APDL Eductation Resources/APDL Eductation Resources.iso/programs/misc/rasmol/!RasMol/HelpFile

Text File | 1996-03-03 | 70.3 KB | 1,691 lines

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, Acorn RISC OS, 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.

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) 1992-1995 by Roger Sayle ([e-mail])


?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          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


?trace
?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 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 ("help sets")
and as a parameter to the `set hbond' and `set ssbond' commands. The RasMol
command `trace' is synonymous with the command `backbone.'

?background
Background
Syntax:  background <colour>

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

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

?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.

?clipboard
Clipboard
Syntax:  clipboard

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

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

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

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

Allowed objects are `atoms,' `bonds,' `backbone,' `ribbons' `labels' `dots,'
`hbonds,' and `ssbonds.' If no object is specified, the default keyword
`atom' is assumed. Some colour schemes are defined for certain object types.
The colour scheme `none' can be applied 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 <colour>.'

?connect
Connect
Syntax:  connect {<boolean>}

The RasMol `connect' command is used to force RasMol to (re)calculate the
connectivity of the current molecule. If the original input file contained
connectivity information, this is discarded. The command `connect false'
uses 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
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.

?dot surface
?surface
?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.

?labels
?label
Label
Syntax:  label {<string>}
         label <boolean>

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

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

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

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

?expansion
?specifiers
?expansion specifiers
?label specifiers
Label Specifiers
Label specifiers are characters sequences that are embedded in the string
parameter passed to the RasMol `label' command. These specifiers are then
expanded as the labels are drawn to display properties associated with the
atom being labelled. The following table lists the current expansion
specifiers. The specifier '%%' is treated as an exception and is displayed
as a single `%' character.

    %a      Atom Name
    %b %t   B-factor/Temperature
    %c %s   Chain Identifier
    %e      Element Atomic Symbol
    %i      Atom Serial Number
    %n      Residue Name
    %r      Residue Number


?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. If the file specifies less bonds than atoms, RasMol
determines connectivity using the `connect' command.

?print
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.

?exit
?quit
Quit
Syntax:  quit
         exit

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

?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 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.

?ribbon
?ribbons
Ribbons
Syntax:  ribbons {<boolean>}
         ribbons <value>

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

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

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

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

?source
?scripts
?script
Script
Syntax:  script <filename>

The RasMol `script' command reads a set of RasMol commands sequentially from
a text file and executes them. This allows sequences of commonly used
commands to be stored and performed by single command. A RasMol script file
may contain a further script command up to a maximum "depth" of 10, allowing
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
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
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         fontsize        hbond
    hetero          hourglass       hydrogen        kinemage
    menus           mouse           radius          shadow
    slabmode        solvent         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. 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.

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

The RasMol `spacefill' command is used to represent all of the currently
selected atoms as solid spheres. This command is used to produce both
union-of-spheres and ball-and-stick models of a molecule. The command,
`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.

?ssbond
?bridges
?disulphide bridges
?ssbonds
SSBonds
Syntax:  ssbonds {<boolean>}
         ssbonds <value>

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

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

?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, strands and turns 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>

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
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
Zap
Syntax:  zap

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

?zoom
Zoom
Syntax:  zoom {<boolean>}
         zoom <value>

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

?parameters
?set parameters
?internal parameters
Internal Parameters
RasMol has a number of internal parameters that may be modified using the
`set' command. These parameters control a number of program options such as
rendering options and mouse button mappings.

A complete list of internal parameter names is given below. Type "help set
<parametername>" for more information on each option.

    ambient         axes            background      bondmode
    boundbox        display         fontsize        hbond
    hetero          hourglass       hydrogen        kinemage
    menus           mouse           radius          shadow
    slabmode        solvent         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.

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

?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.

?fontsize
?set fontsize
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.

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

The RasMol `hetero' parameter is used to modify the `default' behaviour of
the RasMol `select' command, i.e. the behaviour of `select' without any
parameters. When this value is `false,' the default `select' region does not
include 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.'

?hourglass
?set hourglass
Set HourGlass
Syntax:  set hourglass <boolean>

The RasMol `hourglass' parameter allows the user to enable and disable the
use of the `hour glass' cursor used by RasMol to indicate that the program
is currently busy drawing the next frame. The command `set hourglass on'
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>

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.'

?mage
?kinemage
?set kinemage
Set Kinemage
Syntax:  set kinemage <boolean>

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

?set menus
Set Menus
Syntax:  set menus <boolean>

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

?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.

?radius
?set radius
Set Radius
Syntax:  set radius {<value>}

The RasMol `set radius' command is used to alter the behaviour of the RasMol
`dots' command depending upon the value of the `solvent' parameter. When
`solvent' is `true,' the `radius' parameter controls whether a true Van der
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.

?shadow
?shadows
?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.

?slabmode
?set slab
?set slabmode
Set SlabMode
Syntax:  set slabmode <slabmode>

The RasMol `slabmode' parameter controls the rendering method of objects cut
by the slabbing (z-clipping) plane. Valid slabmode parameters are "reject",
"half", "hollow", "solid" and "section".

?solvent
?set solvent
Set Solvent
Syntax:  set solvent <boolean>

The RasMol `set solvent' command is used to control the behaviour of the
RasMol `dots' command. Depending upon the value of the `solvent' parameter,
the `dots' command either generates a Van der 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).

