rasmol - Molecular Graphics Visualisation Tool v2.7.2.1

rasmol [-nodiplay] [[-c format c ] filenamec ] [-script c scriptfilec ]

-pdb

Protein Data Bank

-mdl

MDL's MOL File Format

-mol2

Tripos' Sybyl MOL2 Format

-xyz

MSC's XYZ (XMol) Format

-mopac

MOPAC Input or Output File Format

-alchemy

Alchemy File Format

-charmm

CHARMm File Format

-cif

IUCr CIF or CIF File Format

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

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

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

Copying RasMol

This version is based in large part on RasMol version 2.7.2, RasMol version 2.7.1.1 and RasTop version 1.3 and indirectly on the RasMol 2.5-ucb and 2.6-ucb versions and version 2.6_CIF.2, RasMol 2.6x1 and RasMol_2.6.4.

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:

1. Either include the complete documentation, especially the file NOTICE, with what you distribute or provide a clear indication where people can get a copy of the documentation; and

2. Please give credit where credit is due citing the version and original authors properly; and

3. Please do not give anyone the impression that the original authors are providing a warranty of any kind.

If you would like to use major pieces of RasMol in some other program, make modifications to RasMol, or in some other way make what a lawyer would call a "derived work", you are not only permitted to do so, you are encouraged to do so. In addition to the things we discussed above, please do the following:

4. Please explain in your documentation how what you did differs from this version of RasMol; and

5. Please make your modified source code available.

This version of RasMol is _not_ in the public domain, but it is given freely to the community in the hopes of advancing science. If you make changes, please make them in a responsible manner, and please offer us the opportunity to include those changes in future versions of RasMol.

General Notice

The following notice applies to this work as a whole and to the works included within it:

* Creative endeavors depend on the lively exchange of ideas. There are laws and customs which establish rights and responsibilities for authors and the users of what authors create. This notice is not intended to prevent you from using the software and documents in this package, but to ensure that there are no misunderstandings about terms and conditions of such use.

* Please read the following notice carefully. If you do not understand any portion of this notice, please seek appropriate professional legal advice before making use of the software and documents included in this software package. In addition to whatever other steps you may be obliged to take to respect the intellectual property rights of the various parties involved, if you do make use of the software and documents in this package, please give credit where credit is due by citing this package, its authors and the URL or other source from which you obtained it, or equivalent primary references in the literature with the same authors.

* Some of the software and documents included within this software package are the intellectual property of various parties, and placement in this package does not in any way imply that any such rights have in any way been waived or diminished.

* With respect to any software or documents for which a copyright exists, ALL RIGHTS ARE RESERVED TO THE OWNERS OF SUCH COPYRIGHT.

* Even though the authors of the various documents and software found here have made a good faith effort to ensure that the documents are correct and that the software performs according to its documentation, and we would greatly appreciate hearing of any problems you may encounter, the programs and documents and any files created by the programs are provided **AS IS** without any warranty as to correctness, merchantability or fitness for any particular or general use.

* THE RESPONSIBILITY FOR ANY ADVERSE CONSEQUENCES FROM THE USE OF PROGRAMS OR DOCUMENTS OR ANY FILE OR FILES CREATED BY USE OF THE PROGRAMS OR DOCUMENTS LIES SOLELY WITH THE USERS OF THE PROGRAMS OR DOCUMENTS OR FILE OR FILES AND NOT WITH AUTHORS OF THE PROGRAMS OR DOCUMENTS.

Subject to your acceptance of the conditions stated above, and your respect for the terms and conditions stated in the notices below, if you are not going to make any modifications or create derived works, you are given permission to freely copy and distribute this package, provided you do the following:

1. Either include the complete documentation, especially the file NOTICE, with what you distribute or provide a clear indication where people can get a copy of the documentation; and

2. Give credit where credit is due citing the version and original authors properly; and

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:

4. Explain in your documentation how what you did differs from this version of RasMol; and

5. Make your modified source code available.

RasMol V2.6 Notice

The following notice applies to RasMol V 2.6 and older RasMol versions.

