RasMol 2

RasMol 2.7.2.1 is a molecular graphics program intended for the

visualisation of proteins, nucleic acids and small molecules, based on Roger

Sayles' RasMol_2.6. The program is aimed at display, teaching and generation

of publication quality images. RasMol runs on Microsoft Windows, Apple

Macintosh, UNIX and VMS systems. The UNIX and VMS systems require an 8, 24

or 32 bit colour X Windows display (X11R4 or later). The program reads in a

molecule coordinate file and interactively displays the molecule on the

screen in a variety of colour schemes and molecule representations.

Currently available representations include depth-cued wireframes,

'Dreiding' sticks, spacefilling (CPK) spheres, ball and stick, solid and

strand biomolecular ribbons, atom labels and dot surfaces.

The RasMol help facility can be accessed by typing "help <topic>" or "help

<topic> <subtopic>" from the command line. A complete list of RasMol

commands may be displayed by typing "help commands". A single question mark

may also be used to abbreviate the keyword "help". Please type "help

notices" for important notices.

RasMol Copyright (C) Roger Sayle 1992-1999

Version 2.6x1 Mods Copyright (C) Arne Mueller 1998

Versions 2.5-ucb and 2.6-ucb Mods Copyright (C)

UC Regents/ModularCHEM Consortium 1995, 1996

RasTop 1.3 Copyright (C) Philippe Valadon 2000

Version 2.7.0, 2.7.1, 2.7.1.1, 2.7.2, 2.7.2.1 Mods

rasmol@bernstein-plus-sons.com

?notice

?notices

This software has been created from several sources. Much of the code is

from RasMol 2.6, as created by Roger Sayle. See:

ftp://ftp.dcs.ed.ac.uk/pub/rasmol

The torsion angle code, new POVRAY3 code and other features are derived from

the RasMol2.6x1 revisions by Arne Mueller. See:

ftp://nexus.roko.goe.net/pub/rasmol

The Ramachandran printer plot code was derived from fisipl created by

Frances C. Bernstein. See the Protein Data Bank program tape.

The code to display multiple molecules and to allow bond rotation is derived

in large part from the UCB mods by Gary Grossman and Marco Molinaro,

included with permission of Eileen Lewis of the ModularCHEM Consortium.

The CIF modifications make use of a library based in part on CBFlib by Paul

J. Ellis and Herbert J. Bernstein. See:

http://www.bernstein-plus-sons.com/software/CBF

Parts of CBFlib is loosely based on the CIFPARSE software package from the

NDB at Rutgers university. See:

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

Please type the RasMol commands 'help copying', 'help general', 'help IUCR',

'help CBFlib', and 'help CIFPARSE' for applicable notices. Please type

'help copyright' for copyright notices. If you use RasMol V2.6 or an earlier

version, type the RasMol command 'help oldnotice'.

?copyright

RasMol 2.7.2.1

Molecular Graphics Visualisation Tool

14 April 2001

Based on RasMol 2.6 by Roger Sayle

Biomolecular Structures Group,Glaxo Wellcome Research & Development

Stevenage, Hertfordshire, UK

Version 2.6, August 1995, Version 2.6.4, December 1998

and Based on Mods by

Author Version, Date Copyright

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

Gary Grossman and RasMol 2.5-ucb Nov 95 (C) UC Regents/ModularCHEM

Marco Molinaro RasMol 2.5-ucb Nov 96 Consortium 1995, 1996

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

Herbert J. RasMol 2.7.0 Mar 99 (C) Herbert J. Bernstein

Bernstein RasMol 2.7.1 Jun 99 1998-2001

RasMol 2.7.1.1 Jan 01

RasMol 2.7.2 Aug 00

RasMol 2.7.2.1 Apr 01

and Incorporating Translations by

Author Item Language

Margaret Wong 2.6 Manual Spanish

JosÈ Miguel Fern·ndez Fern·ndez 2.7.1 Manual Spanish

Fernando Gabriel Ranea 2.7.1 menus and messages Spanish

Jean-Pierre Demailly 2.7.1 menus and messages French

Giuseppe Martini, Giovanni Paolella, 2.7.1 menus and messages Italian

A. Davassi, M. Masullo, C. Liotto 2.7.1 help file

This Release by

Herbert J. Bernstein, Bernstein + Sons, P.O. Box 177, Bellport, NY, USA

yaya@bernstein-plus-sons.com

?copying rasmol

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

?generalnotice

?general notice

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.

?old

?oldnotice

?rasmol v2.6 notice

RasMol V2.6 Notice

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

Information in this document is subject to change without notice and does

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.

?iucrpolicy

?iucr policy

IUCR Policy

The IUCr Policy for the Protection and the Promotion of the STAR File and

CIF Standards for Exchanging and Archiving Electronic Data.

Overview

The Crystallographic Information File (CIF)[1] is a standard for information

interchange promulgated by the International Union of Crystallography

(IUCr). CIF (Hall, Allen & Brown, 1991) is the recommended method for

submitting publications to Acta Crystallographica Section C and reports of

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

?cbflib

CBFLIB

The following Disclaimer Notice applies to CBFlib V0.1, from which this code

in part is derived.

* The items furnished herewith were developed under the sponsorship of the

U.S. Government. Neither the U.S., nor the U.S. D.O.E., nor the Leland

Stanford Junior University, nor their employees, makes any warranty, express

or implied, or assumes any liability or responsibility for accuracy,

completeness or usefulness of any information, apparatus, product or process

disclosed, or represents that its use will not infringe privately-owned

rights. Mention of any product, its manufacturer, or suppliers shall not,

nor is it intended to, imply approval, disapproval, or fitness for any

particular use. The U.S. and the University at all times retain the right to

use and disseminate the furnished items for any purpose whatsoever.

Notice 91 02 01

?cifparse

CIFPARSE

Portions of this software are loosely based on the CIFPARSE software package

from the NDB at Rutgers University. See

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

CIFPARSE is part of the NDBQUERY application, a program component of the

Nucleic Acid Database Project [ H. M. Berman, W. K. Olson, D. L. Beveridge,

J. K. Westbrook, A. Gelbin, T. Demeny, S. H. Shieh, A. R. Srinivasan, and B.

Schneider. (1992). The Nucleic Acid Database: A Comprehensive Relational

Database of Three-Dimensional Structures of Nucleic Acids. Biophys J., 63,

751-759.], whose cooperation is gratefully acknowledged, especially in the

form of design concepts created by J. Westbrook.

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

This software is provided WITHOUT WARRANTY OF MERCHANTABILITY OR FITNESS FOR

A PARTICULAR PURPOSE OR ANY OTHER WARRANTY, EXPRESS OR IMPLIED. RUTGERS MAKE

NO REPRESENTATION OR WARRANTY THAT THE SOFTWARE WILL NOT INFRINGE ANY

PATENT, COPYRIGHT OR OTHER PROPRIETARY RIGHT.

RasMol is a molecular graphics program intended for the visualisation of

proteins, nucleic acids and small molecules. The program is aimed at

display, teaching and generation of publication quality images. RasMol runs

on wide range of architectures and operating systems including Microsoft

Windows, Apple Macintosh, UNIX and VMS systems. UNIX and VMS versions

require an 8, 24 or 32 bit colour X Windows display (X11R4 or later). The X

Windows version of RasMol provides optional support for a hardware dials box

and accelerated shared memory communication (via the XInput and MIT-SHM

extensions) if available on the current X Server.

The program reads in a molecule coordinate file and interactively displays

the molecule on the screen in a variety of colour schemes and molecule

representations. Currently available representations include depth-cued

wireframes, 'Dreiding' sticks, spacefilling (CPK) spheres, ball and stick,

solid and strand biomolecular ribbons, atom labels and dot surfaces.

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

the molecules may be rotated and translated.

The RasMol help facility can be accessed by typing "help <topic>" or "help

<topic> <subtopic>" from the command line. A complete list of RasMol

commands may be displayed by typing "help commands". A single question mark

may also be used to abbreviate the keyword "help". Please type "help

notices" for important notices.

RasMol Copyright (C) Roger Sayle 1992-1999

Version 2.6x1 Mods Copyright (C) Arne Mueller 1998

Version 2.5-ucb, 2.6-ucb Mods

RasTop 1.3 Copyright (C) Philippe Valadon 2000

Version 2.7.0. 2.7.1, 2.7.1.1, 2.7.2, 2.7.2.1 Mods

(yaya@bernstein-plus-sons.com)

?commands

?keywords

RasMol allows the execution of interactive commands typed at the 'RasMol>'

prompt in the terminal window. Each command must be given on a separate

line. Keywords are case insensitive and may be entered in either upper or

lower case letters. All whitespace characters are ignored except to separate

keywords and their arguments.

The commands/keywords currently recognised by RasMol are given below.

Type "help <command>" for more information on each RasMol function.

backbone background bond cartoon centre

clipboard colour connect cpk define

depth dots echo english exit

french hbonds help italian label

load molecule monitor pause print

quit refresh renumber reset restrict

ribbons rotate save script select

set show slab source spacefill

spanish ssbonds star stereo strands

structure trace translate unbond wireframe

write zap zoom

?backbone

Backbone

Syntax: backbone {<boolean>}

backbone <value>

backbone dash

The RasMol 'backbone' command permits the representation of a polypeptide

backbone as a series of bonds connecting the adjacent alpha carbons of each

amino acid in a chain. The display of these backbone 'bonds' is turned on

and off by the command parameter in the same way as with the 'wireframe'

command. The command 'backbone off' turns off the selected 'bonds', and

'backbone on' or with a number turns them on. The number can be used to

specify the cylinder radius of the representation in either Angstrom or

RasMol units. A parameter value of 500 (2.0 Angstroms) or above results in a

"Parameter value too large" error. Backbone objects may be coloured using

the RasMol 'colour backbone' command.

The reserved word backbone is also used as a predefined set ("help sets")

and as a parameter to the 'set hbond' and 'set ssbond' commands. The RasMol

command 'trace' renders a smoothed backbone, in contrast to 'backbone' which

connects alpha carbons with straight lines.

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

dash' command.

?background

Background

Syntax: background <colour>

The RasMol 'background' command is used to set the colour of the "canvas"

background. The colour may be given as either a colour name or a comma

separated triple of Red, Green and Blue (RGB) components enclosed in square

brackets. Typing the command 'help colours' will give a list of the

predefined colour names recognised by RasMol. When running under X Windows,

RasMol also recognises colours in the X server's colour name database.

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

command.

?bond

Bond

Syntax: bond <number> <number> +

bond <number> <number> pick

bond rotate {<boolean>}

The RasMol command 'bond <number> <number> +' adds the designated bond to

the drawing, increasing the bond order if the bond already exists. The

command 'bond <number> <number> pick' selects the two atoms specified by the

atom serial numbers as the two ends of a bond around which the 'rotate bond

<angle>' command will be applied. If no bond exists, it is created.

Rotation around a previously picked bond may be specified by the 'rotate

bond <angle>' command, or may also be controlled with the mouse, using the

'bond rotate on/off' or the equivalent 'rotate bond on/off' commands.

?cartoon

Cartoon

Syntax: cartoon {<number>}

The RasMol 'cartoon' command does a display of a molecule 'ribbons' as

Richardson (MolScript) style protein 'cartoons', implemented as thick (deep)

ribbons. The easiest way to obtain a cartoon representation of a protein is

to use the 'Cartoons' option on the 'Display' menu. The 'cartoon' command

represents the currently selected residues as a deep ribbon with width

specified by the command's argument. Using the command without a parameter

results in the ribbon's width being taken from the protein's secondary

structure, as described in the 'ribbons' command. By default, the C-termini

of beta-sheets are displayed as arrow heads. This may be enabled and

disabled using the 'set cartoons' command. The depth of the cartoon may be

adjusted using the 'set cartoons <number>' command. The 'set cartoons'

command without any parameters returns these two options to their default

values.

?center

?centre

Centre

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

center {<expression>} {translate|center}

The RasMol 'centre' command defines the point about which the 'rotate'

command and the scroll bars rotate the current molecule. Without a parameter

the centre command resets the centre of rotation to be the centre of gravity

of the molecule. If an atom expression is specified, RasMol rotates the

molecule about the centre of gravity of the set of atoms specified by the

expression. Hence, if a single atom is specified by the expression, that

atom will remain 'stationary' during rotations.

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

Alternatively the centring may be given as a comma separated triple of

[CenX, CenY, CenZ] offsets in RasMol units (1/250 of an Angstrom) from the

centre of gravity. The triple must be enclosed in square brackets.

The optional forms 'centre ... translate' and 'centre ... center' may be

used to specify use of a translated centre of rotation (not necessarily in

the centre of the canvas) or a centre of rotation which is placed at the

centre of the canvas. Starting with RasMol 2.7.2, the default is to center

the new axis on the canvas.

?clipboard

Clipboard

Syntax: clipboard

The RasMol 'clipboard' command places a copy of the currently displayed

image on the local graphics 'clipboard'. Note: this command is not yet

supported on UNIX or VMS machines. It is intended to make transfering images

between applications easier under Microsoft Windows or on an Apple

Macintosh.

