RASMOL(1) RASMOL(1)
October 1994
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 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
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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 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
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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 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
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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 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.
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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.
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
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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 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
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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.
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.
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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 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 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
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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 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
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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 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
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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
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
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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, 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.
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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.
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
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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".
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.
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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 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
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types.
The logical operators allow complex queries to be constructed out of
simpler ones using the standard boolean connectives and, or and not.
These may be abbreviated by the symbols "&", "|" and "!" respectively.
Parentheses (brackets) may be used to alter the precedence of the
operators. For convenience, a comma may also be used for boolean
disjunction.
The atom expression is evaluated for each atom, hence protein and
backbone selects protein bacbone atoms, not the protein and [nucleic]
acid backbone atoms!
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 less than or equal to,
">" for greater than, and ">" for greater than or equal to.
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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 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
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set is equivalent to the RasMol atom expression amino and not
cyclic
Aliphatic Set
This set contains the aliphatic amino acids. These are the amino
acids Ala, Gly, Ile, Leu and Val. This set is equiavlent to the
RasMol atom expression ala, gly, ile, leu, val
Alpha Set
The set of alpha carbons in the protein molecule. This set is
approximately equivalent to the RasMol atom expression *.CA This
command should not be confused with the predefined set helix
which contains the atoms in the amino acids of the protein's
alpha helices.
Amino Set
This set contains all the atoms contained in amino acid residues.
This is useful for distinguishing the protein from the nucleic
acid and heterogenous atoms in the current molecule database.
Aromatic Set
The set of atoms in amino acids containing aromatic rings. These
are the amino acids His, Phe, Trp and Tyr. Because they contain
aromatic rings all members of this set are member of the
predefined set cyclic. This set is equivalent to the RasMol atom
expressions his, phe, trp, tyr and cyclic and not pro
Backbone Set
This set contains the four atoms of each amino acid that form the
polypeptide N-C-C-O backbone of proteins, and the atoms the sugar
phosphate backbone of nucleic acids. Use the RasMol predefined
sets protein and nucleic to distinguish between the two forms of
backbone. Atoms in nucleic acids and proteins are either
backbone or sidechain. This set is equivalent to the RasMol
expression (protein or nucleic) and not sidechain
The predefined set mainchain is synonymous with the set backbone.
Basic Set
The set of basic amino acids. These are the residue types Arg,
His and Lys. All amino acids are classified as either acidic,
basic or neutral. This set is equivalent to the RasMol atom
expressions arg, his, lys and amino and not (acidic or neutral)
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Bonded Set
This set contain all the atoms in the current molecule database
that are bonded to atleast one other atom.
Buried Set
This set contains the atoms in those amino acids that tend
(prefer) to buried inside protein, away from contact with solvent
molecules. This set refers to the amino acids preference and not
the actual solvent acessibility for the current protein. All
amino acids are classified as either surface or buried. This set
is equivalent to the RasMol atom expression amino and not surface
CG Set
This set contains the atoms in the complementary nucleotides
cytidine and guanoine (C and G respectively). All nucleotides are
classified as either the set at or the set cg This set is
equivalent to the RasMol atom expressions c,g and nucleic and not
at
Charged Set
This set contains the charged amino acids. These are the amino
acids that are either acidic or basic. Amino acids are classified
as being either charged or neutral. This set is equivalent to the
RasMol atom expressions acidic or basic and amino and not neutral
Cyclic Set
The set of atoms in amino acids containing a cycle or rings. All
amino acids are classified as either cyclic or acyclic. This set
consists of the amino acids His, Phe, Pro, Trp and Tyr. The
members of the predefined set aromatic are members of this set.
The only cyclic but non-aromatic amino acid is proline. This set
is equivalent to the RasMol atom expressions his, phe, pro, trp,
tyr and aromatic or pro and amino and not acyclic
Cystine Set
This set contains the atoms of cysteine residues that form part
of a disulphide bridge, i.e. half cystines. RasMol automatically
determines disulphide bridges, if neither the predefined set
cystine nor the RasMol ssbonds command have been used since the
molecule was loaded. The set of free cysteines may be determined
using the RasMol atom expression cys and not cystine
Helix Set
This set contains all atoms that form part of a protein alpha
helix as determined by either the PDB file author or Kabsch and
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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
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
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this set is defined to be all hetero atoms that are not solvent
atoms. Hence this set is equivalent to the RasMol atom expression
hetero and not solvent
Medium Set
All amino acids are classified as either small, medium or large.
This set is equivalent to the RasMol atom expression amino and
not (large or small)
Neutral Set
The set of neutral amino acids. All amino acids are classified
as either acidic, basic or neutral. This set is equivalent to the
RasMol atom expression amino and not (acidic or basic)
Nucleic Set
The set of all atoms in nucleic acids, which consists of the four
nucleotide bases adenosine, cytidine, guanosine and thymidine (A,
C, G and T respectively). All neucleotides are classified as
either purine or pyrimidine. This set is equivalent to the RasMol
atom expressions a,c,g,t and purine or pyrimidine
Polar Set
This set contains the polar amino acids. All amino acids are
classified as either hydrophobic or polar. This set is equivalent
to the RasMol atom expression amino and not hydrophobic
Protein Set
The set of all atoms in proteins. This consists of the RasMol
predefined set amino and common post-translation modifications.
