RASMOL(1) UNIX System V (October 1994) RASMOL(1)
NAME
rasmol - Molecular Graphics Visualisation Tool v2.5
SYNOPSIS
rasmol [-nodiplay] [[-format ] filename] [-script
scriptfile]
FORMATS
-pdb Brookhaven Protein Databank
-mdl MDL's MOL File Format
-mol2 Tripos' Sybyl MOL2 Format
-xyz MSC's XYZ (XMol) Format
-alchemy Alchemy File Format
-charmm CHARMm File Format
DESCRIPTION
RasMol2 is a molecular graphics program intended for the
visualisation of proteins, nucleic acids and small
molecules. The program is aimed at display, teaching and
generation of publication quality images. RasMol runs on
Microsoft Windows, Apple Macintosh, UNIX and VMS systems.
The UNIX and VMS systems require an 8, 24 or 32 bit colour X
Windows display (X11R4 or later). The program reads in a
molecule co-ordinate file and interactively displays the
molecule on the screen in a variety of colour schemes and
molecule representations. Currently available
representations include depth-cued wireframes, 'Dreiding'
sticks, spacefilling (CPK) spheres, ball and stick, solid
and strand biomolecular ribbons, atom labels and dot
surfaces.
COMMANDS
RasMol allows the execution of interactive commands typed at
the RasMol> prompt in the terminal window. Each command must
be given on a separate line. Keywords are case insensitive
and may be entered in either upper or lower case letters.
All whitespace characters are ignored except to separate
keywords and their arguments.
The commands/keywords currently recognised by RasMol are
given below.
Backbone
The RasMol backbone command permits the representation
of a polypeptide backbone as a series of bonds
connecting the adjacent alpha carbons of each amino
acid in a chain. The display of these backbone `bonds'
is turned on and off by the command paramater the same
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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.
Background
The RasMol background command is used to set the colour
of the "canvas" background. The colour may be given as
either a colour name or a comma separated triple of
Red, Green and Blue (RGB) components enclosed in square
brackets. Typing the command help colours will give a
list of the predefined colour names recognised by
RasMol. When running under X Windows, RasMol also
recognises colours in the X server's colour name
database.
The background command is synonymous with the RasMol
set background command.
Centre
The RasMol centre command defines the point about which
the rotate command and the scroll bars rotate the
current molecule. Without a parameter the centre
command resets the centre of rotation to be the centre
of gravity of the molecule. If an atom expression is
specified, RasMol rotates the molecule about the centre
of gravity of the set of atoms specified by the
expression. Hence, if a single atom is specified by the
expression, that atom will remain `stationary' during
rotations.
Type help expression for more information on RasMol
atom expressions.
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
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program using the RasMol write command.
Colour
Colour the atoms (or other objects) of the selected
region. The colour may be given as either a colour name
or a comma separated triple of Red, Green and Blue
(RGB) components enclosed in square brackets. Typing
the command help colours will give a list of all the
predefined colour names recognised by RasMol.
Allowed objects are atoms, bonds, backbone, ribbons
labels dots, hbonds, and ssbonds. If no object is
specified, the default keyword atom is assumed. Some
colour schemes are defined for certain object types.
The colour scheme none can be applied 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 type and
dot surfaces can also be coloured by electrostatic
potential. For more information type help colour
<colour>.
Connect
The RasMol connect command is used to force RasMol to
(re)calculate the connectivity of the current molecule.
If the original input file contained connectivity
information, this is discarded. The command connect
false uses 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
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
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contents of the set do not change, even if the
expression defining them depends on the current
transformation and representation of the molecule.
Dots 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 The RasMol echo command is used to display a message in
the RasMol command/terminal window. The string
parameter may optionally be delimited in double quote
characters. If no parameter is specified, the echo
command displays a blank line. This command is
particularly useful for displaying text from within a
RasMol script file.
HBonds
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
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accepting oxygen and the donating nitrogen. By using
the set hbonds command the alpha carbon positions of
the appropriate residues may be used instead. This is
especially useful when examining proteins in backbone
representation.