When using RasMol on a UNIX or VMS system this functionality may be achieved

by generating a raster image in a format that can be read by the receiving

program using the RasMol 'write' command.

?color

?colour

Colour

Syntax: colour {<object>} <colour>

color {<object>} <colour>

Colour the atoms (or other objects) of the selected region. The colour may

be given as either a colour name or a comma separated triple of Red, Green

and Blue (RGB) components enclosed in square brackets. Typing the command

'help colours' will give a list of all the predefined colour names

recognised by RasMol.

Allowed objects are 'atoms', 'bonds', 'backbone', 'ribbons', 'labels',

'dots', 'hbonds' 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

Connect

Syntax: connect {<boolean>}

The RasMol 'connect' command is used to force RasMol to (re)calculate the

connectivity of the current molecule. If the original input file contained

connectivity information, this is discarded. The command 'connect false'

uses a fast heuristic algorithm that is suitable for determining bonding in

large bio-molecules such as proteins and nucleic acids. The command 'connect

true' uses a slower more accurate algorithm based upon covalent radii that

is more suitable to small molecules containing inorganic elements or

strained rings. If no parameters are given, RasMol determines which

algorithm to use based on the number of atoms in the input file. Greater

than 255 atoms causes RasMol to use the faster implementation. This is the

method used to determine bonding, if necessary, when a molecule is first

read in using the 'load' command.

?define

Define

Syntax: define <identifier> <expression>

The RasMol 'define' command allows the user to associate an arbitrary set of

atoms with a unique identifier. This allows the definition of user-defined

sets. These sets are declared statically, i.e. once defined the contents of

the set do not change, even if the expression defining them depends on the

current transformation and representation of the molecule.

?depth

Depth

Syntax: depth {<boolean>}

depth <value>

The RasMol 'depth' command enables, disables or positions the back-clipping

plane of the molecule. The program only draws those portions of the molecule

that are closer to the viewer than the clipping plane. Integer values range

from zero at the very back of the molecule to 100 which is completely in

front of the molecule. Intermediate values determine the percentage of the

molecule to be drawn.

This command interacts with the 'slab <value>' command, which clips to the

front of a given z-clipping plane.

?dot surface

?surface

?dots

Dots

Syntax: dots {<boolean>}

dots <value>

The RasMol 'dots' command is used to generate a van der Waals' dot surface

around the currently selected atoms. Dot surfaces display regularly spaced

points on a sphere of van der Waals' radius about each selected atom. Dots

that would are 'buried' within the van der Waals' radius of any other atom

(selected or not) are not displayed. The command 'dots on' deletes any

existing dot surface and generates a dots surface around the currently

selected atom set with a default dot density of 100. The command 'dots off'

deletes any existing dot surface. The dot density may be specified by

providing a numeric parameter between 1 and 1000. This value approximately

corresponds to the number of dots on the surface of a medium sized atom.

By default, the colour of each point on a dot surface is the colour of its

closest atom at the time the surface is generated. The colour of the whole

dot surface may be changed using the 'colour dots' command.

?echo

Echo

Syntax: echo {<string>}

The RasMol 'echo' command is used to display a message in the RasMol

command/terminal window. The string parameter may optionally be delimited in

double quote characters. If no parameter is specified, the 'echo' command

displays a blank line. This command is particularly useful for displaying

text from within a RasMol 'script' file.

?english

English

Syntax: English

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

versions. The commands 'French', 'Italian' and 'Spanish' may be used to

select French, Italian and Spanish menus and messages.

?french

French

Syntax: 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.

?hbond

?hbonds

HBonds

Syntax: hbonds {<boolean>}

hbonds <value>

The RasMol 'hbond' command is used to represent the hydrogen bonding of the

protein molecule's backbone. This information is useful in assessing the

protein's secondary structure. Hydrogen bonds are represented as either

dotted lines or cylinders between the donor and acceptor residues. The first

time the 'hbond' command is used, the program searches the structure of the

molecule to find hydrogen bonded residues and reports the number of bonds to

the user. The command 'hbonds on' displays the selected 'bonds' as dotted

lines, and the 'hbonds off' turns off their display. The colour of hbond

objects may be changed by the 'colour hbond' command. Initially, each

hydrogen bond has the colours of its connected atoms.

By default the dotted lines are drawn between the accepting oxygen and the

donating nitrogen. By using the 'set hbonds' command the alpha carbon

positions of the appropriate residues may be used instead. This is

especially useful when examining proteins in backbone representation.

?help

Help

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

? {<topic> {<subtopic>}

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

?italian

Italian

Syntax: Italian

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

versions. The commands 'English', 'French' and 'Spanish' may be used to

select English, French and Spanish menus and messages.

?labels

?label

Label

Syntax: label {<string>}

label <boolean>

The RasMol 'label' command allows an arbitrary formatted text string to be

associated with each currently selected atom. This string may contain

embedded 'expansion specifiers' which display properties of the atom being

labelled. An expansion specifier consists of a '%' character followed by a

single alphabetic character specifying the property to be displayed. An

actual '%' character may be displayed by using the expansion specifier '%%'.

Atom labelling for the currently selected atoms may be turned off with the

command 'label off'. By default, if no string is given as a parameter,

RasMol uses labels appropriate for the current molecule.

The colour of each label may be changed using the 'colour label' command. By

default, each label is drawn in the same colour as the atom to which it is

attached. The size and spacing of the displayed text may be changed using

the 'set fontsize' command. The width of the strokes in the displayed text

may be changed using the 'set fontstroke' command.

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

?expansion

?specifiers

?expansion specifiers

?label specifiers

Label Specifiers

Label specifiers are characters sequences that are embedded in the string

parameter passed to the RasMol 'label' command. These specifiers are then

expanded as the labels are drawn to display properties associated with the

atom being labelled. The following table lists the current expansion

specifiers. The specifier '%%' is treated as an exception and is displayed

as a single '%' character.

%a Atom Name

%b %t B-factor/Temperature

%c %s Chain Identifier

%e Element Atomic Symbol

%i Atom Serial Number

%n Residue Name

%r Residue Number

%M NMR Model Number (with leading "/")

%A Alternate Conformation Identifier (with leading ";")

?load

Load

Syntax: load {<format>} <filename>

Load a molecule coordinate file into RasMol. Valid molecule file formats are

'pdb' (Protein Data Bank format), 'mdl' (Molecular Design Limited's MOL file

format), 'alchemy' (Tripos' Alchemy file format), 'mol2' (Tripos' Sybyl Mol2

file format), 'charmm' (CHARMm file format), 'xyz' (MSC's XMol XYZ file

format), 'mopac' (J. P. Stewart's MOPAC file format) or 'cif' (IUCr CIF or

mmCIF file format). If no file format is specified, 'PDB', 'CIF', or 'mmCIF'

is assumed by default. Up to 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

Molecule

Syntax: molecule <number>

The RasMol 'molecule' command selects one of up to 5 previously loaded

molecules for active manipulation. While all the molcules are displayed and

may be rotated collectively (see the 'rotate all' command), only one

molecule at a time time is active for manipulation by the commands which

control the details of rendering.

?monitor

Monitor

Syntax: monitor <number> <number>

monitor {<boolean>}

The RasMol 'monitor' command allows the display of distance monitors. A

distance monitor is a dashed (dotted) line between an arbitrary pair of

atoms, optionally labelled by the distance between them. The RasMol command

'monitor <number> <number>' adds such a distance monitor between the two

atoms specified by the atom serial numbers given as parameters

Distance monitors are turned off with the command 'monitors off'. By

default, monitors display the distance between its two end points as a label

at the centre of the monitor. These distance labels may be turned off with

the command 'set monitors off', and re-enabled with the command 'set

monitors on'. Like most other representations, the colour of a monitor is

taken from the colour of its end points unless specified by the 'colour

monitors' command.

Distance monitors may also be added to a molecule interactively with the

mouse, using the 'set picking monitor' command. Clicking on an atom results

in its being identified on the rasmol command line. In addition every atom

picked increments a modulo counter such that, in monitor mode, every second

atom displays the distance between this atom and the previous one. The shift

key may be used to form distance monitors between a fixed atom and several

consecutive positions. A distance monitor may also be removed (toggled) by

selecting the appropriate pair of atom end points a second time.

?pause

Pause

Syntax: pause

wait

The RasMol 'pause' command is used in script files to stop the script file

for local manipulation by a mouse, until any key is pushed to restart the

script file. 'Wait' is synonymous with 'pause'. This command may be executed

in RasMol script files to suspend the sequential execution of commands and

allow the user to examine the current image. When RasMol executes a 'pause'

command in a script file, it suspends execution of the rest of the file,

refreshes the image on the screen and allows the manipulation of the image

using the mouse and scroll bars, or resizing of the graphics window. Once a

key is pressed, control returns to the script file at the line following the

'pause' command. While a script is suspended the molecule may be rotated,

translated, scaled, slabbed and picked as usual, but all menu commands are

disabled.

?print

Syntax: print

The RasMol 'print' command sends the currently displayed image to the local

default printer using the operating system's native printer driver. Note:

this command is not yet supported under UNIX or VMS. It is intended to take

advantage of Microsoft Windows and Apple Macintosh printer drivers. For

example, this allows images to be printed directly on a dot matrix printer.

When using RasMol on a UNIX or VMS system this functionality may be achieved

by either generating a PostScript file using the RasMol 'write ps' or 'write

vectps' commands and printing that or generating a raster image file and

using a utility to dump that to the local printer.

?exit

?quit

Quit

Syntax: quit

exit

Exit from the RasMol program. The RasMol commands 'exit' and 'quit' are

synonymous, except within nested scripts. In that case, 'exit' terminates

only the current level, while 'quit' terminates all nested levels of

scripts.

?refresh

Refresh

Syntax: refresh

The RasMol 'refresh' command redraws the current image. This is useful in

scripts to ensure application of a complex list of parameter changes.

?renum

?renumber

Renumber

Syntax: renumber {{-} <value>}

The RasMol 'renumber' command sequentially numbers the residues in a

macromolecular chain. The optional parameter specifies the value of the

first residue in the sequence. By default, this value is one. For proteins,

each amino acid is numbered consecutively from the N terminus to the C

terminus. For nucleic acids, each base is numbered from the 5' terminus to

the 3' terminus. All chains in the current database are renumbered and gaps

in the original sequence are ignored. The starting value for numbering may

be negative.

?reset

Reset

Syntax: reset

The RasMol 'reset' command restores the original viewing transformation and

centre of rotation. The scale is set to its default value, 'zoom 100', the

centre of rotation is set to the geometric centre of the currently loaded

molecule, 'centre all', this centre is translated to the middle of the

screen and the viewpoint set to the default orientation.

This command should not be mistaken for the RasMol 'zap' command which

deletes the currently stored molecule, returning the program to its initial

state.

?restrict

Restrict

Syntax: restrict {<expression>}

The RasMol 'restrict' command both defines the currently selected region of

the molecule and disables the representation of (most of) those parts of the

molecule no longer selected. All subsequent RasMol commands that modify a

molecule's colour or representation affect only the currently selected

region. The parameter of a 'restrict' command is a RasMol atom expression

that is evaluated for every atom of the current molecule. This command is

very similar to the RasMol 'select' command, except 'restrict' disables the

'wireframe', 'spacefill' and 'backbone' representations in the non-selected

region.

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

?ribbon

?ribbons

Ribbons

Syntax: ribbons {<boolean>}

ribbons <value>

The RasMol 'ribbons' command displays the currently loaded protein or

nucleic acid as a smooth solid "ribbon" surface passing along the backbone

of the protein. The ribbon is drawn between each amino acid whose alpha

carbon is currently selected. The colour of the ribbon is changed by the

RasMol 'colour ribbon' command. If the current ribbon colour is 'none' (the

default), the colour is taken from the alpha carbon at each position along

its length.

The width of the ribbon at each position is determined by the optional

parameter in the usual RasMol units. By default the width of the ribbon is

taken from the secondary structure of the protein or a constant value of 720

(2.88 Angstroms) for nucleic acids. The default width of protein alpha

helices and beta sheets is 380 (1.52 Angstroms) and 100 (0.4 Angstroms) for

turns and random coil. The secondary structure assignment is either from the

PDB file or calculated using the DSSP algorithm as used by the 'structure'

command. This command is similar to the RasMol command 'strands' which

renders the biomolecular ribbon as parallel depth-cued curves.

?rotate

Rotate

Syntax: rotate <axis> {-} <value>

rotate bond {<boolean>}

rotate molecule {<boolean>}

rotate all {<boolean>}

Rotate the molecule about the specified axis. Permitted values for the axis

parameter are "x", "y", "z" and "bond". The integer parameter states the

angle in degrees for the structure to be rotated. For the X and Y axes,

positive values move the closest point up and right, and negative values

move it down and left, respectively. For the Z axis, a positive rotation

acts clockwise and a negative angle anti-clockwise.