Information in this document is subject to change without notice and does not represent a commitment on the part of the supplier. This package is sold/distributed subject to the condition that it shall not, by way of trade or otherwise, be lent, re-sold, hired out or otherwise circulated without the supplier's prior consent, in any form of packaging or cover other than that in which it was produced. No part of this manual or accompanying software may be reproduced, stored in a retrieval system on optical or magnetic disk, tape or any other medium, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording or otherwise for any purpose other than the purchaser's personal use.

This product is not to be used in the planning, construction, maintenance, operation or use of any nuclear facility nor the flight, navigation or communication of aircraft or ground support equipment. The author shall not be liable, in whole or in part, for any claims or damages arising from such use, including death, bankruptcy or outbreak of war.

IUCR Policy

The IUCr Policy for the Protection and the Promotion of the STAR File and CIF Standards for Exchanging and Archiving Electronic Data.

Overview

The Crystallographic Information File (CIF)[1] is a standard for information interchange promulgated by the International Union of Crystallography (IUCr). CIF (Hall, Allen & Brown, 1991) is the recommended method for submitting publications to Acta Crystallographica Section C and reports of crystal structure determinations to other sections of Acta Crystallographica and many other journals. The syntax of a CIF is a subset of the more general STAR File[2] format. The CIF and STAR File approaches are used increasingly in the structural sciences for data exchange and archiving, and are having a significant influence on these activities in other fields.

Statement of intent

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

Protection of the standards

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

* holds the copyrights on the standards themselves,

* owns the associated trademarks and service marks, and

* holds a patent on the STAR File.

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

Promotion of the standards

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

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

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

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

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

Glossary of terms

[1] CIF:

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

[2] STAR File:

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

[3] DDL:

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

Last modified: 30 September 2000

IUCr Policy Copyright (C) 2000 International Union of Crystallography

CBFLIB

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

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

Notice 91 02 01

CIFPARSE

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

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

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

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

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

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

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

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

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

RasMol 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.

Backbone

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

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

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

Background

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

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

Bond

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

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

Cartoon

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

Centre

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

Type help expression for more information on RasMol atom expressions.

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

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

Clipboard

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

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

Colour

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

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

Connect

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

Define

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

Depth

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

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

Dots

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

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

Echo

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

English

The RasMol English command sets the menus and messages to the English versions. The commands French, Italian and Spanish may be used to select French, Italian and Spanish menus and messages.

French

The RasMol French command sets the menus and messages to the French versions. The commands English, Italian and Spanish may be used to select English, Italian and Spanish menus and messages.

HBonds

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

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

Help

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

Italian

The RasMol Italian command sets the menus and messages to the Italian versions. The commands English, French and Spanish may be used to select English, French and Spanish menus and messages.

Label

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

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

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

Load

Load a molecule coordinate file into RasMol. Valid molecule file formats are pdb (Protein Data Bank format), mdl (Molecular Design Limited's MOL file format), alchemy (Tripos' Alchemy file format), mol2 (Tripos' Sybyl Mol2 file format), charmm (CHARMm file format), xyz (MSC's XMol XYZ file format), mopac (J. P. Stewart's MOPAC file format) or cif (IUCr CIF or mmCIF file format). If no file format is specified, PDB, CIF, or mmCIF is assumed by default. Up to 5 molecules may be loaded at a time. To delete a molecule prior to loading another use the RasMol zap command. To select a molecule for manipulation use the RasMol molecule <n> command.

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

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

Molecule

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

Monitor

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

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

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

Pause

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

Print

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

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

Quit

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

Refresh

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

Renumber

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

Reset

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

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

Restrict

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

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

Ribbons

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

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

Rotate

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

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

Save

Save the currently selected set of atoms in a Protein Data Bank (PDB), MDL, Alchemy(tm) or XYZ format file. The distinction between this command and the RasMol write command has been dropped. The only difference is that without a format specifier the save command generates a PDB file and the write command generates a GIF image.