Help The RasMol help command provides on-line help on the
given topic.
Label
The RasMol label command allows an arbitrary formatted
text string to be associated with each currently
selected atom. This string may contain embedded
`expansion specifiers' which display properties of the
atom being labelled. An expansion specifier consists of
a `%' character followed by a single alphabetic
character specifying the property to be displayed. An
actual '%' character may be displayed by using the
expansion specifier `%%'.
Atom labelling for the currently selected atoms may be
turned off with the command label off. By default, if
no string is given as a parameter RasMol uses labels
appropriate for the current molecule.
The colour of each label may be changed using the
colour label command. By default, each label is drawn
in the same colour as the atom to which it is attached.
The size of the displayed text may be changed using the
set fontsize command.
Load 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.
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Print
The RasMol print command sends the currently displayed
image to the local default printer using the operating
system's native printer driver. Note: this command is
not yet supported under UNIX or VMS. It is intended to
take advantage of Microsoft Windows and Apple Macintosh
printer drivers. For example, allowing images to be
printed directly on a dot matrix printer.
When using RasMol on a UNIX or VMS system this
functionality may be achieved by either generating a
PostScript file using the RasMol write ps or write
vectps commands and printing that or generating a
raster image file and using a utility to dump that to
the local printer.
Quit Exit from the RasMol program. The RasMol commands exit
and quit are synonymous.
Renumber
The RasMol renumber command sequentially numbers the
residues in a macromolecular chain. The optional
parameter specifies the value of the first residue in
the sequence. By default, this value is one. For
proteins, each amino acid is numbered consecutively
from the N terminus to the C terminus. For nucleic
acids, each base is numbered from the 5' terminus to 3'
terminus. All chains in the current database are
renumbered and gaps in the original sequence are
ignored. The starting value for numbering may be
negative.
Reset
The RasMol reset command restores the original viewing
transformation and centre of rotation. The scale is set
to 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
The RasMol restrict command both defines the currently
selected region of the molecule and disables the
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representation of (most of) those parts of the molecule
no longer selected. All subsequent RasMol commands
that modify a molecule's colour or representation
effect only the currently selected region. The
parameter of a restrict command is a RasMol atom
expression that is evaluated for every atom of the
current molecule. This command is very similar to the
RasMol select command, except restrict disables the
wireframe, spacefill and backbone representations in
the non-selected region.
Type "help expression" for more information on RasMol
atom expressions.
Ribbons
The RasMol ribbons command displays the currently
loaded protein or nucleic acid as a smooth solid
"ribbon" surface passing along the backbone of the
protein. The ribbon is drawn between each amino acid
whose alpha carbon is currently selected. The colour of
the ribbon is changed by the RasMol colour ribbon
command. If the current ribbon colour is none (the
default), the colour is taken from the alpha carbon at
each position along its length.
The width of the ribbon at each position is determined
by the optional parameter in the usual RasMol units. By
default the width of the ribbon is taken from the
secondary structure of the protein or a constant value
of 720 (2.88 Angstroms) for nucleic acids. The default
width of protein alpha helices and beta sheets is 380
(1.52 Angstroms) and 100 (0.4 Angstroms) for turns and
random coil. The secondary structure assignment is
either from the PDB file or calculated using the DSSP
algorithm as used by the structure command. This
command is similar to the RasMol command strands which
renders the biomolecular ribbon as parallel depth-cued
curves.
Rotate
Rotate the molecule about the specified axis. 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.
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Save Save the currently selected set of atoms in either a
Brookhaven Protein Database (PDB) or Alchemy(tm) format
file. The distinction between this command and the
RasMol write command has been dropped. The only
difference is that without a format specifier the save
command generates a PDB file and the write command
generates a GIF image.
Script
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
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 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
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permissible parameter options. Typically, ommiting the
paramter option resets that parameter to its default
value. A list of valid parameter names is given below.
Show The RasMol show command display details of the status
of the currently loaded molecule. The command show
information lists the molecule's name, classification,
PDB code and the number of atoms, chains, groups it
contains. If hydrogen bonding, disulphide bridges or
secondary structure have been determined, the number of
hbonds, ssbonds, helices, ladders and turns are also
displayed respectively. The command show sequence lists
the residues that compose each chain of the molecule.