Alternatively, this command may be used to specify which rotations the mouse

or dials will control. If 'rotate bond true' is selected, the horizontal

scroll bar will control rotation around the axis selected by the 'bond src

dst pick' command. If 'rotate all true' is selected, and multiple molecules

have been loaded, then all molecules will rotate together. In all other

cases, the mouseand dials control the the rotation of the molecule selected

by the 'molecule n' command.

?save

Save

Syntax: save {pdb} <filename>

save mdl <filename>

save alchemy <filename>

save xyz <filename>

Save the currently selected set of atoms in a Protein Data Bank (PDB), MDL,

Alchemy(tm) or XYZ format file. The distinction between this command and the

RasMol 'write' command has been dropped. The only difference is that without

a format specifier the 'save' command generates a 'PDB' file and the 'write'

command generates a 'GIF' image.

?source

?scripts

?script

Script

Syntax: script <filename>

The RasMol 'script' command reads a set of RasMol commands sequentially from

a text file and executes them. This allows sequences of commonly used

commands to be stored and performed by single command. A RasMol script file

may contain a further script command up to a maximum "depth" of 10, allowing

complicated sequences of actions to be executed. RasMol ignores all

characters after the first '#' character on each line allowing the scripts

to be annotated. Script files are often also annotated using the RasMol

'echo' command.

The most common way to generate a RasMol script file is to use the 'write

script' or 'write rasmol' commands to output the sequence of commands that

are needed to regenerate the current view, representation and colouring of

the currently displayed molecule.

The RasMol command 'source' is synonymous with the 'script' command.

?select

Select

Syntax: select {<expression>}

Define the currently selected region of the molecule. All subsequent RasMol

commands that manipulate a molecule or modify its colour or representation

only affect the currently selected region. The parameter of a 'select'

command is a RasMol expression that is evaluated for every atom of the

current molecule. The currently selected (active) region of the molecule are

those atoms that cause the expression to evaluate true. To select the whole

molecule use the RasMol command 'select all'. The behaviour of the 'select'

command without any parameters is determined by the RasMol 'hetero' and

'hydrogen' parameters.

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

?set

Set

Syntax: set <parameter> {<option>}

The RasMol 'set' command allows the user to alter various internal program

parameters such as those controlling rendering options. Each parameter has

its own set or permissible parameter options. Typically, omitting the

paramter option resets that parameter to its default value. A list of valid

parameter names is given below. For more information on each internal

parameter type "help set parameter".

ambient axes background backfade

bondmode bonds boundbox cartoon

cisangle display fontsize fontstroke

hbond hetero hourglass hydrogen

kinemage menus monitor mouse

picking radius shadepower shadow

slabmode solvent specular specpower

stereo ssbonds strands transparent

unitcell vectps write

?show

Show

Syntax: show information

show centre

show phipsi

show RamPrint

show rotation

show selected { group | chain |atom }

show sequence

show symmetry

show translation

show zoom

The RasMol 'show' command display details of the status of the currently

loaded molecule. The command 'show information' lists the molecule's name,

classification, PDB code and the number of atoms, chains, groups it

contains. If hydrogen bonding, disulphide bridges or secondary structure

have been determined, the number of hbonds, ssbonds, helices, ladders and

turns are also displayed, respectively. The command 'show centre' shows any

non-zero centering values selected by the 'centre [CenX, CenY, CenZ]'

command. The command 'show phipsi' shows the phi and psi angles of the

currently selected residues and the omega angles of cis peptide bonds. The

command 'show RamPrint' (or 'show RPP' or 'show RamachandranPrinterPlot')

shows a simple Ramachandran printer plot in the style of Frances Bernstein's

fisipl program. The command 'show rotation' (or 'show rot' or 'show

'rotate') shows the currently selected values of z, y, x and bond rotations,

if any. The command 'show selected' (or 'show selected group' or 'show

selected chain' or 'show selected atom' ) shows the groups (default), chains

or atoms of the current selection. The command 'show sequence' lists the

residues that comprise each chain of the molecule. The command 'show

symmetry' shows the space group and unit cell of the molecule. The command

'show translation' shows any non-zero translation values selected by the

'translate <axis> <value>' command. The command 'show zoom' shows any

non-zero zoom value selected by the 'zoom <value>' command.

?slab

Slab

Syntax: slab {<boolean>}

slab <value>

The RasMol 'slab' command enables, disables or positions the z-clipping

plane of the molecule. The program only draws those portions of the molecule

that are further from the viewer than the slabbing plane. Integer values

range from zero at the very back of the molecule to 100 which is completely

in front of the molecule. Intermediate values determine the percentage of

the molecule to be drawn.

This command interacts with the 'depth <value>' command, which clips to the

rear of a given z-clipping plane.

?cpk

?spacefill

Spacefill

Syntax: spacefill {<boolean>}

spacefill temperature

spacefill user

spacefill <value>

The RasMol 'spacefill' command is used to represent all of the currently

selected atoms as solid spheres. This command is used to produce both

union-of-spheres and ball-and-stick models of a molecule. The command,

'spacefill true', the default, represents each atom as a sphere of van der

Waals radius. The command 'spacefill off' turns off the representation of

the selected atom as spheres. A sphere radius may be specified as an integer

in RasMol units (1/250th Angstrom) or a value containing a decimal point. A

value of 500 (2.0 Angstroms) or greater results in a "Parameter value too

large" error.

The 'temperature' option sets the radius of each sphere to the value stored

in its temperature field. Zero or negative values have no effect and values

greater than 2.0 are truncated to 2.0. The 'user' option allows the radius

of each sphere to be specified by additional lines in the molecule's PDB

file using Raster 3D's COLOUR record extension.

The RasMol command 'cpk' is synonymous with the 'spacefill' command.

?spanish

Spanish

Syntax: 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.

?ssbond

?bridges

?disulphide bridges

?ssbonds

SSBonds

Syntax: ssbonds {<boolean>}

ssbonds <value>

The RasMol 'ssbonds' command is used to represent the disulphide bridges of

the protein molecule as either dotted lines or cylinders between the

connected cysteines. The first time that the 'ssbonds' command is used, the

program searches the structure of the protein to find half-cysteine pairs

(cysteines whose sulphurs are within 3 Angstroms of each other) and reports

the number of bridges to the user. The command 'ssbonds on' displays the

selected "bonds" as dotted lines, and the command 'ssbonds off' disables the

display of ssbonds in the currently selected area. Selection of disulphide

bridges is identical to normal bonds, and may be adjusted using the RasMol

'set bondmode' command. The colour of disulphide bonds may be changed using

the 'colour ssbonds' command. By default, each disulphide bond has the

colours of its connected atoms.

By default disulphide bonds are drawn between the sulphur atoms within the

cysteine groups. By using the 'set ssbonds' command the position of the

cysteine's alpha carbons may be used instead.

?star

Star

Syntax: star {<boolean>}

star temperature

star user

star <value>

The RasMol 'star' command is used to represent all of the currently selected

atoms as stars (six strokes, one each in the x, -x, y, -y, z and -z

directions). The commands 'select not bonded' followed by 'star 75' are

useful to mark unbonded atoms in a 'wireframe' display with less overhead

than provided by 'spacefill 75'. This can be done automatically for all

subsequent wireframe displays with the command 'set bondmode not bonded'.

The command 'star true', the default, represents each atom as a star with

strokes length equal to van der Waals radius. The command 'star off' turns

off the representation of the selected atom as stars. A star stroke length

may be specified as an integer in RasMol units (1/250th Angstrom) or a value

containing a decimal point. A value of 500 (2.0 Angstroms) or greater

results in a "Parameter value too large" error.

The 'temperature' option sets the stroke length of each star to the value

stored in its temperature field. Zero or negative values have no effect and

values greater than 2.0 are truncated to 2.0. The 'user' option allows the

stroke length of each star to be specified by additional lines in the

molecule's PDB file using Raster 3D's COLOUR record extension.

The RasMol 'spacefill' command can be used for more artistic rendering of

atoms as spheres.

?stereo

Stereo

Syntax: stereo on

stereo [-] <number>

stereo off

The RasMol 'stereo' command provides side-by-side stereo display of images.

Stereo viewing of a molecule may be turned on (and off) either by selecting

'Stereo' from the 'Options' menu, or by typing the commands 'stereo on' or

'stereo off'.

Starting with RasMol version 2.7.2.1, the 'Stereo' menu selection and the

command 'stereo' without arguments cycle from the initial state of 'stereo

off' to 'stereo on' in cross-eyed mode to 'stereo on' in wall-eyed mode and

then back to 'stereo off'.

The separation angle between the two views may be adjusted with the 'set

stereo [-] <number>' command, where positive values result in crossed eye

viewing and negative values in relaxed (wall-eyed) viewing. The inclusion of

'[-] <number>' in the 'stereo' command, as for example in 'stereo 3' or

'stereo -5', also controls angle and direction.

The stereo command is only partially implemented. When stereo is turned on,

the image is not properly recentred. (This can be done with a 'translate x

-<number>' command.) It is not supported in vector PostScript output files,

is not saved by the 'write script' command, and in general is not yet

properly interfaced with several other features of the program.

?strands

Strands

Syntax: strands {<boolean>}

strands <value>

The RasMol 'strands' command displays the currently loaded protein or

nucleic acid as a smooth "ribbon" of depth-cued curves passing along the

backbone of the protein. The ribbon is composed of a number of strands that

run parallel to one another along the peptide plane of each residue. The

ribbon is drawn between each amino acid whose alpha carbon is currently

selected. The colour of the ribbon is changed by the RasMol 'colour ribbon'

command. If the current ribbon colour is 'none' (the default), the colour is

taken from the alpha carbon at each position along its length. The central

and outermost strands may be coloured independently using the 'colour

ribbon1' and 'colour ribbon2' commands, respectively. The number of strands

in the ribbon may be altered using the RasMol 'set strands' command.

The width of the ribbon at each position is determined by the optional

parameter in the usual RasMol units. By default the width of the ribbon is

taken from the secondary structure of the protein or a constant value of 720

for nucleic acids (which produces a ribbon 2.88 Angstroms wide). The default

width of protein alpha helices and beta sheets is 380 (1.52 Angstroms) and

100 (0.4 Angstroms) for turns and random coil. The secondary structure

assignment is either from the PDB file or calculated using the DSSP

algorithm as used by the 'structure' command. This command is similar to the

RasMol command 'ribbons' which renders the biomolecular ribbon as a smooth

shaded surface.

?structure

Structure

Syntax: structure

The RasMol 'structure' command calculates secondary structure assignments

for the currently loaded protein. If the original PDB file contained

structural assignment records (HELIX, SHEET and TURN) these are discarded.

Initially, the hydrogen bonds of the current molecule are found, if this

hasn't been done already. The secondary structure is then determined using

Kabsch and Sander's DSSP algorithm. Once finished the program reports the

number of helices, strands and turns found.

?trace

Trace

Syntax: trace {<boolean>}

trace <value>

trace temperature

The RasMol 'trace' command displays a smooth spline between consecutive

alpha carbon positions. This spline does not pass exactly through the alpha

carbon position of each residue, but follows the same path as 'ribbons',

'strands' and 'cartoons'. Note that residues may be displayed as 'ribbons',

'strands', 'cartoons' or as a 'trace'. Enabling one of these representations

disables the others. However, a residue may be displayed simultaneously as

backbone and as one of the above representations. This may change in future

versions of RasMol. Prior to version 2.6, 'trace' was synonymous with

'backbone'.

'Trace temperature' displays the backbone as a wider cylinder at high

temperature factors and thinner at lower. This representation is useful to

X-ray crystallographers and NMR spectroscopists.

?translate

Translate

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

The RasMol 'translate' command moves the position of the centre of the

molecule on the screen. The axis parameter specifies along which axis the

molecule is to be moved and the integer parameter specifies the absolute

position of the molecule centre from the middle of the screen. Permitted

values for the axis parameter are "x", "y" and "z". Displacement values must

be between -100 and 100 which correspond to moving the current molecule just

off the screen. A positive "x" displacement moves the molecule to the right,

and a positive "y" displacement moves the molecule down the screen. The pair

of commands 'translate x 0' and 'translate y 0' centres the molecule on the

screen.

?unbond

UnBond

Syntax: unbond <number> <number>

unbond

The RasMol command 'unbond <number> <number>' removes the designated bond

from the drawing.

The command 'unbond' without arguments removes a bond previously picked by

the 'bond <number> <number> pick' command.

?wireframe

Wireframe

Syntax: wireframe {<boolean>}

wireframe <value> {<value>}

The RasMol 'wireframe' command represents each bond within the selected

region of the molecule as a cylinder, a line or a depth-cued vector. The

display of bonds as depth-cued vectors (drawn darker the further away from

the viewer) is turned on by the command 'wireframe' or 'wireframe on'. The

selected bonds are displayed as cylinders by specifying a radius either as

an integer in RasMol units or containing a decimal point as a value in

Angstroms. A parameter value of 500 (2.0 Angstroms) or above results in an

"Parameter value too large" error. Bonds may be coloured using the 'colour

bonds' command. If the selected bonds involved atoms of alternate conformers

then the bonds are narrowed in the middle to a radius of .8 of the specified

radius (or to the radius specifed as the optional second parameter).

