RasMol2 is a molecular graphics program intended for the visualisation of 
proteins, nucleic acids and small molecules. The program is aimed at 
teaching, display and generation of publication quality images. RasMol runs 
under Microsoft Windows and also UNIX and VMS systems with an 8bit or 24bit 
(32bit) 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 representations and colour schemes. Currently 
available molecule representations include depth-cued wireframes, 'Dreiding' 
sticks, spacefilling (CPK) spheres, ball and stick, biomolecular ribbon 
(either solid or strands) and dots. 

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".

Copyright (c) 1992-1996 by Roger Sayle (rasmol@ggr.co.uk)


?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      centre          colour
    dots            define          exit            hbonds
    help            load            quit            renumber
    reset           restrict        ribbons         rotate
    save            script          select          set
    show            slab            spacefill       strands
    structure       ssbonds         translate       wireframe
    write           zap             zoom


?backbone
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 determine the 
cylinder radius of the representation in 0.004 angstrom units. Backbone 
objects may be coloured using the RasMol `colour backbone' command. A 
parameter value of 500 (2 angstroms) or above results in an "Integer 
argument too large" error. 

The reserved work backbone is also used as a predefined set ("help sets") 
and as a parameter to the `set hbond' and `set ssbond' commands. 

?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. 

?center
?centre
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. 

?color
?colour
Colour
Syntax:  colour {<object>} <colour>
         color {<object>} <colour>

Colour the atoms (or other objects) of the selected zone. 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,' `dots,' `hbonds,' 
`ribbons' 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 `amino,' `cpk,' `chain,' `group,' `shapely,' 
`structure,' `temperature' and `user' and hydrogen bond objects can also be 
coloured by `type.' For more information type `help colour <colour>.' 

?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. 

?dots
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
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. 

?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. 

?load
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. 

?exit
?quit
Quit
Syntax:  quit
         exit

Exit from the RasMol program. 

?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 
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 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
Restrict
Syntax:  restrict {<expression>}

The RasMol `restrict' command both defines the currently active zone 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 zone. 
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-active 
zone. 

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 
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 `strands' which renders the biomolecular ribbon as parallel 
depth-cued curves. 

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

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

?save
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. This command should not be 
confused with the RasMol `write' command which generates either image or 
script files. 

?script
Script
Syntax:  script <filename>

The RasMol `script' command reads a set of commands sequentially from a text 
file and executes them. This allows sequences of commonly used commands to 
be stored and performed by a 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. 

?select
Select
Syntax:  select {<expression>}

Define the currently active zone of the molecule. All subsequent RasMol 
commands that manipulate a molecule or modify its colour or representation, 
only effects the currently selected zone. The parameter of a `select' 
command is a RasMol expression that is evaluated for every atom of the 
current molecule. The currently selected (active) zone of the molecule are 
those atoms that cause the expression to evaluate true. To select the whole 
molecule use the RasMol command `select all.' 

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, ommiting 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      bondmode
    boundbox        display         hbond           hetero
    hourglass       hydrogen        menus           mouse
    shadow          slabmode        specular        specpower
    ssbonds         strands         unitcell        vectps


?show
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
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. 

?spacefill
Spacefill
Syntax:  spacefill {<boolean>}
         spacefill temperature
         spacefill user
         spacefill <value>

Represent the currently selected zone as a spacefilling union of spheres 
model. An integer parameter may be used to specify the radius of each atom 
given in 4nm units. If no parameter is given, each atom is drawn as a sphere 
of its Van der Waals radius. 

The `temperature' option is used to set the radius of each selected sphere 
to the value in the temperature field of the molecule file. A zero or 
negative value causes no change in the selected atom. Temperature values 
greater than 2.00 are truncated to 2.00 Angstrom radius. 

The `user' option allows the radius of the selected spheres to be determined 
by matching each atom against optional lines in the input data file. Details 
of the wildcard pattern matching used by Raster3D's COLOR records is given 
in the manual. 

?ssbond
?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. 

?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 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
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 and ladders found. 

?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. Permited 
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. 

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

Represent each bond within the selected zone of the molecule as either a 
cylinder or depth-cued vector. If no parameter is given, RasMol draws each 
bond as a hither-and-yon shaded narrow vector. An integer parameter 
specifies the radius of a cylinder, given in 4nm units, to be used as a 
stick bond. 

?write
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) and "bmp" (Microsoft bitmap). 
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. 

This command should not be confused with the RasMol `save' command which 
save the currently selected portion of the molecule. 

?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 between 10 and 200 specifies the desired magnification as a 
percentage of the default scale. 

?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      bondmode
    boundbox        display         hbond           hetero
    hourglass       hydrogen        menus           mouse
    shadow          slabmode        specular        specpower
    ssbonds         strands         unitcell        vectps


?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 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. 

?axis
?axes
?set axis
?set axes
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
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. 

?bondmode
?set bondmode
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. 

?boundbox
?boundingbox
?bounding box
?set boundbox
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. 

?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). 

?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.' his parameter is similar to the RasMol `ssbonds' parameter. 

?set hetero
Set Hetero
Syntax:  set hetero <boolean>

set hetero 

?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' 
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. 

?hydrogen
?set hydrogen
Set Hydrogen
Syntax:  set hydrogen <boolean>

set hydrogen 

?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 as image as possible. 

?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' 
provide the same mouse bindings as other packages for experienced users. 

?set shadow
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
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". 

?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. 

?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 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
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
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
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
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' 

?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 bacbone atoms, not the protein and [nucleic] acid backbone 
atoms! 

Examples:    backbone and not helix
             within( 800, ser70 )
             not (hydrogen or hetero)
             not *.FE and hetero
             8, 12, 16, 20-28
             arg, his, lys


?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 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
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 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, `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 "=" 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 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 RasMol 0.004 Angstrom units. 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(800,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 sets
Predefined Sets
RasMol atom expressions may contain predefined sets. Thsese 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. 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 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 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 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 set
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
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
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
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
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" 

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

?buried set
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
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
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
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
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
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
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
Hydrogen Set
This predefined set contains all the hydrogen and deuterium atoms of the 
current molecule. 

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

?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 purine" 

?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 pyrimidine" 

?selected set
Selected Set
This set contains the set of atoms in the currently active zone. The 
currently active zone is defined by the preceding `select' or `restrict' 
command and not the atom expression containing the `selected' keyword. 

?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 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 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 set
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
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
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
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.' 

?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 `cpk,' `amino,' `chain,' `group,' `shapely,' 
`structure,' `temperature,' `user' and `hbond type' colour schemes. 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]


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


?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. 

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

?shapely
?shapely colors
?shapely colours
?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. 

?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 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
?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. 

?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]


?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
?booleans
?boolean expression
?boolean expressions
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. 

.