Slab The RasMol slab command enables, disables or positions
the z-clipping plane of the molecule. The program only
draws those portions of the molecule that are further
from the viewer than the slabbing plane. 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
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.
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SSBonds
The RasMol ssbonds command is used to represent the
disulphide bridges of the protein molecule as either
dotted lines or cylinders between the connected
cysteines. The first time that the ssbonds command is
used, the program searches the structure of the protein
to find half-cysteine pairs (cysteines whose sulphurs
are within 3 angstroms of each other) and reports the
number of bridges to the user. The command ssbonds on
displays the selected `bonds' as dotted lines, and the
command ssbonds off disables the display of ssbonds in
the currently selected area. Selection of disulphide
bridges is identical to normal bonds, and may be
adjusted using the RasMol set bondmode command. The
colour of disulphide bonds may be changed using the
colour ssbonds command. By default, each disulphide
bond has the colours of its connected atoms.
By default disulphide bonds are drawn between the
sulphur atoms within the cysteine groups. By using the
set ssbonds command the position of the cysteine's
alpha carbons may be used instead.
Strands
The RasMol strands command displays the currently
loaded protein or nucleic acid as a smooth "ribbon" of
depth-cued curves passing along the backbone of the
protein. The ribbon is composed of a number of strands
that run parallel to one another along the peptide
plane of each residue. The ribbon is drawn between each
amino acid whose alpha carbon is currently selected.
The colour of the ribbon is changed by the RasMol
colour ribbon command. If the current ribbon colour is
none (the default), the colour is taken from the alpha
carbon at each position along its length. The 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
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the structure command. This command is similar to the
RasMol command ribbons which renders the biomolecular
ribbon as a smooth shaded surface.
Structure
The RasMol structure command calculates secondary
structure assignments for the currently loaded protein.
If the original PDB file contained structural
assignment records (HELIX 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
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
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 the current image to a file in a standard raster
format. Currently supported image file formats include
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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 Deletes the contents of the current database and resets
parameter variables to their initial default state.
Zoom Change the magnification of the currently displayed
image. Boolean parameters either magnify or reset the
scale of current molecule. An integer parameter between
10 and 200 specifies the desired magnification as a
percentage of the default scale.
SET 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.
Set Ambient
The RasMol ambient parameter is used to control the
amount of ambient (or surrounding) light in the scene.
The ambient value must be between 0 and 100 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
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ribbon representations.
Set Axes
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
The RasMol background parameter is used to set the
colour of the "canvas" background. The colour may be
given as either a colour name or a comma separated
triple of Red, Green, Blue (RGB) components enclosed in
square brackets. Typing the command help colours will
give a list of the predefined colour names recognised
by RasMol. When running under X Windows, RasMol also
recognises colours in the X server's colour name
database.
The command set background is synonymous with the
RasMol command background.
Set BondMode
The RasMol set bondmode command controls the mechanism
used to select individual bonds. When using the select
and restrict commands, a given bond will be selected if
i) the bondmode is or and either of the connected atoms
is selected, or ii) the bondmode is and and both atoms
connected by the bond are selected. Hence an individual
bond may be uniquely identified by using the command
set bondmode and and then uniquely selecting the atoms
at both ends.
Set BoundBox
The RasMol boundbox parameter controls the display of
the current molecules bounding box on the display. The
bounding box is orthogonal to the data file's original
co-ordinate axes. The set boundbox command is similar
the the commands set axes and set unitcell that display
orthogonal co-ordinate axes and the bounding box
respectively.
Set Display
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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
The RasMol hbonds parameter determines whether hydrogen
bonds are drawn between the donor and acceptor atoms of
the hydrogen bond, set hbonds sidechain or between the
alpha carbon atoms of the protein backbone and between
the phosphorous atoms of the nucleic acid backbone, set
hbonds backbone. The actual display of hydrogen bonds
is controlled by the hbonds command. Drawing hydrogen
bonds between protein alpha carbons or nucleic acid
phosphorous atoms is useful when the rest of the
molecule is shown in only a schematic representation
such as backbone, ribbons or strands. his parameter is
similar to the RasMol ssbonds parameter.