Non-bonded atoms, which could become invisible in an ordinary 'wireframe'

display can be marked by a preceding 'set bondmode not bonded' command. If

nearly co-linear bonds to atoms cause them to be difficult to see in a

wireframe display, the 'set bondmode all' command will add markers for 'all'

atoms in subsequent 'wireframe' command executions.

?write

Write

Syntax: write {<format>} <filename>

Write the current image to a file in a standard format. Currently supported

image file formats include 'bmp' (Microsoft bitmap) and 'gif' (Compuserve

GIF), 'iris' (IRIS RGB), 'ppm' (Portable Pixmap), 'ras' (Sun rasterfile),

'ps' and 'epsf' (Encapsulated PostScript), 'monops' (Monochrome Encapsulated

PostScript), 'pict' (Apple PICT), 'vectps' (Vector Postscript). The 'write'

command may also be used to generate command scripts for other graphics

programs. The format 'script' writes out a file containing the RasMol

'script' commands to reproduce the current image. The format 'molscript'

writes out the commands required to render the current view of the molecule

as ribbons in Per Kraulis' Molscript program and the format 'kinemage' the

commands for David Richardson's program Mage. The following formats are

useful for further processing: 'povray' (POVRay 2), 'povray3' (POVRay 3 --

under development), 'vrml' (VRML file). Finally, several formats are

provided to provide phi-psi data for listing or for 'phipsi' (phi-psi data

as an annotated list with cis omegas), 'ramachan' and 'RDF' and

'RamachandranDataFile' (phi-psi data as columns of numbers for gnuplot),

'RPP' and 'RamachandranPrinterPlot' (phi-psi data as a printer plot).

The distinction between this command and the RasMol 'save' command has been

dropped. The only difference is that without a format specifier the 'save'

command generates a 'PDB' file and the 'write' command generates a 'GIF'

image.

?zap

Zap

Syntax: zap

Deletes the contents of the current database and resets parameter variables

to their initial default state.

?zoom

Zoom

Syntax: zoom {<boolean>}

zoom <value>

Change the magnification of the currently displayed image. Boolean

parameters either magnify or reset the scale of current molecule. An integer

parameter specifies the desired magnification as a percentage of the default

scale. The minimum parameter value is 10; the maximum parameter value is

dependent upon the size of the molecule being displayed. For medium sized

proteins this is about 500.

?parameters

?set parameters

?internal parameters

Internal Parameters

RasMol has a number of internal parameters that may be modified using the

'set' command. These parameters control a number of program options such as

rendering options and mouse button mappings.

A complete list of internal parameter names is given below. Type "help set

<parametername>" for more information on each option.

ambient axes background backfade

bondmode bonds boundbox cartoon

cisangle display fontsize fontstroke

hbond hetero hourglass hydrogen

kinemage menus monitor mouse

picking radius shadow slabmode

solvent specular specpower stereo

ssbonds strands transparent unitcell

vectps write

?ambient

?set ambient

Set Ambient

Syntax: set ambient {<value>}

The RasMol 'ambient' parameter is used to control the amount of ambient (or

surrounding) light in the scene. The 'ambient' value must be between 0 and

100. It controls the percentage intensity of the darkest shade of an object.

For a solid object, this is the intensity of surfaces facing away from the

light source or in shadow. For depth-cued objects this is the intensity of

objects furthest from the viewer.

This parameter is commonly used to correct for monitors with different

"gamma values" (brightness), to change how light or dark a hardcopy image

appears when printed or to alter the feeling of depth for wireframe or

ribbon representations.

?axis

?axes

?set axis

?set axes

Set Axes

Syntax: set axes <boolean>

The RasMol 'axes' parameter controls the display of orthogonal coordinate

axes on the current display. The coordinate axes are those used in the

molecule data file, and the origin is the centre of the molecule's bounding

box. The 'set axes' command is similar to the commands 'set boundbox' and

'set unitcell' that display the bounding box and the crystallographic unit

cell, respectively.

?set backfade

Set Backfade

Syntax: set backfade <boolean>

The RasMol 'backfade' parameter is used to control backfade to the specified

background colour, rather than black. This is controlled by the commands

'set backfade on' and 'set backfade off'. For example, this may be used to

generate depth-cued images that fade to white, rather than black.

?set background

Set Background

Syntax: set background <colour>

The RasMol 'background' parameter is used to set the colour of the "canvas"

background. The colour may be given as either a colour name or a comma

separated triple of Red, Green, Blue (RGB) components enclosed in square

brackets. Typing the command 'help colours' will give a list of the

predefined colour names recognised by RasMol. When running under X Windows,

RasMol also recognises colours in the X server's colour name database.

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

'background'.

?bondmode

?set bondmode

Set BondMode

Syntax: set bondmode and

set bondmode or

set bondmode all

set bondmode none

set bondmode not bonded

The RasMol 'set bondmode' command controls the mechanism used to select

individual bonds and modifies the display of bonded and non-bonded atoms by

subsequent 'wireframe' commands.

When using the 'select' and 'restrict' commands, a given bond will be

selected if i) the bondmode is 'or' and either of the connected atoms is

selected, or ii) the bondmode is 'and' and both atoms connected by the bond

are selected. Hence an individual bond may be uniquely identified by using

the command 'set bondmode and' and then uniquely selecting the atoms at both

ends.

The 'bondmode [all | none | not bonded]' commands add 'star 75' or

'spacefill 75' markers for the designated atoms to 'wireframe' displays.

Stars are used when the specified wireframe radius is zero.

?setbond

?set bonds

Set Bonds

Syntax: set bond <boolean>

The RasMol 'bonds' parameter is used to control display of double and triple

bonds as multiple lines or cylinders. Currently bond orders are only read

from MDL Mol files, Sybyl Mol2 format files, Tripos Alchemy format files,

CIF and mmCIF, and suitable PDB files. Double (and triple) bonds are

specified in some PDB files by specifying a given bond twice (and three

times) in CONECT records. The command 'set bonds on' enables the display of

bond orders, and the command 'set bonds off' disables them.

?boundbox

?boundingbox

?bounding box

?set boundbox

Set BoundBox

Syntax: set boundbox <boolean>

The RasMol 'boundbox' parameter controls the display of the current

molecule's bounding box on the display. The bounding box is orthogonal to

the data file's original coordinate axes. The 'set boundbox' command is

similar to the commands 'set axes' and 'set unitcell' that display

orthogonal coordinate axes and the bounding box, respectively.

?set cartoon

Set Cartoon

Syntax: set cartoon {<boolean>}

set cartoon {<number>}

The RasMol 'cartoon' parameter is used to control display of the cartoon

version of the 'ribbons' display. By default, the C-termini of beta-sheets

are displayed as arrow heads. This may be enabled and disabled using the

'set cartoons <boolean>' command. The depth of the cartoon may be adjusted

using the 'cartoons <number>' command. The 'set cartoons' command without

any parameters returns these two options to their default values.

?cisangle

?cis

?cis angle

?set cisangle

Set CisAngle

Syntax: set cisangle {<value>}

The RasMol 'cisangle' parameter controls the cutoff angle for identifying

cis peptide bonds. If no value is given, the cutoff is set to 90 degrees.

?display

?set display

Set Display

Syntax: set display selected

set display normal

This command controls the display mode within RasMol. By default, 'set

display normal', RasMol displays the molecule in the representation

specified by the user. The command 'set display selected' changes the

display mode such that the molecule is temporarily drawn so as to indicate

currently selected portion of the molecule. The user specified colour scheme

and representation remains unchanged. In this representation all selected

atoms are shown in yellow and all non selected atoms are shown in blue. The

colour of the background is also changed to a dark grey to indicate the

change of display mode. This command is typically only used by external

Graphical User Interfaces (GUIs).

?fontsize

?set fontsize

Set FontSize

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

The RasMol 'set fontsize' command is used to control the size of the

characters that form atom labels. This value corresponds to the height of

the displayed character in pixels. The maximum value of 'fontsize' is 48

pixels, and the default value is 8 pixels high. Fixed or proportional

spacing may be selected by appending the "FS" or "PS" modifiers,

respectively. The default is "FS". To display atom labels on the screen use

the RasMol 'label' command and to change the colour of displayed labels, use

the 'colour labels' command.

?fontstroke

?set fontstroke

Set FontStroke

Syntax: set fontstroke {<value>}

The RasMol 'set fontstroke' command is used to control the size of the

stroke width of the characters that form atom labels. This value is the

radius in pixels of cylinders used to form the strokes. The special value of

"0" is the default used for the normal single pixel stroke width, which

allows for rapid drawing and rotation of the image. Non-zero values are

provided to allow for more artistic atom labels for publication at the

expense of extra time in rendering the image.

When wider strokes are used, a larger font size is recommend, e.g. by using

the RasMol 'set fontsize 24 PS' command, followed by 'set fontstroke 2'

To display atom labels on the screen use the RasMol 'label' command, and to

change the colour of displayed labels use the 'colour labels' command.

?set hbonds

Set HBonds

Syntax: set hbonds backbone

set hbonds sidechain

The RasMol 'hbonds' parameter determines whether hydrogen bonds are drawn

between the donor and acceptor atoms of the hydrogen bond, 'set hbonds

sidechain' or between the alpha carbon atoms of the protein backbone and

between the phosphorous atoms of the nucleic acid backbone, 'set hbonds

backbone'. The actual display of hydrogen bonds is controlled by the

'hbonds' command. Drawing hydrogen bonds between protein alpha carbons or

nucleic acid phosphorous atoms is useful when the rest of the molecule is

shown in only a schematic representation such as 'backbone', 'ribbons' or

'strands'. This parameter is similar to the RasMol 'ssbonds' parameter.

?hetero

?set hetero

Set Hetero

Syntax: set hetero <boolean>

The RasMol 'hetero' parameter is used to modify the 'default' behaviour of

the RasMol 'select' command, i.e. the behaviour of 'select' without any

parameters. When this value is 'false', the default 'select' region does not

include any heterogeneous atoms (refer to the predefined set 'hetero' ).

When this value is 'true', the default 'select' region may contain hetero

atoms. This parameter is similar to the RasMol 'hydrogen' parameter which

determines whether hydrogen atoms should be included in the default set. If

both 'hetero' and 'hydrogen' are 'true', 'select' without any parameters is

equivalent to 'select all'.

?hourglass

?set hourglass

Set HourGlass

Syntax: set hourglass <boolean>

The RasMol 'hourglass' parameter allows the user to enable and disable the

use of the 'hour glass' cursor used by RasMol to indicate that the program

is currently busy drawing the next frame. The command 'set hourglass on'

enables the indicator, whilst 'set hourglass off' prevents RasMol from

changing the cursor. This is useful when spinning the molecule, running a

sequence of commands from a script file or using interprocess communication

to execute complex sequences of commands. In these cases a 'flashing' cursor

may be distracting.

?hydrogen

?set hydrogen

Set Hydrogen

Syntax: set hydrogen <boolean>

The RasMol 'hydrogen' parameter is used to modify the "default" behaviour of

the RasMol 'select' command, i.e. the behaviour of 'select' without any

parameters. When this value is 'false', the default 'select' region does not

include any hydrogen, deuterium or tritium atoms (refer to the predefined

set 'hydrogen' ). When this value is 'true', the default 'select' region may

contain hydrogen atoms. This parameter is similar to the RasMol 'hetero'

parameter which determines whether heterogeneous atoms should be included in

the default set. If both 'hydrogen' and 'hetero' are 'true', 'select'

without any parameters is equivalent to 'select all'.

?mage

?kinemage

?set kinemage

Set Kinemage

Syntax: set kinemage <boolean>

The RasMol 'set kinemage' command controls the amount of detail stored in a

Kinemage output file generated by the RasMol 'write kinemage' command. The

output kinemage files are intended to be displayed by David Richardson's

Mage program. 'set kinemage false', the default, only stores the currently

displayed representation in the generated output file. The command 'set

kinemage true', generates a more complex Kinemage that contains both the

wireframe and backbone representations as well as the coordinate axes,

bounding box and crystal unit cell.

?set menus

Set Menus

Syntax: set menus <boolean>

The RasMol 'set menus' command enables the canvas window's menu buttons or

menu bar. This command is typically only used by graphical user interfaces

or to create as large an image as possible when using Microsoft Windows.

?set monitor

Set Monitor

Syntax: set monitor <boolean>

?setmonitors

The RasMol 'set monitor' command enables 'monitors'. The distance monitor

labels may be turned off with the command 'set monitor off', and re-enabled

with the command 'set monitor on'.

