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1 RasMol
2 Introduction
RasMol2 is a molecular graphics program intended for the
visualisation of proteins, nucleic acids and small molecules. The
program is aimed at display, teaching and generation of publication
quality images. RasMol runs on Microsoft Windows, Apple Macintosh,
UNIX and VMS systems. The UNIX and VMS systems require an 8, 24 or
32 bit colour X Windows display (X11R4 or later). The program reads
in a molecule co-ordinate file and interactively displays the
molecule on the screen in a variety of colour schemes and molecule
representations. Currently available representations include
depth-cued wireframes, 'Dreiding' sticks, spacefilling (CPK)
spheres, ball and stick, solid and strand biomolecular ribbons, atom
labels and dot surfaces.
2 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.
3 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 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.
3 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.
3 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.
3 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.
3 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' `dot surfaces can also be coloured by'
`electrostatic potential.' For more information type `help colour
.'
3 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.
3 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 contents of the set do not change, even if the
expression defining them depends on the current transformation and
representation of the molecule.
3 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.
3 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.
3 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 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.
3 Help
The RasMol `help' command provides on-line help on the given topic.
3 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 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.
3 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.
3 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.
3 Quit
Exit from the RasMol program. The RasMol commands `exit' and `quit'
are synonymous.
3 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.
3 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.
3 Restrict
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.
3 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.
3 Rotate
Rotate the molecule about the specified axis. Permited values for
the axis parameter are 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.
3 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.
3 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.
3 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.
3 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 permissible parameter options.
Typically, ommiting the paramter option resets that parameter to its
default value. A list of valid parameter names is given below.
3 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.
3 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.
3 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.
3 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.
3 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 the `structure' command. This command is
similar to the RasMol command `ribbons' which renders the
biomolecular ribbon as a smooth shaded surface.
3 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.
3 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 Displacement
values must be between -100 and 100 which correspond to moving the
current molecule just off the screen. A positive displacement moves
the molecule to the right, and a positive displacement moves the
molecule down the screen. The pair of commands `translate x 0' and
`translate y 0' centres the molecule on the screen.
3 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.
3 Write
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.
3 Zap
Deletes the contents of the current database and resets parameter
variables to their initial default state.
3 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.
2 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.
3 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 ribbon representations.
3 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.
3 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.'
3 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.
3 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.
3 Display
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).
3 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.
3 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.
3 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,' `select' without any
parameters is equivalent to `select all.'
3 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.
3 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.'
3 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.
3 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.
3 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.
3 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.
3 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.
3 SlabMode
The RasMol `slabmode' parameter controls the rendering method of
objects cut by the slabbing (z-clipping) plane. Valid slabmode
parameters are
3 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).
3 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.
3 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.
3 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 such as `backbone,' `ribbons' or `strands.'
his parameter is similar to the RasMol `hbonds' parameter.
3 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.
3 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.
3 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'
2 Atom_Expressions
RasMol atom expressions uniquely identify an arbitrary group of
atoms within a molecule. Atom expressions are composed of either
primitive expressions, predefined sets, comparison operators,
`within' expressions, or logical (boolean) combinations of the above
expression types.
The logical operators allow complex queries to be constructed out of
simpler ones using the standard boolean connectives `and, or' and
`not.' These may be abbreviated by the symbols 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
3 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.
3 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 The inequality operator as
either The ordering operators are for less than, for less than or
equal to, for greater than, and for greater than or equal to.
3 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.
2 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.'
3 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"
3 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)"
3 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"
3 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"
3 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.
3 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.
3 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"
3 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.'
3 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)"
3 Bonded_Set
This set contain all the atoms in the current molecule database that
are bonded to atleast one other atom.
3 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"
3 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"
3 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"
3 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"
3 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"
3 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.
3 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.'
3 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"
3 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"
3 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.'
3 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)"
3 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"
3 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)"
3 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)"
3 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"
3 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"
3 Protein_Set
The set of all atoms in proteins. This consists of the RasMol
predefined set `amino' and common post-translation modifications.
3 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"
3 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"
3 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.
3 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.
3 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"
3 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)"
3 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"
3 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"
3 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.
3 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.'
2 Colours_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]
3 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]
3 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.
3 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
3 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.
3 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.
3 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.
3 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.
3 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.
3 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.
3 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]
3 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.
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]
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