Set FontSize
The RasMol set fontsize command is used to control the
size of the characters that form atom labels. This
value corresponds to the height of the displayed
character in pixels. The maximum value of fontsize is
32 pixels, and the default value is 8 pixels high. To
display atom labels on the screen use the RasMol label
command and to change the colour of displayed labels,
use the colour labels command.
Set Hetero
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,
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select without any parameters is equivalent to select
all.
Set HourGlass
The RasMol hourglass parameter allows the user to
enable and disable the use of the `hour glass' cursor
used by RasMol to indicate that the program is
currently busy drawing the next frame. The command set
hourglass on enable the indicator, whilst set hourglass
off prevents RasMol from changing the cursor. This is
useful when spinning the molecule, running a sequence
of commands from a script file or using interprocess
communication to execute complex sequences of commands.
In these cases a `flashing' cursor may be distracting.
Set Hydrogen
The RasMol hydrogen parameter is used to modify the
`default' behaviour of the RasMol select command, i.e.
the behaviour of select without any parameters. When
this value is false, the default select region does not
include any hydrogen or deuterium atoms (refer to the
predefined set hydrogen ). When this value is true, the
default select region may contain hydrogen atoms. This
parameter is similar to the RasMol hetero parameter
which determines whether heterogenous atoms should be
included in the default set. If both hydrogen and
hetero are true, select without any parameters is
equivalent to select all.
Set Kinemage
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
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.
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Set Mouse
The RasMol set mouse command sets the rotation,
translation, scaling and zooming mouse bindings. The
default value is rasmol which is suitable for two
button mice (for three button mice the second and third
buttons are synonymous); X-Y rotation is controlled by
the first button, and X-Y translation by the second.
Additional functions are controlled by holding a
modifier key on the keyboard. [Shift] and the first
button performs scaling, [shift] and the second button
performs Z-rotation, and [control] and the first mouse
button controls the clipping plane. The insight and
quanta provide the same mouse bindings as other
packages for experienced users.
Set Radius
The RasMol set radius command is used to alter the
behaviour of the RasMol dots command depending upon the
value of the solvent parameter. When solvent is true,
the radius parameter controls whether a true Van der
Waal's surface is generated by the dots command. If the
value of radius is anything other than zero, that value
is used as the radius of each atom instead of it true
VdW value. When the value of solvent is true, this
parameter determines the `probe sphere' (solvent)
radius. The parameter may be given as an integer in
rasmol units or containing a decimal point in
Angstroms. The default value of this parameter is
determined by the value of solvent and changing solvent
resets radius to its new default value.
Set Shadow
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
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".
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Set Solvent
The RasMol set solvent command is used to control the
behaviour of the RasMol dots command. Depending upon
the value of the solvent parameter, the dots command
either generates a Van der Waal's or a solvent
acessible surface around the currently selected set of
atoms. Changing this parameter automatically resets the
value of the RasMol radius parameter. The command set
solvent false, the default value, indicates that a Van
der Waal's surface should be generated and resets the
value of radius to zero. The command set solvent true
indicates that a `Connolly' or `Richards' solvent
accessible surface should be drawn and sets the radius
parameter, the solvent radius, to 1.2 Angstroms (or 300
RasMol units).
Set Specular
The RasMol set specular command enables and disables
the display of specular highlights on solid objects
drawn by RasMol. Specular highlights appear as white
reflections of the light source on the surface of the
object. The current RasMol implementation uses an
approximation function to generate this highlight.
The specular highlights on the surfaces of solid
objects may be altered by using the specular reflection
coefficient, which is altered using the RasMol set
specpower command.
Set SpecPower
The specpower parameter determines the shininess of
solid objects rendered by RasMol. This value between 0
and 100 adjusts the reflection 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
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
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such as backbone, ribbons or strands. his parameter is
similar to the RasMol hbonds parameter.