?mouse

?set mouse

Set Mouse

Syntax: set mouse rasmol

set mouse insight

set mouse quanta

The RasMol 'set mouse' command sets the rotation, translation, scaling and

zooming mouse bindings. The default value is 'rasmol' which is suitable for

two button mice (for three button mice the second and third buttons are

synonymous); X-Y rotation is controlled by the first button, and X-Y

translation by the second. Additional functions are controlled by holding a

modifier key on the keyboard. [Shift] and the first button performs scaling,

[shift] and the second button performs Z-rotation, and [control] and the

first mouse button controls the clipping plane. The 'insight' and 'quanta'

options provide the same mouse bindings as other packages for experienced

users.

?pick

?picking

?setpick

?set picking

Set Picking

Syntax: set picking <boolean>

set picking off

set picking none

set picking ident

set picking distance

set picking monitor

set picking angle

set picking torsion

set picking label

set picking centre

set picking center

set picking coord

set picking bond

set picking atom

set picking group

set picking chain

The RasMol 'set picking' series of commands affects how a user may interact

with a molecule displayed on the screen in RasMol.

Enabling/Disabling Atom Identification Picking: Clicking on an atom with the

mouse results in identification and the display of its residue name, residue

number, atom name, atom serial number and chain in the command window. This

behavior may be disabled with the command 'set picking none' and restored

with the command 'set picking ident'. The command 'set picking coord' adds

the atomic coordinates of the atom to the display.

Disabling picking, by using 'set picking off' is useful when executing the

'pause' command in RasMol scripts as it prevents the display of spurious

message on the command line while the script is suspended.

Measuring Distances, Angles and Torsions: Interactive measurement of

distances, angles and torsions is achieved using the commands: 'set picking

distance', 'set picking monitor', 'set picking angle' and 'set picking

torsion', respectively. In these modes, clicking on an atom results in it

being identified on the rasmol command line. In addition every atom picked

increments a modulo counter such that in distance mode, every second atom

displays the distance (or distance monitor) between this atom and the

previous one. In angle mode, every third atom displays the angle between the

previous three atoms and in torsion mode every fourth atom displays the

torsion between the last four atoms. By holding down the shift key while

picking an atom, this modulo counter is not incremented and allows, for

example, the distances of consecutive atoms from a fixed atom to be

displayed. See the 'monitor' command for how to control the display of

distance monitor lines and labels.

Labelling Atoms with the Mouse: The mouse may also be used to toggle the

display of an atom label on a given atom. The RasMol command 'set picking

label' removes a label from a picked atom if it already has one or displays

a concise label at that atom position otherwise.

Centring Rotation with the Mouse: A molecule may be centred on a specified

atom position using the RasMol commands 'set picking centre' or 'set picking

center'. In this mode, picking an atom causes all futher rotations to be

about that point.

Picking a Bond as a Rotation Axis: Any bond may be picked as an axis of

rotation for the portion of the molecule beyond the second atom selected.

This feature should be used with caution, since, naturally, it changes the

conformation of the molecule. After executing 'set picking bond' or using

the equivalent "Pick Bond" in the "Settings" menu, a bond to be rotated is

picked with the same sort of mouse clicks as are used for picking atoms for

a distance measurement. Normally this should be done where a bond exists,

but if no bond exists, it will be added. The bond cannot be used for

rotation if it is part of a ring of any size. All bonds selected for

rotation are remembered so that they can be properly reported when writing a

script, but only the most recently selected bond may be actively rotated.

Enabling Atom/Group/Chain Selection Picking: Atoms, groups and chains may be

selected (as if with the 'select' command), with the 'set picking atom',

'set picking group', 'set picking chain' commands. For each of these

commands, the shift key may be used to have a new selection added to the

old, and the control key may be used to have a new selection deleted from

the old. When the 'set picking atom' command is given, the mouse can be used

to pick or to drag a box around the atoms for which selection is desired.

When the 'set picking group' command is given, picking any an atom will

cause selection of all atoms which agree in residue number with the picked

atom, even if in different chains. When the 'set picking chain' command is

given, picking any atom will cause selection of all atoms which agree in

chain identifier with the picked atom.

?radius

?set radius

Set Radius

Syntax: set radius {<value>}

The RasMol 'set radius' command is used to alter the behaviour of the RasMol

'dots' command depending upon the value of the 'solvent' parameter. When

'solvent' is 'true', the 'radius' parameter controls whether a true van der

Waals' surface is generated by the 'dots' command. If the value of 'radius'

is anything other than zero, that value is used as the radius of each atom

instead of its true vdW value. When the value of 'solvent' is 'true', this

parameter determines the 'probe sphere' (solvent) radius. The parameter may

be given as an integer in rasmol units or containing a decimal point in

Angstroms. The default value of this parameter is determined by the value of

'solvent' and changing 'solvent' resets 'radius' to its new default value.

?shadepower

?set shadepower

Set ShadePower

Syntax: set shadepower {<value>}

The 'shadepower' parameter (adopted from RasTop) determines the shade

repartition (the contrast) used in rendering solid objects. This value

between 0 and 100 adjusts shading on an object surface oriented along the

direction to the light source. Changing the shadepower parameter does not

change the maximum or the minimum values of this shading, as does changing

the 'ambient' parameter. A value of 100 concentrates the light on the top of

spheres, giving a highly specular, glassy rendering (see the 'specpower'

parameter). A value of 0 distributes the light on the entire object.

This implementation of shadepower differs from the one in RasTop only in the

choice of range (0 to 100 versus -20 to 20 in RasTop).

?shadow

?shadows

?set shadow

Set Shadow

Syntax: set shadow <boolean>

The RasMol 'set shadow' command enables and disables ray-tracing of the

currently rendered image. Currently only the spacefilling representation is

shadowed or can cast shadows. Enabling shadowing will automatically disable

the Z-clipping (slabbing) plane using the command 'slab off'. Ray-tracing

typically takes about several seconds for a moderately sized protein. It is

recommended that shadowing be normally disabled whilst the molecule is being

transformed or manipulated, and only enabled once an appropiate viewpoint is

selected, to provide a greater impression of depth.

?slabmode

?set slab

?set slabmode

Set SlabMode

Syntax: set slabmode <slabmode>

The RasMol 'slabmode' parameter controls the rendering method of objects cut

by the slabbing (z-clipping) plane. Valid slabmode parameters are "reject",

"half", "hollow", "solid" and "section".

?solvent

?set solvent

Set Solvent

Syntax: set solvent <boolean>

The RasMol 'set solvent' command is used to control the behaviour of the

RasMol 'dots' command. Depending upon the value of the 'solvent' parameter,

the 'dots' command either generates a van der Waals' or a solvent accessible

surface around the currently selected set of atoms. Changing this parameter

automatically resets the value of the RasMol 'radius' parameter. The command

'set solvent false', the default value, indicates that a van der Waals'

surface should be generated and resets the value of 'radius' to zero. The

command 'set solvent true' indicates that a 'Connolly' or 'Richards' solvent

accessible surface should be drawn and sets the 'radius' parameter, the

solvent radius, to 1.2 Angstroms (or 300 RasMol units).

?specular

?set specular

Set Specular

Syntax: set specular <boolean>

The RasMol 'set specular' command enables and disables the display of

specular highlights on solid objects drawn by RasMol. Specular highlights

appear as white reflections of the light source on the surface of the

object. The current RasMol implementation uses an approximation function to

generate this highlight.

The specular highlights on the surfaces of solid objects may be altered by

using the specular reflection coefficient, which is altered using the RasMol

'set specpower' command.

?specpower

?set specpower

Set SpecPower

Syntax: set specpower {<value>}

The 'specpower' parameter determines the shininess of solid objects rendered

by RasMol. This value between 0 and 100 adjusts the reflection coefficient

used in specular highlight calculations. The specular highlights are enabled

and disabled by the RasMol 'set specular' command. Values around 20 or 30

produce plastic looking surfaces. High values represent more shiny surfaces

such as metals, while lower values produce more diffuse/dull surfaces.

?set ssbonds

Set SSBonds

Syntax: set ssbonds backbone

set ssbonds sidechain

The RasMol 'ssbonds' parameter determines whether disulphide bridges are

drawn between the sulphur atoms in the sidechain (the default) or between

the alpha carbon atoms in the backbone of the cysteines residues. The actual

display of disulphide bridges is controlled by the 'ssbonds' command.

Drawing disulphide bridges between alpha carbons is useful when the rest of

the protein is shown in only a schematic representation such as 'backbone',

'ribbons' or 'strands'. This parameter is similar to the RasMol 'hbonds'

parameter.

?set stereo

Set Stereo

Syntax: set stereo <boolean>

set stereo [-] <number>

The RasMol 'set stereo' parameter controls the separation between the left

and right images. Turning stereo on and off doesn't reposition the centre of

the molecule.

Stereo viewing of a molecule may be turned on (and off) either by selecting

'Stereo' from the 'Options' menu, or by typing the commands 'stereo on' or

'stereo off'.

The separation angle between the two views may be adjusted with the 'set

stereo [-] <number>' command, where positive values result in crossed eye

viewing and negative values in relaxed (wall-eyed) viewing. Currently,

stereo viewing is not supported in 'vector PostScript' output files.

?set strands

Set Strands

Syntax: set strands {<value>}

The RasMol 'strands' parameter controls the number of parallel strands that

are displayed in the ribbon representations of proteins. The permissible

values for this parameter are 1, 2, 3, 4, 5 and 9. The default value is 5.

The number of strands is constant for all ribbons being displayed. However,

the ribbon width (the separation between strands) may be controlled on a

residue by residue basis using the RasMol 'ribbons' command.

?set transparent

Set Transparent

Syntax: set transparent <boolean>

The RasMol 'transparent' parameter controls the writing of transparent GIFs

by the 'write gif <filename>' command. This may be controlled by the 'set

transparent on' and 'set transparent off' commands.

?unitcell

?unit cell

?set unitcell

Set UnitCell

Syntax: set unitcell <boolean>

The RasMol 'unitcell' parameter controls the display of the crystallographic

unit cell on the current display. The crystal cell is only enabled if the

appropriate crystal symmetry information is contained in the PDB, CIF or

mmCIF data file. The RasMol command 'show symmetry' display details of the

crystal's space group and unit cell axes. The 'set unitcell' command is

similar to the commands 'set axes' and 'set boundbox' that display

orthogonal coordinate axes and the bounding box, respectively.

?vectps

?set vectps

Set VectPS

Syntax: set vectps <boolean>

The RasMol 'vectps' parameter is use to control the way in which the RasMol

'write' command generates vector PostScript output files. The command 'set

vectps on' enables the use of black outlines around spheres and cylinder

bonds producing "cartoon-like" high resolution output. However, the current

implementation of RasMol incorrectly cartoons spheres that are intersected

by more than one other sphere. Hence "ball and stick" models are rendered

correctly but not large spacefilling spheres models. Cartoon outlines can be

disabled, the default, by the command 'set vectps off'.

?set write

Set Write

Syntax: set write <boolean>

The RasMol 'write' parameter controls the use of the 'save' and 'write'

commands within scripts, but it may only be executed from the command line.

By default, this value is 'false', prohibiting the generation of files in

any scripts executed at start-up (such as those launched from a WWW

browser). However, animators may start up RasMol interactively: type 'set

write on' and then execute a script to generate each frame using the source

command.

?expression

?expressions

?atom expressions

Atom Expressions

RasMol atom expressions uniquely identify an arbitrary group of atoms within

a molecule. Atom expressions are composed of either primitive expressions,

(for more details type "help primitives"), predefined sets, (type "help

sets"), comparison operators, ("help comparisons"), 'within' expressions,

("help within") or logical (boolean) combinations of the above expression

types.

The logical operators allow complex queries to be constructed out of simpler

ones using the standard boolean connectives 'and', 'or' and 'not'. These may

be abbreviated by the symbols "&", "|" and "!", respectively. Parentheses

(brackets) may be used to alter the precedence of the operators. For

convenience, a comma may also be used for boolean disjunction.

The atom expression is evaluated for each atom, hence 'protein and backbone'

selects protein backbone atoms, not the protein and [nucleic] acid backbone

atoms!

Examples: backbone and not helix

within( 8.0, ser70 )

not (hydrogen or hetero)

not *.FE and hetero

8, 12, 16, 20-28

arg, his, lys

?examples

?example expressions

Example Expressions

The following table gives some useful examples of RasMol atom expressions.

For examples of the precise syntax, type "help expressions".

Expression Interpretation

* All atoms

cys Atoms in cysteines

hoh Atoms in heterogeneous water molecules

as? Atoms in either asparagine or aspartic acid

*120 Atoms at residue 120 of all chains

*p Atoms in chain P

*.n? Nitrogen atoms

cys.sg Sulphur atoms in cysteine residues

ser70.c? Carbon atoms in serine-70

hem*p.fe Iron atoms in the Heme groups of chain P

*.*;A All atoms in alternate conformation A

*/4 All atoms in model 4

?primitive

?primitives

?primitive expression

?primitive expressions

Primitive Expressions

RasMol primitive expressions are the fundamental building blocks of atom

expressions. There are two types of primitive expression. The first type is

used to identify a given residue number or range of residue numbers. A

single residue is identified by its number (position in the sequence), and a

range is specified by lower and upper bounds separated by a hyphen

character. For example 'select 5,6,7,8' is also 'select 5-8'. Note that this

selects the given residue numbers in all macromolecule chains.