Script

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

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

The RasMol command source is synonymous with the script command.

Select

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

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

Set

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

Show

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

Slab

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

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

Spacefill

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

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

The RasMol command cpk is synonymous with the spacefill command.

Spanish

The RasMol Spanish command sets the menus and messages to the Spanish versions. The commands English, French and Italian may be used to select English, French and Italian menus and messages.

SSBonds

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

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

Star

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

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

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

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

Stereo

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

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

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

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

Strands

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

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

Structure

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

Trace

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

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

Translate

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

UnBond

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

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

Wireframe

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

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

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

Write

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

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

Zap

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

Zoom

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

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.

Set Ambient

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

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

Set Axes

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

Set Backfade

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

Set Background

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

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

Set BondMode

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

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

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

Set Bonds

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

Set BoundBox

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

Set Cartoon

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

Set CisAngle

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

Set Display

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

Set FontSize

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

Set FontStroke

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

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

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

Set HBonds

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

Set Hetero

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

Set HourGlass

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

Set Hydrogen

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

Set Kinemage

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

Set Menus

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

Set Monitor

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

Set Mouse

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

Set Picking

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

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

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

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

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

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

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

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

Set 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 ShadePower

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

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

Set Shadow

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

Set Specular

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

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

Set SpecPower

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

Set SSBonds

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

Set Stereo

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

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

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

Set Strands

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

Set Transparent

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

Set UnitCell

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

Set VectPS

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

Set Write

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

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

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

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

Primitive Expressions

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

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

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

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

Comparison Operators

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

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

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

Within Expressions

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

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

Predefined Sets

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

AT Set

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

Acidic Set

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

Acyclic Set

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

Aliphatic Set

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

Alpha Set

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

Amino Set

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

Aromatic Set

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

Backbone Set

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

The predefined set mainchain is synonymous with the set backbone.

Basic Set

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

Bonded Set

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

Buried Set

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

CG Set

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

Charged Set

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

Cyclic Set

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

Cystine Set

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

Helix Set

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

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

Hetero Set

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

Hydrogen Set

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

Hydrophobic Set

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

Ions Set

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

Large Set

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

Ligand Set

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

Medium Set

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

Neutral Set

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

Nucleic Set

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

Polar Set

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

Protein Set

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

Purine Set

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

Pyrimidine Set

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

Selected Set

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

Sheet Set

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

Sidechain Set

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

Small Set

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

Solvent Set

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

Surface Set

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

Turn Set

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

Water Set

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

Set Summary

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

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

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

Alt Colours

The RasMol alt (Alternate Conformer) colour scheme codes the base structure with one colour and applies a limited number of colours to each alternate conformer. In a RasMol built for 8-bit 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

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

Charge Colours

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

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

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

CPK Colours

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

Group Colours

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

If a chain has a large number of heterogeneous molecules associated with it, the macromolecule may not be drawn in the full range of the spectrum. When RasMol performs group 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 Colours

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

Shapely Colours

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

Structure Colours

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

Temperature Colours

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

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

User Colours

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

HBond Type Colours

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

Potential Colours

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

Amino Acid Codes

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

Booleans

A boolean parameter is a truth value. Valid boolean values are 'true' and used by RasMol to either enable or disable a representation or option.

Protein Data Bank Files

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

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

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

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

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

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

RasMol Interpretation of PDB fields

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

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

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

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

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

PDB Colour Scheme Specification

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

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

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

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

Multiple NMR Models

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

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

CIF and mmCIF Format Files

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

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

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

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

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

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

Monochrome X-Windows Support

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

Tcl/Tk IPC support

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

UNIX sockets based IPC

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

Compiling RasWin with Borland and MetroWerks

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

Molecular Graphics

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

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

Molecular Graphics Programs

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

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

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

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

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

Molecular Biology Algorithms

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

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

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

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

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

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

Graphics Algorithms

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

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

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

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

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

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

File Formats

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

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

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

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

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

The RasMol User Manual!

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