Set Strands
The RasMol strands parameter controls the number of
parallel strands that are displayed in the ribbon
representations of proteins. The permissible values for
this parameter are 1, 2, 3, 4, 5 and 9. The default
value is 5. The number of strands is constant for all
ribbons being displayed. However, the ribbon width
(the separation between strands) may be controlled on a
residue by residue basis using the RasMol ribbons
command.
Set UnitCell
The RasMol unitcell parameter controls the display of
the crystallographic unit cell on the current display.
The crystal cell is only enabled if the appropriate
crystal symmetry information is contained in the PDB
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
The RasMol vectps parameter is use to control the way
in which the RasMol write command generates vector
PostScript output files. The command set vectps on
enables to use of black outlines around spheres and
cylinder bonds producing `cartoon-like' high resolution
output. However, the current implementation of RasMol
incorrectly cartoons spheres that are intersected by
more than one other sphere. Hence `ball and stick'
models are rendered correctly by not large spacefilling
spheres models. Cartoon outlines can be disabled, the
default, by the command set vectps off
ATOM EXPRESSIONS
RasMol atom expressions uniquely identify an arbitrary group
of atoms within a molecule. Atom expressions are composed of
either primitive expressions, predefined sets, comparison
operators, within expressions, or logical (boolean)
combinations of the above expression types.
The logical operators allow complex queries to be
constructed out of simpler ones using the standard boolean
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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!
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.
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
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less than or equal to, ">" for greater than, and ">"
for greater than or equal to.
Within Expressions
A RasMol within expression allows atoms to be selected
on their proximity to another set of atoms. A within
expression takes two parameters separated by a comma
and surrounded by parenthesis. The first argument is an
integer value called the "cut-off" distance of the
within expression and the second argument is any valid
atom expression. The cut-off distance is expressed in
either integer RasMol units or Angstroms containing a
decimal point. An atom is selected if it is within the
cut-off distance of any of the atoms defined by the
second argument. This allows complex expressions to be
constructed containing nested within expressions.
For example, the command select within(3.2,backbone)
selects any atom within a 3.2 Angstrom radius of any
atom in a protein or nucleic acid backbone. Within
expressions are particularly useful for selecting the
atoms around an active site.
Predefined Sets
RasMol atom expressions may contain predefined sets.
These sets are single keywords that represent portions
of a molecule of interest. Predefined sets are often
abbreviations primitive atom expressions, and in some
cases of selecting areas of a molecule that could not
otherwise be distinguished. A list of the currently
predefined sets is given below. In addition to the
sets listed here, RasMol also treats element names (and
their plurals) as predefined sets containing all atoms
of that element type, i.e. the command select oxygen is
equivalent to the command select elemno=8.
Predefined Sets
AT Set
This set contains the atoms in the complementary
nucleotides adenosine and thymidine (A and T
respectively). All nucleotides are classified as either
the set at or the set cg This set is equivalent to the
RasMol atom expressions a,t and nucleic and not cg
Acidic Set
The set of acidic amino acids. These are the residue
types Asp and Glu. All amino acids are classified as
either acidic, basic or neutral. This set is equivalent
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to the RasMol atom expressions asp, glu and amino and
not (basic or neutral)
Acyclic Set
The set of atoms in amino acids not containing a cycle
or ring. All amino acids are classified as either
cyclic or acyclic. This set is equivalent to the RasMol
atom expression amino and not cyclic
Aliphatic Set
This set contains the aliphatic amino acids. These are
the amino acids Ala, Gly, Ile, Leu and Val. This set
is equiavlent to the RasMol atom expression ala, gly,
ile, leu, val
Alpha Set
The set of alpha carbons in the protein molecule. This
set is approximately equivalent to the RasMol atom
expression *.CA This command should not be confused
with the predefined set helix which contains the atoms
in the amino acids of the protein's alpha helices.
Amino Set
This set contains all the atoms contained in amino acid
residues. This is useful for distinguishing the
protein from the nucleic acid and heterogenous atoms in
the current molecule database.