The second type of primitive expression specifies a sequence of fields that

must match for a given atom. The first part specifies a residue (or group of

residues) and an optional second part specifies the atoms within those

residues. The first part consists of a residue name, optionally followed by

a residue number and/or chain identifier.

The second part consists of a period character followed by an atom name. An

atom name may be up to four alphabetic or numeric characters. An optional

semicolon followed by an alternate conformation identifier may be appended.

An optional slash followed by a model number may also be appended.

An asterisk may be used as a wild card for a whole field and a question mark

as a single character wildcard.

For examples of RasMol expressions type "help examples".

?comparison

?comparisons

?comparison expressions

?comparison operators

Comparison Operators

Parts of a molecule may also be distinguished using equality, inequality and

ordering operators on their properties. The format of such comparison

expression is a property name, followed by a comparison operator and then an

integer value.

The atom properties that may be used in RasMol are 'atomno' for the atom

serial number, 'elemno' for the atom's atomic number (element), 'resno' for

the residue number, 'radius' for the spacefill radius in RasMol units (or

zero if not represented as a sphere) and 'temperature' for the PDB isotropic

temperature value.

The equality operator is denoted either "=" or "==". The inequality operator

as either "<>", "!=" or "/=". The ordering operators are "<" for less than,

"<=" for less than or equal to, ">" for greater than, and ">" for greater

than or equal to.

Examples: resno < 23

temperature >= 900

atomno == 487

?within expressions

Within Expressions

A RasMol 'within' expression allows atoms to be selected on their proximity

to another set of atoms. A 'within' expression takes two parameters

separated by a comma and surrounded by parentheses. The first argument is an

integer value called the "cut-off" distance of the within expression and the

second argument is any valid atom expression. The cut-off distance is

expressed in either integer RasMol units or Angstroms containing a decimal

point. An atom is selected if it is within the cut-off distance of any of

the atoms defined by the second argument. This allows complex expressions to

be constructed containing nested 'within' expressions.

For example, the command 'select within(3.2,backbone)' selects any atom

within a 3.2 Angstrom radius of any atom in a protein or nucleic acid

backbone. 'Within' expressions are particularly useful for selecting the

atoms around an active site.

?sets

?predefined

?predefined sets

Predefined Sets

RasMol atom expressions may contain predefined sets. These sets are single

keywords that represent portions of a molecule of interest. Predefined sets

are often abbreviations of primitive atom expressions. In some cases the use

of predefined sets allows selection of areas of a molecule that could not

otherwise be distinguished. A list of the currently predefined sets is given

below. In addition to the sets listed here, RasMol also treats element names

(and their plurals) as predefined sets containing all atoms of that element

type, i.e. the command 'select oxygen' is equivalent to the command 'select

elemno=8'. Type "help sets setname" for more information about a given set.

at acidic acyclic aliphatic

alpha amino aromatic backbone

basic bonded buried cg

charged cyclic cystine helix

hetero hydrogen hydrophobic ions

large ligand medium neutral

nucleic polar protein purine

pyrimidine selected sheet sidechain

small solvent surface turn

water

?at

?sets at

?at set

AT Set

This set contains the atoms in the complementary nucleotides adenosine and

thymidine (A and T, respectively). All nucleotides are classified as either

the set 'at' or the set 'cg' This set is equivalent to the RasMol atom

expressions "a,t", and "nucleic and not cg".

?acidic

?sets acidic

?acidic set

Acidic Set

The set of acidic amino acids. These are the residue types Asp and Glu. All

amino acids are classified as either 'acidic', 'basic' 'or' 'neutral'. This

set is equivalent to the RasMol atom expressions "asp, glu" and "amino and

not (basic or neutral)".

?acyclic

?sets acyclic

?acyclic set

Acyclic Set

The set of atoms in amino acids not containing a cycle or ring. All amino

acids are classified as either 'cyclic' or 'acyclic'. This set is equivalent

to the RasMol atom expression "amino and not cyclic".

?aliphatic

?sets aliphatic

?aliphatic set

Aliphatic Set

This set contains the aliphatic amino acids. These are the amino acids Ala,

Gly, Ile, Leu and Val. This set is equivalent to the RasMol atom expression

"ala, gly, ile, leu, val".

?alpha

?alpha carbon

?alpha carbons

?sets alpha

?alpha set

Alpha Set

The set of alpha carbons in the protein molecule. This set is approximately

equivalent to the RasMol atom expression "*.CA". This command should not be

confused with the predefined set 'helix' which contains the atoms in the

amino acids of the protein's alpha helices.

?amino

?sets amino

?amino set

Amino Set

This set contains all the atoms contained in amino acid residues. This is

useful for distinguishing the protein from the nucleic acid and

heterogeneous atoms in the current molecule database.

?aromatic

?sets aromatic

?aromatic set

Aromatic Set

The set of atoms in amino acids containing aromatic rings. These are the

amino acids His, Phe, Trp and Tyr. Because they contain aromatic rings all

members of this set are member of the predefined set 'cyclic'. This set is

equivalent to the RasMol atom expressions "his, phe, trp, tyr" and "cyclic

and not pro".

?mainchain

?sets backbone

?sets mainchain

?backbone set

Backbone Set

This set contains the four atoms of each amino acid that form the

polypeptide N-C-C-O backbone of proteins, and the atoms of the sugar

phosphate backbone of nucleic acids. Use the RasMol predefined sets

'protein' and 'nucleic' to distinguish between the two forms of backbone.

Atoms in nucleic acids and proteins are either 'backbone' or 'sidechain'.

This set is equivalent to the RasMol expression "(protein or nucleic) and

not sidechain".

The predefined set 'mainchain' is synonymous with the set 'backbone'.

?basic

?sets basic

?basic set

Basic Set

The set of basic amino acids. These are the residue types Arg, His and Lys.

All amino acids are classified as either 'acidic', 'basic' or 'neutral'.

This set is equivalent to the RasMol atom expressions "arg, his, lys" and

"amino and not (acidic or neutral)".

?bonded

?sets bonded

?bonded set

Bonded Set

This set contain all the atoms in the current molecule database that are

bonded to at least one other atom.

?buried

?sets buried

?buried set

Buried Set

This set contains the atoms in those amino acids that tend (prefer) to be

buried inside protein, away from contact with solvent molecules. This set

refers to the amino acids preference and not the actual solvent

accessibility for the current protein. All amino acids are classified as

either 'surface' or 'buried'. This set is equivalent to the RasMol atom

expression "amino and not surface".

?cg

?sets cg

?cg set

CG Set

This set contains the atoms in the complementary nucleotides cytidine and

guanosine (C and G, respectively). All nucleotides are classified as either

the set 'at' or the set 'cg' This set is equivalent to the RasMol atom

expressions "c,g" and "nucleic and not at".

?charged

?sets charged

?charged set

Charged Set

This set contains the charged amino acids. These are the amino acids that

are either 'acidic' or 'basic'. Amino acids are classified as being either

'charged' or 'neutral'. This set is equivalent to the RasMol atom

expressions "acidic or basic" and "amino and not neutral".

?cyclic

?sets cyclic

?cyclic set

Cyclic Set

The set of atoms in amino acids containing a cycle or rings. All amino acids

are classified as either 'cyclic' or 'acyclic'. This set consists of the

amino acids His, Phe, Pro, Trp and Tyr. The members of the predefined set

'aromatic' are members of this set. The only cyclic but non-aromatic amino

acid is proline. This set is equivalent to the RasMol atom expressions "his,

phe, pro, trp, tyr" and "aromatic or pro" and "amino and not acyclic".

?cystine

?sets cystine

?cystine set

Cystine Set

This set contains the atoms of cysteine residues that form part of a

disulphide bridge, i.e. half cystines. RasMol automatically determines

disulphide bridges, if neither the predefined set 'cystine' nor the RasMol

'ssbonds' command have been used since the molecule was loaded. The set of

free cysteines may be determined using the RasMol atom expression "cys and

not cystine".

?helix

?helices

?alpha helix

?alpha helices

?sets helix

?sets helices

?helix set

Helix Set

This set contains all atoms that form part of a protein alpha helix as

determined by either the PDB file author or Kabsch and Sander's DSSP

algorithm. By default, RasMol uses the secondary structure determination

given in the PDB file if it exists. Otherwise, it uses the DSSP algorithm as

used by the RasMol 'structure' command.

This predefined set should not be confused with the predefined set 'alpha'

which contains the alpha carbon atoms of a protein.

?hetero

?sets hetero

?hetero set

Hetero Set

This set contains all the heterogeneous atoms in the molecule. These are the

atoms described by HETATM entries in the PDB file. These typically contain

water, cofactors and other solvents and ligands. All 'hetero' atoms are

classified as either 'ligand' or 'solvent' atoms. These heterogeneous

'solvent' atoms are further classified as either 'water' or 'ions'.

?hydrogen

?sets hydrogen

?hydrogen set

Hydrogen Set

This predefined set contains all the hydrogen, deuterium and tritium atoms

of the current molecule. This predefined set is equivalent to the RasMol

atom expression "elemno=1".

?hydrophobic

?sets hydrophobic

?hydrophobic set

Hydrophobic Set

This set contains all the hydrophobic amino acids. These are the amino acids

Ala, Leu, Val, Ile, Pro, Phe, Met and Trp. All amino acids are classified as

either 'hydrophobic' or 'polar'. This set is equivalent to the RasMol atom

expressions "ala, leu, val, ile, pro, phe, met, trp" and "amino and not

polar".

?ions

?sets ions

?ions set

Ions Set

This set contains all the heterogeneous phosphate and sulphate ions in the

current molecule data file. A large number of these ions are sometimes

associated with protein and nucleic acid structures determined by X-ray

crystallography. These atoms tend to clutter an image. All 'hetero' atoms

are classified as either 'ligand' or 'solvent' atoms. All 'solvent' atoms

are classified as either 'water' or 'ions'.

?large

?sets large

?large set

Large Set

All amino acids are classified as either 'small', 'medium' or 'large'. This

set is equivalent to the RasMol atom expression "amino and not (small or

medium)".

?ligand

?sets ligand

?ligand set

Ligand Set

This set contains all the heterogeneous cofactor and ligand moieties that

are contained in the current molecule data file. This set is defined to be

all 'hetero' atoms that are not 'solvent' atoms. Hence this set is

equivalent to the RasMol atom expression "hetero and not solvent".

?medium

?sets medium

?medium set

Medium Set

All amino acids are classified as either 'small', 'medium' or 'large'. This

set is equivalent to the RasMol atom expression "amino and not (large or

small)".

?neutral

?sets neutral

?neutral set

Neutral Set

The set of neutral amino acids. All amino acids are classified as either

'acidic', 'basic' or 'neutral'. This set is equivalent to the RasMol atom

expression "amino and not (acidic or basic)".

?nucleic

?sets nucleic

?nucleic set

Nucleic Set

The set of all atoms in nucleic acids, which consists of the four nucleotide

bases adenosine, cytidine, guanosine and thymidine (A, C, G and T,

respectively). All neucleotides are classified as either 'purine' or

'pyrimidine'. This set is equivalent to the RasMol atom expressions

"a,c,g,t" and "purine or pyrimidine". The symbols for RNA nucleotides (U,

+U, I, 1MA, 5MC, OMC, 1MG, 2MG, M2G, 7MG, OMG, YG, H2U, 5MU, and PSU) are

also recognized as members of this set.

?polar

?sets polar

?polar set

Polar Set

This set contains the polar amino acids. All amino acids are classified as

either 'hydrophobic' or 'polar'. This set is equivalent to the RasMol atom

expression "amino and not hydrophobic".

?protein

?sets protein

?protein set

Protein Set

The set of all atoms in proteins. This consists of the RasMol predefined set

'amino' and common post-translation modifications.

?purine

?sets purine

?purine set

Purine Set

The set of purine nucleotides. These are the bases adenosine and guanosine

(A and G, respectively). All nucleotides are either 'purines' or

'pyrimidines'. This set is equivalent to the RasMol atom expressions "a,g"

and "nucleic and not pyrimidine".

?pyrimidine

?sets pyrimidine

?pyrimidine set

Pyrimidine Set

The set of pyrimidine nucleotides. These are the bases cytidine and

thymidine (C and T, respectively). All nucleotides are either 'purines' or

'pyrimidines'. This set is equivalent to the RasMol atom expressions "c,t"

and "nucleic and not purine".

?selected

?sets selected

?selected set

Selected Set

This set contains the set of atoms in the currently selected region. The

currently selected region is defined by the preceding 'select' or 'restrict'

command and not the atom expression containing the 'selected' keyword.

?sheet

?sheets

?beta sheet

?beta sheets

?sets sheet

?sets sheets

?sheet set

Sheet Set

This set contains all atoms that form part of a protein beta sheet as

determined by either the PDB file author or Kabsch and Sander's DSSP

algorithm. By default, RasMol uses the secondary structure determination

given in the PDB file if it exists. Otherwise, it uses the DSSP algorithm as

used by the RasMol 'structure' command.

