of a CIF, and
for validating the data name definitions contained within a CIF. Detailed
information on this software, and the associated dictionaries, may be obtained
from the IUCr Office at 5 Abbey Square, Chester CH1 2HU, England.
- 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
- Portions of this software are loosely based
on the CIFPARSE software package from the NDB at Rutgers University. See
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.
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
The RasMol help facility can be accessed by typing "help
<topic>" or "help <topic> <subtopic>" from the command line. A complete list of
RasMol commands may be displayed by typing "help commands". A single question
mark may also be used to abbreviate the keyword "help". Please type "help
notices" for important notices.
RasMol 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.
The commands/keywords currently recognised by RasMol are given below.
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.
- 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.
- 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.
- 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.
- 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 RasMol clipboard command places a copy of the currently displayed
image on the local graphics 'clipboard'. Note: this command is not yet supported
on UNIX or VMS machines. It is intended to make transfering images between
applications easier under Microsoft Windows or on an Apple Macintosh.
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 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.
are atoms, bonds, backbone, ribbons, labels, dots, hbonds 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
- 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.
- 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.
- 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.
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.
- 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
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.
- The RasMol
help command provides on-line help on the given topic.
- 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
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 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. Only a single molecule may be loaded at a time. To delete a molecule
prior to loading another use the RasMol zap 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
- 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
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.
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.
- 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.
- 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
- 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
- The RasMol refresh command redraws the current image.
This is useful in scripts to ensure application of a complex list of parameter
- 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.
- 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.
- 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.
- 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
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 the molecule about the specified axis. Permitted values for the axis
parameter are "x", "y" and "z". 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.
- 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.
- 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.
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
The RasMol command source is synonymous with the script
- 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.
- The RasMol set command allows the user
to alter various internal program parameters such as those controlling
rendering options. Each parameter has its own set or permissible parameter
options. Typically, omitting the paramter option resets that parameter to
its default value. A list of valid parameter names is given below.
- 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 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 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 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.
- 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.
command cpk is synonymous with the spacefill command.
- 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
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.
- 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"
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.
spacefill command can be used for more artistic rendering of atoms as spheres.
- 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. 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.
- 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.
- 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.
- 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.
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.
- 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.
- 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.
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
- 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
- Deletes the contents of the current database and resets
parameter variables to their initial default state.
- 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.
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.
- 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
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
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
- 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.
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
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
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
- Set Picking
- The RasMol set picking series of commands
affects how a user may interact with a molecule displayed on the screen
Enabling/Disabling Atom 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.
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
- 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 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 appropiate 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
- 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
- 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
- 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
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.
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.
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
- 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.
- 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.
- 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.
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
- 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
- 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.
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.
- 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
- 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
- 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
- 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
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
- Set Summary
- The table below summarises RasMol's classification
of the common amino acids.
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 color 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
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
- 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
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 coloring it decides the range of colors 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
color 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 color scaling.
- NMR Model
- 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.
- 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
- 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.
- A boolean parameter is a truth value. Valid boolean values are
'true' and used by RasMol to either enable or disable a representation or
- 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.
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
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
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
- 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
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
- 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
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
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.
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.
In the following sections, support for Monochrome X-Windows, Tcl/Tk
IPC, UNIX sockets based IPC, Compiling RasWin with Borland and MetroWerks
- 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
- 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.
The RasMol User Manual!
- Molecular Graphics
-  Nelson Max, "Computer Representation of Molecular
Surfaces", IEEE Computer Graphics and Applications, pp.21-29, August 1983.
 Arthur M. Lesk, "Protein Architecture: A Practical Approach", IRL Press
- Molecular Graphics Programs
-  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.
 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
 David C. Richardson and Jane S. Richardson, "The Kinemage: A tool
for Scientific Communication", Protein Science, Vol.1, No.1,pp.3-9, January
 Mike Carson, "RIBBONS 2.0", Journal of Applied Crystallography,
Vol.24, pp.958-961, 1991.
 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,
- Molecular Biology Algorithms
-  Wolfgang Kabsch and Christian
Sander, "Dictionary of Protein Secondary Structure: Pattern Recognition
of Hydrogen-Bonded and Geometrical Features", Biopolymers, Vol.22, pp.2577-2637,
 Michael L. Connolly, "Solvent-Accessible Surfaces of Proteins and
Nucleic Acids", Science, Vol.221, No.4612, pp.709-713, August 1983.
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.
 Mike Carson, "Ribbon Models of
Macromolecules", Journal of Molecular Graphics, Vol.5, No.2, pp.103-106, June
 Mike Carson and Charles E. Bugg, "Algorithm for Ribbon Models
of Proteins", Journal of Molecular Graphics, Vol.4, No.2, pp.121-122, June
 H. Iijima, J. B. Dunbar Jr. and G. Marshall, "Calibration of Effective
van der Waals Atomic Contact Radii for Proteins and Peptides", Proteins:
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1992-1998 by Roger Sayle (email@example.com)
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