Aromatic Set
The set of atoms in amino acids containing aromatic
rings. These are the amino acids His, Phe, Trp and
Tyr. Because they contain aromatic rings all members
of this set are member of the predefined set cyclic.
This set is equivalent to the RasMol atom expressions
his, phe, trp, tyr and cyclic and not pro
Backbone Set
This set contains the four atoms of each amino acid
that form the polypeptide N-C-C-O backbone of proteins,
and the atoms the sugar phosphate backbone of nucleic
acids. Use the RasMol predefined sets protein and
nucleic to distinguish between the two forms of
backbone. Atoms in nucleic acids and proteins are
either backbone or sidechain. This set is equivalent to
the RasMol expression (protein or nucleic) and not
sidechain
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The predefined set mainchain is synonymous with the set
backbone.
Basic Set
The set of basic amino acids. These are the residue
types Arg, His and Lys. All amino acids are classified
as either acidic, basic or neutral. This set is
equivalent to the RasMol atom expressions arg, his, lys
and amino and not (acidic or neutral)
Bonded Set
This set contain all the atoms in the current molecule
database that are bonded to atleast one other atom.
Buried Set
This set contains the atoms in those amino acids that
tend (prefer) to buried inside protein, away from
contact with solvent molecules. This set refers to the
amino acids preference and not the actual solvent
acessibility for the current protein. All amino acids
are classified as either surface or buried. This set is
equivalent to the RasMol atom expression amino and not
surface
CG Set
This set contains the atoms in the complementary
nucleotides cytidine and guanoine (C and G
respectively). All nucleotides are classified as either
the set at or the set cg This set is equivalent to the
RasMol atom expressions c,g and nucleic and not at
Charged Set
This set contains the charged amino acids. These are
the amino acids that are either acidic or basic. Amino
acids are classified as being either charged or
neutral. This set is equivalent to the RasMol atom
expressions acidic or basic and amino and not neutral
Cyclic Set
The set of atoms in amino acids containing a cycle or
rings. All amino acids are classified as either cyclic
or acyclic. This set consists of the amino acids His,
Phe, Pro, Trp and Tyr. The members of the predefined
set aromatic are members of this set. The only cyclic
but non-aromatic amino acid is proline. This set is
equivalent to the RasMol atom expressions his, phe,
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pro, trp, tyr and aromatic or pro and amino and not
acyclic
Cystine Set
This set contains the atoms of cysteine residues that
form part of a disulphide bridge, i.e. half cystines.
RasMol automatically determines disulphide bridges, if
neither the predefined set cystine nor the RasMol
ssbonds command have been used since the molecule was
loaded. The set of free cysteines may be determined
using the RasMol atom expression cys and not cystine
Helix Set
This set contains all atoms that form part of a protein
alpha helix as determined by either the PDB file author
or Kabsch and Sander's DSSP algorithm. By default,
RasMol uses the secondary structure determination given
in the PDB file if it exists. Otherwise, it uses the
DSSP algorithm as used by the RasMol structure command.
This predefined set should not be confused with the
predefined set alpha which contains the alpha carbon
atoms of a protein.
Hetero Set
This set contains all the heterogenous atoms in the
molecule. These are the atoms described by HETATM
entries in the PDB file. These typically contain water,
cofactors and other solvents and ligands. All hetero
atoms are classified as either ligand or solvent atoms.
These heterogenous solvent atoms are further classified
as either water or ions.
Hydrogen Set
This predefined set contains all the hydrogen and
deuterium atoms of the current molecule. This
predefined set is equivalent to the RasMol atom
expression elemno=1
Hydrophobic Set
This set contains all the hydrophobic amino acids.
These are the amino acids Ala, Leu, Val, Ile, Pro, Phe,
Met and Trp. All amino acids are classified as either
hydrophobic or polar. This set is equivalent to the
RasMol atom expressions ala, leu, val, ile, pro, phe,
and amino and not polar
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Ions Set
This set contains all the heterogenous phosphate and
sulphate ions in the current molecule data file. A
large number of these ions are sometimes associated
with protein and nucleic acid structures determined by
X-ray crystallography. These atoms tend to clutter an
image. All hetero atoms are classified as either ligand
or solvent atoms. All solvent atoms are classified as
either water or ions.