?specular
?set specular
Set Specular
Syntax:  set specular <boolean>

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

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

?specpower
?set specpower
Set SpecPower
Syntax:  set specpower {<value>}

The `specpower' parameter determines the shininess of solid objects rendered
by RasMol. This value between 0 and 100 adjusts the reflection 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.

?unitcell
?unit cell
?set unitcell
Set UnitCell
Syntax:  set unitcell <boolean>

The RasMol `unitcell' parameter controls the display of the crystallographic
unit cell on the current display. The crystal cell is only enabled if the
appropriate crystal symmetry information is contained in the PDB 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.

?vectps
?set vectps
Set VectPS
Syntax:  set vectps <boolean>

The RasMol `vectps' parameter is use to control the way in which the RasMol
`write' command generates vector PostScript output files. The command `set
vectps on' enables 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( 8.0, ser70 )
             not (hydrogen or hetero)
             not *.FE and hetero
             8, 12, 16, 20-28
             arg, his, lys


?examples
?example expressions
Example Expressions
The following table gives some useful examples of RasMol atom expressions.
For examples of the precise syntax, type "help expressions".

    Expression      Interpretation

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

The second type of primitive expression specifies a sequence of fields that
must match for a given atom. The first part specifies a residue (or group of
residues) and an optional second part specifies the atoms within those
residues. The first part consists of a residue name, optionally followed by
a residue number and/or chain identifier. The second part consists of a
period character followed by an atom name. An asterisk may be used as a wild
card for a whole field and a question mark as a single character wildcard.

For examples of RasMol expressions type "help examples".

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

The atom properties that may be used in RasMol are `atomno' for the atom
serial number, `elemno' for the atom's atomic number (element), `resno' for
the residue number, `radius' for the spacefill radius in RasMol units (or
zero if not represented as a sphere) and `temperature' for the PDB
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 either integer RasMol units or Angstroms containing a decimal
point. An atom is selected if it is within the cut-off distance of any of
the atoms defined by the second argument. This allows complex expressions to
be constructed containing nested `within' expressions.

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

?sets
?predefined
?predefined sets
Predefined Sets
RasMol atom expressions may contain predefined sets. These sets are single
keywords that represent portions of a molecule of interest. Predefined sets
are often abbreviations 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.' 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
?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
?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
?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
?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
?alpha carbon
?alpha carbons
?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
?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
?aromatic set
Aromatic Set
The set of atoms in amino acids containing aromatic rings. These are the
amino acids His, Phe, Trp and Tyr. Because they contain aromatic rings all
members of this set are member of the predefined set `cyclic.' This set is
equivalent to the RasMol atom expressions "his, phe, trp, tyr" and "cyclic
and not pro"

?mainchain
?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"

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

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

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

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

?helix
?helices
?alpha helix
?alpha helices
?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. This predefined set is equivalent to the RasMol atom
expression "elemno=1"

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

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

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

?water
?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,' `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]


?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.

?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.

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

The difference between the `charge' and `temperature' colour schemes is that
increasing temperature values proceed from blue to red, whereas increasing
charge 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
?color user
?colour user
?user colours
User Colours
The RasMol `user' colour scheme allows RasMol to use the colour scheme
stored in the PDB file. The colours for each atom are stored in COLO records
placed in the PDB data file. This convention was introduced by David Bacon's
Raster3D program.

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

      Offset    Colour    Triple
        +2      white     [255,255,255]
        +3      magenta   [255,0,255]
        +4      red       [255,0,0]
        +5      orange    [255,165,0]
        -3      cyan      [0,255,255]
        -4      green     [0,255,0]
      default   yellow    [255,255,0]


?potential
?electrostatic
?electrostatic potential
?potential colours
Potential Colours
The RasMol `potential' colour scheme applies only to dot surfaces, hence is
used in the command "colour dots potential" This scheme colours each
currently displayed dot by the electrostatic potential at that point in
space. This potential is calculated using Coulomb's law taking the
temperature/charge field of the input file to be the charge assocated with
that atom. This is the same interpretation used by the `colour charge'
command. Like the `charge' colour scheme low values are blue/white and high
values are red. The table below shows the static assignment of colours using
a dielectric constant value of 10.

     25 < V          red       [255,0,0]
     10 < V <  25    orange    [255,165,0]
      3 < V <  10    yellow    [255,255,0]
      0 < V <   3    green     [0,255,0]
     -3 < V <   0    cyan      [0,255,255]
    -10 < V <   3    blue      [0,0,255]
    -25 < V < -10    purple    [160,32,240]
          V < -25    white     [255,255,255]


?codes
?amino codes
?amino acid codes
Amino Acid Codes
The following table lists the names, single letter and three letter codes of
each of the amino acids.

    Alanine         A  ALA         Arginine        R  ARG
    Asparagine      N  ASN         Aspartic acid   D  ASP
    Cysteine        C  CYS         Glutamic acid   E  GLU
    Glutamine       Q  GLN         Glycine         G  GLY
    Histidine       H  HIS         Isoleucine      I  ILE
    Leucine         L  LEU         Lysine          K  LYS
    Methionine      M  MET         Phenylalanine   F  PHE
    Proline         P  PRO         Serine          S  SER
    Threonine       T  THR         Tryptophan      W  TRP
    Tyrosine        Y  TYR         Valine          V  VAL


?boolean
?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.