RasMol V2.6 Molecular Visualisation Program

# RasMol V2.6

## Molecular Visualisation Program

### Roger Sayle

### Glaxo Wellcome Research and Development

### Stevenage, Hertfordshire, U.K.

## Table of Contents

1. Introduction
2. Command Reference
3. Internal Parameters
4. Atom Expressions
5. Predefined Sets
6. Colour Schemes

<p><p>Copyright (c) 1992-1995 by Roger Sayle <address>rasmol@ggr.co.uk</address>

The information supplied in this document is believed to be true but no liability is assumed for its use or for the infringements of the rights of the others resulting from its use.

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, bancruptcy or outbreak of war.

## Introduction

RasMol2 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 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 co-ordinate 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.

## Command Reference

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

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

        Backbone        Background      Centre
        Clipboard       Colour          Connect
        CPK             Dots            Define
        Echo            Exit            HBonds
        Help            Label           Load
        Print           Quit            Renumber
        Reset           Restrict        Ribbons
        Rotate          Save            Script
        Select          Set             Show
        Slab            Source          Spacefill
        SSBonds         Strands         Structure
        Trace           Translate       Wireframe
        Write           Zap             Zoom

### Backbone

    Syntax:  backbone {<boolean>}
             backbone <value>

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 paramater the same as 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 work `backbone` is also used as a predefined set and as a parameter to the `set hbond` and `set ssbond` commands. The RasMol command `trace` is synonymous with the command `backbone.`

### 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.

### Centre

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

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.

### 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.

### 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 all objects accept 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 `cpk,` `amino,` `chain,` `group,` `shapely,` `structure,` `temperature` `charge` and `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 .`

### 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 an extremely fast heuristic algorithmm that is suitable for determing 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 for 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 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

    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.

### Dots

    Syntax:  dots {<boolean>}
             dots <value>

The RasMol `dots` command is used to generate a Van der Waal's 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 Waal's 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 it's 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

    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.

### 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

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

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

### 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 (similar to C's printf syntax). 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. RasMol uses the label "%n%r:%c.%a" if the molecule contains more than one chain, "%e%i" if the molecule has only a single residue (a small molecule) and "%n%r.%a" otherwise.

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 of the displayed text may be changed using the `set fontsize` command.

The following table lists the current expansion specifiers:

        %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

### Load

    Syntax:  load {<format>} <filename>

Load a molecule co-ordinate file into RasMol2. Valid molecule file formats are `pdb` (Brookhaven Protein Databank), `mdl` (Molecular Design Limited's MOL file format), `alchemy` (Tripos' Alchemy file format), `mol2` (Tripos' Sybyl Mol2 file format), `charmm` (CHARMm file format) or `xyz` (MSC's XMol XYZ file format). If no file format is specified, `pdb` is assumed by default. Only a single molecule may be loaded at a time. To delete a molecule prior to loading another use the RasMol `zap` command.

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

### 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, allowing images to be printed directly on a dot matrix printer.

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

### Quit

    Syntax:  quit
             exit

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

### 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 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

    Syntax:  reset

The RasMol `reset` command restores the original viewing transformation and centre of rotation. The scale is set to it 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

    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 effect only the currently selected region. The parameter of a `restrict` command is a RasMol atom expression that is evaluated for every atom of the current molecule. This command is very similar to the RasMol `select` command, except restrict disables the `wireframe,` `spacefill` and `backbone` representations in the non-selected region.

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

### Ribbons

    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

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

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

### Save

    Syntax:  save {pdb} <filename>
             save alchemy <filename>

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

### Script

    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 compilicated 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

    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 effects 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

    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, ommiting the paramter option resets that parameter to its default value. A list of valid parameter names is given below.

        Ambient         Axes            Background
        BondMode        BoundBox        Display
        FontSize        HBonds          Hetero
        HourGlass       Hydrogen        Kinemage
        Menus           Mouse           Radius
        Shadow          SlabMode        Solvent
        Specular        SpecPower       SSBonds
        Strands         UnitCell        VectPS

### Show

    Syntax:  show information
             show sequence
             show symmetry

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 sequence` lists the residues that compose each chain of the molecule.

### 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. 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.

### 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, `spacefilll 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 causes have no effect and values greater than 2.0 are truncated to 2. The `user` option allows the radius of each spheres to be specified by additional lines in the molecule's PDB file using Raster 3D's COLOR record extension.

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

### 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.

### 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 colour of 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

    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 and SHEET) these are discarded. Initially, the hydrogen bonds of the current molecule are found, if this hasn't been done already. The secondary structure is the determined using Kabsch and Sander's DSSP algorithm. Once finished the program reports the number of helices, strands and turns found.