?sidechain

?sets sidechain

?sidechain set

Sidechain Set

This set contains the functional sidechains of any amino acids and the base

of each nucleotide. These are the atoms not part of the polypeptide N-C-C-O

backbone of proteins or the sugar phosphate backbone of nucleic acids. Use

the RasMol predefined sets 'protein' and 'nucleic' to distinguish between

the two forms of sidechain. Atoms in nucleic acids and proteins are either

'backbone' or 'sidechain'. This set is equivalent to the RasMol expression

"(protein or nucleic) and not backbone".

?small

?sets small

?small set

Small Set

All amino acids are classified as either 'small', 'medium' or 'large'. This

set is equivalent to the RasMol atom expression "amino and not (medium or

large)".

?solvent

?sets solvent

?solvent set

Solvent Set

This set contains the solvent atoms in the molecule coordinate file. These

are the heterogeneous water molecules, phosphate and sulphate ions. All

'hetero' atoms are classified as either 'ligand' or 'solvent' atoms. All

'solvent' atoms are classified as either 'water' or 'ions'. This set is

equivalent to the RasMol atom expressions "hetero and not ligand" and "water

or ions".

?surface

?sets surface

?surface set

Surface Set

This set contains the atoms in those amino acids that tend (prefer) to be on

the surface of proteins, in contact with solvent molecules. This set refers

to the amino acids preference and not the actual solvent accessibility for

the current protein. All amino acids are classified as either 'surface' or

'buried'. This set is equivalent to the RasMol atom expression "amino and

not buried".

?turn

?turns

?sets turn

?sets turns

?turn set

Turn Set

This set contains all atoms that form part of a protein turns as determined

by either the PDB file author or Kabsch and Sander's DSSP algorithm. By

default, RasMol uses the secondary structure determination given in the PDB

file if it exists. Otherwise, it uses the DSSP algorithm as used by the

RasMol 'structure' command.

?water

?waters

?sets water

?sets waters

?water set

Water Set

This set contains all the heterogeneous water molecules in the current

database. A large number of water molecules are sometimes associated with

protein and nucleic acid structures determined by X-ray crystallography.

These atoms tend to clutter an image. All 'hetero' atoms are classified as

either 'ligand' or 'solvent' atoms. The 'solvent' atoms are further

classified as either 'water' or 'ions'.

?set summary

Set Summary

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

acids.

Residues ALA ASN CYS GLN HIS LEU MET PRO THR TYR

ARG ASP GLU GLY ILE LYS PHE SER TRP VAL

A R N D C E Q G H I L K M F P S T W Y V

====================================================

Predefined

Set:

acidic * *

acyclic * * * * * * * * * * * * * * *

aliphatic * * * * *

aromatic * * * *

basic * * *

buried * * * * * * * *

charged * * * * *

cyclic * * * * *

hydrophobic * * * * * * * * * *

large * * * * * * * * * * *

medium * * * * * *

negative * *

neutral * * * * * * * * * * * * * * * *

polar * * * * * * * * * *

positive * * *

small * * *

surface * * * * * * * * * * * *

?colors

?colours

?color schemes

?colour schemes

?color names

?colour names

?predefined colors

?predefined colours

Colour Schemes

The RasMol 'colour' command allows different objects (such as atoms, bonds

and ribbon segments) to be given a specified colour. Typically this colour

is either a RasMol predefined colour name or an RGB triple. Additionally

RasMol also supports 'alt', 'amino', 'chain', 'charge', 'cpk', 'group',

'model', 'shapely', 'structure', 'temperature' or 'user' colour schemes for

atoms, and 'hbond type' colour scheme for hydrogen bonds and 'electrostatic

potential' colour scheme for dot surfaces. The 24 currently predefined

colour names are listed below with their corresponding RGB triplet.

Black [0,0,0] Orange [255,165,0]

Blue [0,0,255] Pink [255,101,117]

BlueTint [175,214,255] PinkTint [255,171,187]

Brown [175,117,89] Purple [160,32,240]

Cyan [0,255,255] Red [255,0,0]

Gold [255,156,0] RedOrange [255,69,0]

Grey [125,125,125] SeaGreen [0,250,109]

Green [0,255,0] SkyBlue [58,144,255]

GreenBlue [46,139,87] Violet [238,130,238]

GreenTint [152,255,179] White [255,255,255]

HotPink [255,0,101] Yellow [255,255,0]

Magenta [255,0,255] YellowTint [246,246,117]

If you frequently wish to use a colour not predefined, you can write a

one-line script. For example, if you make the file 'grey.col' containing the

line, 'colour [180,180,180] #grey', then the command 'script grey.col'

colours the currently selected atom set grey.

?alt

?color alt

?colour alt

?alt colours

?alternate

?alternate conformer

?alt colours

Alt Colours

The RasMol 'alt' (Alternate Conformer) colour scheme codes the base

structure with one colour and applies a limited number of colours to each

alternate conformer. In a RasMol built for 8-bit color systems, 4 colours

are allowed for alternate conformers. Otherwise, 8 colours are available.

?color amino

?colour amino

?amino colours

Amino Colours

The RasMol 'amino' colour scheme colours amino acids according to

traditional amino acid properties. The purpose of colouring is to identify

amino acids in an unusual or surprising environment. The outer parts of a

protein that are polar are visible (bright) colours and non-polar residues

darker. Most colours are hallowed by tradition. This colour scheme is

similar to the 'shapely' scheme.

ASP,GLU Bright Red [230,10,10] CYS,MET Yellow [230,230,0]

LYS,ARG Blue [20,90,255] SER,THR Orange [250,150,0]

PHE,TYR Mid Blue [50,50,170] ASN,GLN Cyan [0,220,220]

GLY Light Grey [235,235,235] LEU,VAL,ILE Green [15,130,15]

ALA Dark Grey [200,200,200] TRP Purple [180,90,180]

HIS Pale Blue [130,130,210] PRO Flesh [220,150,130]

Others Tan [190,160,110]

?chain

?color chain

?colour chain

?chain colours

Chain Colours

The RasMol 'chain' colour scheme assigns each macromolecular chain a unique

colour. This colour scheme is particularly useful for distinguishing the

parts of multimeric structure or the individual 'strands' of a DNA chain.

'Chain' can be selected from the RasMol 'Colours' menu.

?charge

?color charge

?colour temperature

?charge colours

Charge Colours

The RasMol 'charge' colour scheme colour codes each atom according to the

charge value stored in the input file (or beta factor field of PDB files).

High values are coloured in blue (positive) and lower values coloured in red

(negative). Rather than use a fixed scale this scheme determines the maximum

and minimum values of the charge/temperature field and interpolates from red

to blue appropriately. Hence, green cannot be assumed to be 'no net charge'

charge.

The difference between the 'charge' and 'temperature' colour schemes is that

increasing temperature values proceed from blue to red, whereas increasing

charge values go from red to blue.

If the charge/temperature field stores reasonable values it is possible to

use the RasMol 'colour dots potential' command to colour code a dot surface

(generated by the 'dots' command) by electrostatic potential.

?color cpk

?colour cpk

?cpk colours

CPK Colours

The RasMol 'cpk' colour scheme is based upon the colours of the popular

plastic spacefilling models which were developed by Corey, Pauling and later

improved by Kultun. This colour scheme colours 'atom' objects by the atom

(element) type. This is the scheme conventionally used by chemists. The

assignment of the most commonly used element types to colours is given

below.

Carbon light grey Chlorine green

Oxygen red Bromine, Zinc brown

Hydogen white Sodium blue

Nitrogen light blue Iron orange

Sulphur yellow Magnesium forest green

Phosphorous orange Calcium dark grey

Unknown deep pink

?group

?color group

?colour group

?group colours

Group Colours

The RasMol 'group' colour scheme colour codes residues by their position in

a macromolecular chain. Each chain is drawn as a smooth spectrum from blue

through green, yellow and orange to red. Hence the N terminus of proteins

and 5' terminus of nucleic acids are coloured red and the C terminus of

proteins and 3' terminus of nucleic acids are drawn in blue. If a chain has

a large number of heterogeneous molecules associated with it, the

macromolecule may not be drawn in the full 'range' of the spectrum. 'Group'

can be selected from the RasMol 'Colours' menu.

If a chain has a large number of heterogeneous molecules associated with it,

the macromolecule may not be drawn in the full range of the spectrum. When

RasMol performs group 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.

?model

?color model

?colour model

?modelcolours

?modelcolors

?model colors

?NMR

?NMR model

?nmr model colours

NMR Model Colours

The RasMol 'model' colour scheme codes each NMR model with a distinct

colour. The NMR model number is taken as a numeric value. High values are

coloured in blue and lower values coloured in red. Rather than use a fixed

scale this scheme determines the maximum value of the NMR model number and

interpolates from red to blue appropriately.

?shapely

?shapely colors

?shapely colours

Shapely Colours

The RasMol 'shapely' colour scheme colour codes residues by amino acid

property. This scheme is based upon Bob Fletterick's "Shapely Models". Each

amino acid and nucleic acid residue is given a unique colour. The 'shapely'

colour scheme is used by David Bacon's Raster3D program. This colour scheme

is similar to the 'amino' colour scheme.

ALA Medium Green [140,255,140] GLY White [255,255,255]

LEU Olive Green [ 69, 94, 69] SER Medium Orange [255,112, 66]

VAL Light Purple [255,140,255] THR Dark Orange [184, 76, 0]

LYS Royal Blue [ 71, 71,184] ASP Dark Rose [160, 0, 66]

ILE Dark Green [ 0, 76, 0] ASN Light Salmon [255,124,112]

GLU Dark Brown [102, 0, 0] PRO Dark Grey [ 82, 82, 82]

ARG Dark Blue [ 0, 0,124] PHE Olive Grey [ 83, 76, 66]

GLN Dark Salmon [255, 76, 76] TYR Medium Brown [140,112, 76]

HIS Medium Blue [112,112,255] CYS Medium Yellow [255,255,112]

MET Light Brown [184,160, 66] TRP Olive Brown [ 79, 70, 0]

ASX,GLX,PCA,HYP

Medium Purple [255, 0,255]

A Light Blue [160,160,255] C Light Orange [255,140, 75]

G Medium Salmon [255,112,112] T Light Green [160,255,160]

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

Default Medium Purple [255, 0,255]

?color structure

?colour structure

?structure colours

Structure Colours

The RasMol 'structure' colour scheme colours the molecule by protein

secondary structure. Alpha helices are coloured magenta, [240,0,128], beta

sheets are coloured yellow, [255,255,0], turns are coloured pale blue,

[96,128,255] and all other residues are coloured white. The secondary

structure is either read from the PDB file (HELIX, SHEET and TURN records),

if available, or determined using Kabsch and Sander's DSSP algorithm. The

RasMol 'structure' command may be used to force DSSP's structure assignment

to be used.

?temperature

?color temperature

?colour temperature

?temperature colours

Temperature Colours

The RasMol 'temperature' colour scheme colour codes each atom according to

the anisotropic temperature (beta) value stored in the PDB file. Typically

this gives a measure of the mobility/uncertainty of a given atom's position.

High values are coloured in warmer (red) colours and lower values in colder

(blue) colours. This feature is often used to associate a "scale" value

[such as amino acid variability in viral mutants] with each atom in a PDB

file, and colour the molecule appropriately.

The difference between the 'temperature' and 'charge' colour schemes is that

increasing temperature values proceed from blue to red, whereas increasing

charge values go from red to blue.

?user

?color user

?colour user

?user colours

User Colours

The RasMol 'user' colour scheme allows RasMol to use the colour scheme

stored in the PDB file. The colours for each atom are stored in COLO records

placed in the PDB data file. This convention was introduced by David Bacon's

Raster3D program.

?type

?color type

?colour type

?hbond type colours

HBond Type Colours

The RasMol 'type' colour scheme applies only to hydrogen bonds, hence is

used in the command 'colour hbonds type'. This scheme colour codes each

hydrogen bond according to the distance along a protein chain between

hydrogen bond donor and acceptor. This schematic representation was

introduced by Belhadj-Mostefa and Milner-White. This representation gives a

good insight into protein secondary structure (hbonds forming alpha helices

appear red, those forming sheets appear yellow and those forming turns

appear magenta).

Offset Colour Triple

+2 white [255,255,255]

+3 magenta [255,0,255]

+4 red [255,0,0]

+5 orange [255,165,0]

-3 cyan [0,255,255]

-4 green [0,255,0]

default yellow [255,255,0]

?potential

?electrostatic

?electrostatic potential

?potential colours

Potential Colours

The RasMol 'potential' colour scheme applies only to dot surfaces, hence is

used in the command 'colour dots potential'. This scheme colours each

currently displayed dot by the electrostatic potential at that point in

space. This potential is calculated using Coulomb's law taking the

temperature/charge field of the input file to be the charge assocated with

that atom. This is the same interpretation used by the 'colour charge'

command. Like the 'charge' colour scheme low values are blue/white and high

values are red. The table below shows the static assignment of colours using

a dielectric constant value of 10.