Large Set
All amino acids are classified as either small, medium
or large. This set is equivalent to the RasMol atom
expression amino and not (small or medium)
Ligand Set
This set contains all the heterogenous cofactor and
ligand moieties that are contained in the current
molecule data file. At this set is defined to be all
hetero atoms that are not solvent atoms. Hence this set
is equivalent to the RasMol atom expression hetero and
not solvent
Medium Set
All amino acids are classified as either small, medium
or large. This set is equivalent to the RasMol atom
expression amino and not (large or small)
Neutral Set
The set of neutral amino acids. All amino acids are
classified as either acidic, basic or neutral. This set
is equivalent to the RasMol atom expression amino and
not (acidic or basic)
Nucleic Set
The set of all atoms in nucleic acids, which consists
of the four nucleotide bases adenosine, cytidine,
guanosine and thymidine (A, C, G and T respectively).
All neucleotides are classified as either purine or
pyrimidine. This set is equivalent to the RasMol atom
expressions a,c,g,t and purine or pyrimidine
Polar Set
This set contains the polar amino acids. All amino
acids are classified as either hydrophobic or polar.
This set is equivalent to the RasMol atom expression
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amino and not hydrophobic
Protein Set
The set of all atoms in proteins. This consists of the
RasMol predefined set amino and common post-translation
modifications.
Purine Set
The set of purine nucleotides. These are the bases
adenosine and guanosine (A and G respectively). All
nucleotides are either purines or pyrimidines. This set
is equivalent to the RasMol atom expressions a,g and
nucleic and not purine
Pyrimidine Set
The set of pyrimidine nucleotides. These are the bases
cytidine and thymidine (C and T respectively). All
nucleotides are either purines or pyrimidines. This set
is equivalent to the RasMol atom expressions c,t and
nucleic and not pyrimidine
Selected Set
This set contains the set of atoms in the currently
selected region. The currently selected region is
defined by the preceding select or restrict command and
not the atom expression containing the selected
keyword.
Sheet Set
This set contains all atoms that form part of a protein
beta sheet as determined by either the PDB file author
or Kabsch and Sander's DSSP algorithm. By default,
RasMol uses the secondary structure determination given
in the PDB file if it exists. Otherwise, it uses the
DSSP algorithm as used by the RasMol structure command.
Sidechain Set
This set contains the functional sidechains of any
amino acids and the base of each nucleotide. These are
the atoms not part of the polypeptide N-C-C-O backbone
of proteins or the sugar phosphate backbone of nucleic
acids. Use the RasMol predefined sets protein and
nucleic to distinguish between the two forms of
sidechain. Atoms in nucleic acids and proteins are
either backbone or sidechain. This set is equivalent to
the RasMol expression (protein or nucleic) and not
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backbone
Small Set
All amino acids are classified as either small, medium
or large. This set is equivalent to the RasMol atom
expression amino and not (medium or large)
Solvent Set
This set contains the solvent atoms in the molecule
co-ordinate file. These are the heterogenous water
molecules, phosphate and sulphate ions. All hetero
atoms are classified as either ligand or solvent atoms.
All solvent atoms are classified as either water or
ions. This set is equivalent to the RasMol atom
expressions hetero and not ligand and water or ions
Surface Set
This set contains the atoms in those amino acids that
tend (prefer) to be on the surface of proteins, in
contact with solvent molecules. This set refers to the
amino acids preference and not the actual solvent
accessibility for the current protein. All amino acids
are classified as either surface or buried. This set is
equivalent to the RasMol atom expression amino and not
buried
Turn Set
This set contains all atoms that form part of a protein
turns as determined by either the PDB file author or
Kabsch and Sander's DSSP algorithm. By default, RasMol
uses the secondary structure determination given in the
PDB file if it exists. Otherwise, it uses the DSSP
algorithm as used by the RasMol structure command.