### 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. Permited values for the axis parameter are "<tt><b>x</b></tt>", "<tt><b>y</b></tt>" and "<tt><b>z</b></tt>". Displacement values must be between -100 and 100 which correspond to moving the current molecule just off the screen. A positive "<tt><b>x</b></tt>" displacement moves the molecule to the right, and a positive "<tt><b>y</b></tt>" displacement moves the molecule down the screen. The pair of commands `translate x 0` and `translate y 0` centres the molecule on the screen.

### Wireframe

    Syntax:  wireframe {<boolean>}
             wireframe <value>

The RasMol `wireframe` command represents each bond within the selected region of the molecule as either a cylinder, a line or 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.

### Write

    Syntax:  write {<format>} <filename>

Write the current image to a file in a standard raster format. Currently supported image file formats include "`gif`" (Compuserve GIF), "`ppm`" (Portable Pixmap), "`ras`" (Sun rasterfile), "`ps`" and "`epsf`" (Encapsulated PostScript), "`monops`" (Monochrome Encapsulated PostScript), "`bmp`" (Microsoft bitmap) and "`pict`" (Apple PICT). 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 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

    Syntax:  zap

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

### 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.

## 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.

        Ambient         Axes            Background
        BondMode        BoundBox        Display
        FontSize        HBonds          Hetero
        HourGlass       Hydrogen        Kinemage
        Menus           Mouse           Radius
        Shadow          SlabMode        Solvent
        Specular        SpecPower       SSBonds
        Strands         UnitCell        VectPS

### 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 that controls the percentage intensity of the darkest shade of an object. For a solid object, this is the intensity of surfaces facing away from the light source or in shadow. For depth-cued objects this is the intensity of objects furthest from the viewer.

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

### Set Axes

    Syntax:  set axes <boolean>

The RasMol `axes` parameter controls the display of orthogonal co-ordinate axes on the current display. The co-ordinate 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 the the commands `set boundbox` and `set unitcell` that display the bounding box and the crystallographic unit cell respectively.

### 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.`

### Set BondMode

    Syntax:  set bondmode and
             set bondmode or

The RasMol `set bondmode` command controls the mechanism used to select individual bonds. 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.

### Set BoundBox

    Syntax:  set boundbox <boolean>

The RasMol `boundbox` parameter controls the display of the current molecules bounding box on the display. The bounding box is orthogonal to the data file's original co-ordinate axes. The `set boundbox` command is similar the the commands `set axes` and `set unitcell` that display orthogonal co-ordinate axes and the bounding box respectively.

### 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).

### 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.` his parameter is similar to the RasMol `ssbonds` parameter.

### Set FontSize

    Syntax:  set fontsize {<value>}

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 32 pixels, and the default value is 8 pixels high. 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 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 an heterogenous atoms (refer to the predefined set `hetero` ). When this value is `true,` the default `select` region may contain hetero atoms. This parameter is similar to the RasMol `hydrogen` parameter which determines whether hydrogen atoms should be included in the default set. If both `hetero` and `hydrogen` are `true,` `select` without any parameters is equivalent to `select all.`

### Set HourGlass

    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` enable the indicator, whilst `set hourglass off` prevents RasMol from changing the cursor. This is useful when spinning the molecule, running a sequence of commands from a script file or using interprocess communication to execute complex sequences of commands. In these cases a `flashing' cursor may be distracting.

### Set Hydrogen

    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 or deuterium 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 heterogenous atoms should be included in the default set. If both `hydrogen` and `hetero` are `true,` `select` without any parameters is equivalent to `select all.`

### Set Kinemage

    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 co-ordinate axes, bounding box and crystal unit cell.

### 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 as image as possible when using Microsoft Windows.

### 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` provide the same mouse bindings as other packages for experienced users.

### 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 Waal's 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 it true VdW value. When the value of `solvent` is `true,` this parameter determines the `probe sphere' (solvent) radius. The parameter may be given as an integer in rasmol units or containing a decimal point in Angstroms. The default value of this parameter is determined by the value of `solvent` and changing `solvent` resets `radius` to its new default value.

### Set Shadow

    Syntax:  set shadow <boolean>

The RasMol `set shadow` command enables and disables raytracing 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.` Raytracing typically takes about 10s for a moderately sized protein. It is recommended that shadowing is normally disabled whilst the molecule is being transformed or manipulated, and only enabled once an appropiate viewpoint is selected, to provide a greater impression of depth.

### Set SlabMode

    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 "<tt><b>reject</b></tt>", "<tt><b>half</b></tt>", "<tt><b>hollow</b></tt>", "<tt><b>solid</b></tt>" and "<tt><b>section</b></tt>".

### 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 Waal's or a solvent acessible 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 Waal's surface should be generated and resets the value of `radius` to zero. The command `set solvent true` indicates that a `Connolly' or `Richards' solvent accessible surface should be drawn and sets the `radius` parameter, the solvent radius, to 1.2 Angstroms (or 300 RasMol units).