25 < V red [255,0,0]

10 < V < 25 orange [255,165,0]

3 < V < 10 yellow [255,255,0]

0 < V < 3 green [0,255,0]

-3 < V < 0 cyan [0,255,255]

-10 < V < 3 blue [0,0,255]

-25 < V < -10 purple [160,32,240]

V < -25 white [255,255,255]

?codes

?amino codes

?amino acid codes

Amino Acid Codes

The following table lists the names, single letter and three letter codes of

each of the amino acids.

Alanine A ALA Arginine R ARG

Asparagine N ASN Aspartic acid D ASP

Cysteine C CYS Glutamic acid E GLU

Glutamine Q GLN Glycine G GLY

Histidine H HIS Isoleucine I ILE

Leucine L LEU Lysine K LYS

Methionine M MET Phenylalanine F PHE

Proline P PRO Serine S SER

Threonine T THR Tryptophan W TRP

Tyrosine Y TYR Valine V VAL

?boolean expression

?boolean expressions

?booleans

Booleans

A boolean parameter is a truth value. Valid boolean values are 'true' and

'false', and their synonyms 'on' and 'off'. Boolean parameters are commonly

used by RasMol to either enable or disable a representation or option.

?file

?chfile

?fileformats

?file formats

File Formats

?protein data bank files

Protein Data Bank Files

If you do not have the PDB documentation, you may find the following summary

of the PDB file format useful. The Protein Data Bank is a computer-based

archival database for macromolecular structures. The database was

established in 1971 by Brookhaven National Laboratory, Upton, New York, as a

public domain repository for resolved crystallographic structures. The Bank

uses a uniform format to store atomic coordinates and partial bond

connectivities as derived from crystallographic studies. In 1999 the Protein

Data Bank moved to the Research Collaboratory for Structural Biology.

PDB file entries consist of records of 80 characters each. Using the punched

card analogy, columns 1 to 6 contain a record-type identifier, the columns 7

to 70 contain data. In older entries, columns 71 to 80 are normally blank,

but may contain sequence information added by library management programs.

In new entries conforming to the 1996 PDB format, there is other information

in those columns. The first four characters of the record identifier are

sufficient to identify the type of record uniquely, and the syntax of each

record is independent of the order of records within any entry for a

particular macromolecule.

The only record types that are of major interest to the RasMol program are

the ATOM and HETATM records which describe the position of each atom.

ATOM/HETATM records contain standard atom names and residue abbreviations,

along with sequence identifiers, coordinates in Angstrom units, occupancies

and thermal motion factors. The exact details are given below as a FORTRAN

format statement. The "fmt" column indicates use of the field in all PDB

formats, in the 1992 and earlier formats or in the 1996 and later formats.

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

Column Content fmt

1-6 'ATOM' or 'HETATM' all

7-11 Atom serial number (may have gaps) all

13-16 Atom name, in IUPAC standard format all

17 Alternate location indicator indicated by A, B or C all

18-20 Residue name, in IUPAC standard format all

23-26 Residue sequence number all

27 Code for insertions of residues (i.e. 66A & 66B) all

31-38 X coordinate all

39-46 Y coordinate all

47-54 Z coordinate all

55-60 Occupancy all

61-66 Temperature factor all

68-70 Footnote number 92

73-76 Segment Identifier (left-justified) 96

77-78 Element Symbol (right-justified) 96

79-80 Charge on the Atom 96

Residues occur in order starting from the N-terminal residue for proteins

and 5'-terminus for nucleic acids. If the residue sequence is known, certain

atom serial numbers may be omitted to allow for future insertion of any

missing atoms. Within each residue, atoms are ordered in a standard manner,

starting with the backbone (N-C-C-O for proteins) and proceeding in

increasing remoteness from the alpha carbon, along the side chain.

HETATM records are used to define post-translational modifications and

cofactors associated with the main molecule. TER records are interpreted as

breaks in the main molecule's backbone.

If present, RasMol also inspects HEADER, COMPND, HELIX, SHEET, TURN, CONECT,

CRYST1, SCALE, MODEL, ENDMDL, EXPDTA and END records. Information such as

the name, database code, revision date and classification of the molecule

are extracted from HEADER and COMPND records, initial secondary structure

assignments are taken from HELIX, SHEET and TURN records, and the end of the

file may be indicated by an END record.

?rasmol interpretation of pdb fields

RasMol Interpretation of PDB fields

Atoms located at 9999.000, 9999.000, 9999.000 are assumed to be Insight

pseudo atoms and are ignored by RasMol. Atom names beginning ' Q' are also

assumed to be pseudo atoms or position markers.

When a data file contains an NMR structure, multiple conformations may be

placed in a single PDB file delimited by pairs of MODEL and ENDMDL records.

RasMol displays all the NMR models contained in the file.

Residue names "CSH", "CYH" and "CSM" are considered pseudonyms for cysteine

"CYS". Residue names "WAT", "H20", "SOL" and "TIP" are considered pseudonyms

for water "HOH". The residue name "D20" is consider heavy water "DOD". The

residue name "SUL" is considered a sulphate ion "SO4". The residue name

"CPR" is considered to be cis-proline and is translated as "PRO". The

residue name "TRY" is considered a pseudonym for tryptophan "TRP".

RasMol uses the HETATM fields to define the sets hetero, water, solvent and

ligand. Any group with the name "HOH", "DOD", "SO4" or "PO4" (or aliased to

one of these names by the preceding rules) is considered a solvent and is

considered to be defined by a HETATM field.

RasMol only respects CONECT connectivity records in PDB files containing

fewer than 256 atoms. This is explained in more detail in the section on

determining molecule connectivity. CONECT records that define a bond more

than once are interpreted as specifying the bond order of that bond, i.e. a

bond specified twice is a double bond and a bond specified three (or more)

times is a triple bond. This is not a standard PDB feature.

?pdb colour scheme specification

PDB Colour Scheme Specification

RasMol also accepts the supplementary COLO record type in the PDB files.

This record format was introduced by David Bacon's Raster3D program for

specifying the colour scheme to be used when rendering the molecule. This

extension is not currently supported by the PDB. The COLO record has the

same basic record type as the ATOM and HETATM records described above.

Colours are assigned to atoms using a matching process. The Mask field is

used in the matching process as follows. First RasMol reads in and remembers

all the ATOM, HETATM and COLO records in input order. When the user-defined

('User') colour scheme is selected, RasMol goes through each remembered

ATOM/HETATM record in turn, and searches for a COLO record that matches in

all of columns 7 through 30. The first such COLO record to be found

determines the colour and radius of the atom.

Column Content

1-6 'COLOR' or 'COLOUR'

7-30 Mask (described below)

31-38 Red component

39-46 Green component

47-54 Blue component

55-60 Sphere radius in Angstroms

61-70 Comments

Note that the Red, Green and Blue components are in the same positions as

the X, Y, and Z components of an ATOM or HETA record, and the van der Waals

radius goes in the place of the Occupancy. The Red, Green and Blue

components must all be in the range 0 to 1.

In order that one COLO record can provide colour and radius specifications

for more than one atom (e.g. based on residue, atom type, or any other

criterion for which labels can be given somewhere in columns 7 through 30),

a 'don't-care' character, the hash mark "#" (number or sharp sign) is used.

This character, when found in a COLO record, matches any character in the

corresponding column in a ATOM/HETATM record. All other characters must

match identically to count as a match. As an extension to the specification,

any atom that fails to match a COLO record is displayed in white.

?multiple nmr models

Multiple NMR Models

RasMol loads all of the NMR models from a PDB file no matter which command

is used: 'load pdb <filename>' or 'load nmrpdb <filename>'

Once multiple NMR conformations have been loaded they may be manipulated

with the atom expression extensions described in 'Primitive Expressions'. In

particular, the command 'restrict */1' will restrict the display to the

first model only.

?cif and mmcif format files

CIF and mmCIF Format Files

CIF is the IUCr standard for presentation of small molecules and mmCIF is

intended as the replacement for the fixed-field PDB format for presentation

of macromolecular structures. RasMol can accept data sets in either format.

There are many useful sites on the World Wide Web where information tools

and software related to CIF, mmCIF and the PDB can be found. The following

are good starting points for exploration:

The International Union of Crystallography (IUCr) provides access to

software, dictionaries, policy statements and documentation relating to CIF

and mmCIF at: IUCr, Chester, England (www.iucr.org/iucr-top/cif/) with many

mirror sites.

The Nucleic Acid Database Project provides access to its entries, software

and documentation, with an mmCIF page giving access to the dictionary and

mmCIF software tools at Rutgers University, New Jersey, USA

(http://ndbserver.rutgers.edu/NDB/mmcif) with many mirror sites.

This version of RasMol restricts CIF or mmCIF tag values to essentially the

same conventions as are used for the fixed-field PDB format. Thus chain

identifiers and alternate conformation identifiers are limited to a single

character, atom names are limited to 4 characters, etc. RasMol interprets

the following CIF and mmCIF tags:

mmCIF tag CIF tag Used for

_struct_biol.details Info.classification

_database_2.database_code Info.identcode

_entry.id

_struct_biol.id

_struct.title Info.moleculename

_chemical_name_common

_chemical_name_systematic

_chemical_name_mineral

_symmetry.space_group_name_H-M

_symmetry_space_group_name_H-M

Info.spacegroup

_cell.length_a _cell_length_a Info.cell

_cell.length_b _cell_length_b

_cell.length_c _cell_length_c

_cell.angle_alpha _cell_angle_alpha

_cell.angle_beta _cell_angle_beta

_cell.angle_gamma _cell_angle_gamma

_atom_sites.fract_transf_matrix[1][1]

_atom_sites_fract_tran_matrix_11

Used to compute

orthogonal coords

... ...

_atom_sites.fract_transf_vector[1]

_atom_sites_fract_tran_vector_1

... ...

_atom_sites.cartn_transf_matrix[1][1]

_atom_sites_cartn_tran_matrix_11

Alternative to

compute orth. coords

... ...

_atom_sites.cartn_transf_vector[1]

_atom_sites_cartn_tran_vector_1

... ...

_atom_site.cartn_x _atom_site_cartn_x

atomic coordinates

... ...

_atom_site.fract_x _atom_site_fract_x

... ...

_struct_conn.id bonds

...

_geom_bond.atom_site_id_1

_geom_bond_atom_site_label_1

... ...

_struct_conf.id helices, sheets, turns

_struct_sheet_range.id

... ...

A search is made through multiple data blocks for the desired tags, so a

single dataset may be composed from multiple data blocks, but multiple data

sets may not be stacked in the same file.

?machine specific support

?chmacspec

Machine-Specific Support

In the following sections, support for 'Monochrome X-Windows', 'Tcl/Tk IPC',

'UNIX sockets based IPC', 'Compiling RasWin with Borland and MetroWerks' are

described.

?monochrome x windows support

?monochrome x-windows support

Monochrome X-Windows Support

RasMol supports the many monochrome UNIX workstations typically found in

academia, such as low-end SUN workstations and NCD X-terminals. The X11

version of RasMol (when compiled in 8 bit mode) now detects black and white

X-Windows displays and enables dithering automatically. The use of run-time

error diffusion dithering means that all display modes of RasMol are

available when in monochrome mode. For best results, users should experiment

with the set ambient command to ensure the maximum contrast in resulting

images.

?tcltk

?tcl/tk ipc support

Tcl/Tk IPC support

Version 4 of Tk graphics library changed the protocol used to communicate

between Tk applications. RasMol version 2.6 was modified such that it could

communicate with both this new protocol and the previous version 3 protocol

supported by RasMol v2.5. Although Tcl/Tk 3.x applications may only

communicate with other 3.x applications and Tcl/Tk 4.x applications with

other 4.x applications, these changes allow RasMol to communicate between

processes with both protocols (potentially concurrently).

?sockets

?ipc

?unix sockets based ipc

UNIX sockets based IPC

The UNIX implementation of RasMol supports BSD-style socket communication.

An identical socket mechanism is also being developed for VMS, Apple

Macintosh and Microsoft Windows systems. This should allow RasMol to

interactively display results of a computation on a remote host. The current

protocol acts as a TCP/IP server on port 21069 that executes command lines

until either the command 'exit' or the command 'quit' is typed. The command

exit from the RasMol server, the command 'quit' both disconnects the current

session and terminates RasMol. This functionality may be tested using the

UNIX command 'telnet <hostname> 21069'.

?borland

?metrowerks

?compiling raswin with borland and metrowerks

Compiling RasWin with Borland and MetroWerks

A number of changes were made to the source code in the transition from

version 2.5 to 2.6 to allow the Microsoft Windows version of RasMol to

compile using the Borland C/C++ compiler. These fixes include name changes

for the standard library and special code to avoid a bug in _fmemset.

Additional changes were made in the transition from 2.6 to 2.7 to allow

compilation with the MetroWerks compilers.

?bibliography

?chbib

Bibliography

?molecular graphics

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

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

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

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

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.