Water Set
This set contains all the heterogenous water molecules
in the current database. A large number of water
molecules are sometimes associated with protein and
nucleic acid structures determined by X-ray
crystallography. These atoms tend to clutter an image.
All hetero atoms are classified as either ligand or
solvent atoms. The solvent atoms are further classified
as either water or ions.
COLOUR SCHEMES
The RasMol colour command allows different objects (such as
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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 blue, black, cyan,
green, greenblue, magenta, orange, purple, red, redorange,
violet, white and yellow.
Amino Colours
The RasMol amino colour scheme colours amino acids
according to traditional amino acid properties. The
purpose of colouring is to identify amino acids in an
unusual or surprising environment. The outer parts of a
protein that are polar are visible (bright) colours and
non-polar residues darker. Most colours are hallowed by
tradition. This colour scheme is similar to the shapely
scheme.
Chain Colours
The RasMol chain colour scheme assigns each
macromolecular chain a unique colour. This colour
scheme is particularly useful for distinguishing the
parts of multimeric structure or the individual
`strands' of a DNA chain.
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.
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.
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Shapely Colours
The RasMol shapely colour scheme colour codes residues
by amino acid property. This scheme is based upon Bob
Fletterick's "Shapely Models". Each amino acid and
nucleic acid residue is given a unique colour. The
shapely colour scheme is used by David Bacon's Raster3D
program. This colour scheme is similar to the amino
colour scheme.
Structure Colours
The RasMol structure colour scheme colours the molecule
by protein secondary structure. Alpha helices are
coloured magenta, [240,0,128], beta sheets are coloured
yellow, [255,255,0], turns are coloured pale blue,
[96,128,255] and all other residues are coloured white.
The secondary structure is either read from the PDB
file (HELIX and SHEET records), if available, or
determined using Kabsch and Sander's DSSP algorithm.
The RasMol structure command may be used to force
DSSP's structure assignment to be used.
Temperature Colours
The RasMol temperature colour scheme colour codes each
atom according to the anisotropic temperature (beta)
value stored in the PDB file. Typically this gives a
measure of the mobility/uncertainty of a given atom's
position. High values are coloured in warmer (red)
colours and lower values in colder (blue) colours. This
feature is often used to associate a "scale" value
[such as amino acid variability in viral mutants] with
each atom in a PDB file, and colour the molecule
appropriately.
The difference between the temperature and charge
colour schemes is that increasing temperature values
proceed from blue to red, whereas increasing charge
valuse go from red to blue.
Charge Colours
The RasMol charge colour scheme colour codes each atom
according to the charge value stored in the input file
(or beta factor field of PDB files). High values are
coloured in blue (positive) and lower values coloured
in red (negative). Rather than use a fixed scale this
scheme determines the maximum and minimum values of the
charge/temperature field and interpolates from red to
blue appropriately. Hence, green cannot be assumed to
be `no net charge' charge.
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The difference between the charge and temperature
colour schemes is that increasing temperature values
proceed from blue to red, whereas increasing charge
valuse go from red to blue.
If the charge/temperature field stores reasonable
values it is possible to use the RasMol colour dots
potential command to colour code a dot surface
(generated by the dots command) by electrostatic
potential.
User Colours
The RasMol user colour scheme allows RasMol to use the
colour scheme stored in the PDB file. The colours for
each atom are stored in COLO records placed in the PDB
data file. This convention was introduced by David
Bacon's Raster3D program.
HBond Type Colours
The RasMol type colour scheme applies only to hydrogen
bonds, hence is used in the command colour hbonds type
This scheme colour codes each hydrogen bond according
to the distance along a protein chain between hydrogen
bond donor and acceptor. This schematic representation
was introduced by Belhadj-Mostefa and Milner-White.
This representation gives a good insight into protein
secondary structure (hbonds forming alpha helices
appear red, those forming sheets appear yellow and
those forming turns appear magenta).
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.
SEE ALSO
The RasMol User Manual!
AUTHOR
Copyright (C) 1992-94 by Roger Sayle. All rights reserved.
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(rasmol@ggr.co.uk)
Page 30 (printed 12/11/98)