### Set Specular

    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.

### 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 coeffient 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

    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.` his parameter is similar to the RasMol `hbonds` parameter.

### 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 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 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 the the commands `set axes` and `set boundbox` that display orthogonal co-ordinate axes and the bounding box respectively.

### 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 to 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 by not large spacefilling spheres models. Cartoon outlines can be disabled, the default, by the command `set vectps off`

## Atom Expressions

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

The logical operators allow complex queries to be constructed out of simpler ones using the standard boolean connectives `and, or` and `not.` These may be abbreviated by the symbols "<tt>&amp;</tt>", "<tt>|</tt>" and "<tt>!</tt>" 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 bacbone 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

- Primitive Expressions
- Predefined Sets
- Comparison Operators
- `Within` Expressions

- Examples

### Example Expressions

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

        Expression      Interpretation

        *               All atoms
        cys             Atoms in cysteines
        hoh             Atoms in heterogenous 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

### 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.

A residue name typically consists of up to three alphabetic characters, which are case insensitive. Hence the primitive expressions `SER` and `ser` are equivalent, identifying all serine residues. Residue names that contain non-alphabetic characters, such as sulphate groups, may be delimited using square brackets, i.e. `[SO4]`

The residue number is the residue's position in the macromolecule sequence. Negative sequence numbers are permited. For example, `SER70` Care must be taken when specifying both residue name and number, it the group at the specified position isn't the specified residue no atoms are selected.

The chain identifier is typically a single case-insensitive alphabetic or numeric character. Numeric chain identifiers must be distinguished or separated from residue numbers by a colon character. For example, `SER70A` or `SER70:1`

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

### Comparison Operators

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

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

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

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

### 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 parenthesis. The first argument is an integer value called the "cut-off" distance of the within expression and the second argument is any valid atom expression. The cut-off distance is expressed in either integer RasMol units or Angstroms containing a decimal point. An atom is selected if it is within the cut-off distance of any of the atoms defined by the second argument. This allows complex expressions to be constructed containing nested `within` expressions.

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

### Predefined Sets

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

        AT              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 Set

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

### Acidic Set

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

### Acyclic Set

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

### Aliphatic Set

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

### Alpha Set

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

### Amino Set

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

### Aromatic Set

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

### Backbone Set

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

The predefined set `mainchain` is synonymous with the set `backbone.`

### Basic Set

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

### Bonded Set

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

### Buried Set

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

### CG Set

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

### Charged Set

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

### Cyclic Set

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

### Cystine Set

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

### Helix Set

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

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

### Hetero Set

This set contains all the heterogenous 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 heterogenous `solvent` atoms are further classified as either `water` or `ions.`

### Hydrogen Set

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

### Hydrophobic Set

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

### Ions Set

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

### Large Set

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

### Ligand Set

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

### Medium Set

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

### Neutral Set

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

### Nucleic Set

The set of all atoms in nucleic acids, which consists of the four nucleotide bases adenosine, cytidine, guanosine and thymidine (A, C, G and T respectively). All neucleotides are classified as either `purine` or `pyrimidine.` This set is equivalent to the RasMol atom expressions "`a,c,g,t`" and "`purine or pyrimidine`"

### Polar Set

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

### Protein Set

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

### Purine Set

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

### 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 pyrimidine`"

### Selected Set

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

### Sheet Set

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

### Sidechain Set

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

### Small Set

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

### Solvent Set

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

### Surface Set

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

### Turn Set

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

### Water Set

This set contains all the heterogenous 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.`

## 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 `cpk,` `amino,` `chain,` `group,` `shapely,` `structure,` `temperature,` `charge` and `user` colour schemes for atoms, a `hbond type` colour scheme for hydrogen bonds and `electrostatic potential` colour scheme for dot surfaces. The currently predefined colour names are listed below with their corresponding RGB triplet.

        blue         [0,0,255]          black        [0,0,0]
        cyan         [0,255,255]        green        [0,255,0]
        greenblue    [46,139,87]        magenta      [255,0,255]
        orange       [255,165,0]        purple       [160,32,240]
        red          [255,0,0]          redorange    [255,69,0]
        violet       [238,130,238]      white        [255,255,255]
        yellow       [255,255,0]

### 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         pink   [180,90,180]
       HIS     pale blue  [130,130,210]   PRO         flesh  [220,150,130]

### 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.

### 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 colour `atom' objects by the atom (element) type. This is the scheme conventionally used by chemists. The assignment of element type to colours is given below.

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

### 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 heterogenous molecules associated with it, the macromolecule may not be drawn in the full `range' of the spectrum.

### Shapely Colours

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

### Structure Colours

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

### Temperature Colours

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

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

### 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 valuse 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.

### User Colours

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

### HBond Type Colours

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

          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 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]