Purine Set
The set of purine nucleotides. These are the bases adenosine and
guanosine (A and G respectively). All nucleotides are either
purines or pyrimidines. This set is equivalent to the RasMol atom
expressions a,g and nucleic and not purine
Pyrimidine Set
The set of pyrimidine nucleotides. These are the bases cytidine
and thymidine (C and T respectively). All nucleotides are either
purines or pyrimidines. This set is equivalent to the RasMol atom
expressions c,t and nucleic and not pyrimidine
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Selected Set
This set contains the set of atoms in the currently selected
region. The currently selected region is defined by the preceding
select or restrict command and not the atom expression containing
the selected keyword.
Sheet Set
This set contains all atoms that form part of a protein beta
sheet as determined by either the PDB file author or Kabsch and
Sander's DSSP algorithm. By default, RasMol uses the secondary
structure determination given in the PDB file if it exists.
Otherwise, it uses the DSSP algorithm as used by the RasMol
structure command.
Sidechain Set
This set contains the functional sidechains of any amino acids
and the base of each nucleotide. These are the atoms not part of
the polypeptide N-C-C-O backbone of proteins or the sugar
phosphate backbone of nucleic acids. Use the RasMol predefined
sets protein and nucleic to distinguish between the two forms of
sidechain. Atoms in nucleic acids and proteins are either
backbone or sidechain. This set is equivalent to the RasMol
expression (protein or nucleic) and not backbone
Small Set
All amino acids are classified as either small, medium or large.
This set is equivalent to the RasMol atom expression amino and
not (medium or large)
Solvent Set
This set contains the solvent atoms in the molecule co-ordinate
file. These are the heterogenous water molecules, phosphate and
sulphate ions. All hetero atoms are classified as either ligand
or solvent atoms. All solvent atoms are classified as either
water or ions. This set is equivalent to the RasMol atom
expressions hetero and not ligand and water or ions
Surface Set
This set contains the atoms in those amino acids that tend
(prefer) to be on the surface of proteins, in contact with
solvent molecules. This set refers to the amino acids preference
and not the actual solvent accessibility for the current protein.
All amino acids are classified as either surface or buried. This
set is equivalent to the RasMol atom expression amino and not
buried
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Turn Set
This set contains all atoms that form part of a protein turns as
determined by either the PDB file author or Kabsch and Sander's
DSSP algorithm. By default, RasMol uses the secondary structure
determination given in the PDB file if it exists. Otherwise, it
uses the DSSP algorithm as used by the RasMol structure command.
Water Set
This set contains all the heterogenous water molecules in the
current database. A large number of water molecules are sometimes
associated with protein and nucleic acid structures determined by
X-ray crystallography. These atoms tend to clutter an image. All
hetero atoms are classified as either ligand or solvent atoms.
The solvent atoms are further classified as either water or ions.
COLOUR SCHEMES
The RasMol colour command allows different objects (such as atoms,
bonds and ribbon segments) to be given a specified colour. Typically
this colour is either a RasMol predefined colour name or an RGB
triple. Additionally RasMol also supports cpk, amino, chain, group,
shapely, structure, temperature, charge and user colour schemes for
atoms, a hbond type colour scheme for hydrogen bonds and electrostatic
potential colour scheme for dot surfaces. The currently predefined
colour names are 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
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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.
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.
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Charge Colours
The RasMol charge colour scheme colour codes each atom according
to the charge value stored in the input file (or beta factor
field of PDB files). High values are coloured in blue (positive)
and lower values coloured in red (negative). Rather than use a
fixed scale this scheme determines the maximum and minimum values
of the charge/temperature field and interpolates from red to blue
appropriately. Hence, green cannot be assumed to be `no net
charge' charge.
The difference between the charge and temperature colour schemes
is that increasing temperature values proceed from blue to red,
whereas increasing charge valuse go from red to blue.
If the charge/temperature field stores reasonable values it is
possible to use the RasMol colour dots potential command to
colour code a dot surface (generated by the dots command) by
electrostatic potential.
User Colours
The RasMol user colour scheme allows RasMol to use the colour
scheme stored in the PDB file. The colours for each atom are
stored in COLO records placed in the PDB data file. This
convention was introduced by David Bacon's Raster3D program.
HBond Type Colours
The RasMol type colour scheme applies only to hydrogen bonds,
hence is used in the command colour hbonds type This scheme
colour codes each hydrogen bond according to the distance along a
protein chain between hydrogen bond donor and acceptor. This
schematic representation was introduced by Belhadj-Mostefa and
Milner-White. This representation gives a good insight into
protein secondary structure (hbonds forming alpha helices appear
red, those forming sheets appear yellow and those forming turns
appear magenta).
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.
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SEE ALSO
The RasMol User Manual!
AUTHOR
Copyright (C) 1992-94 by Roger Sayle. All rights reserved.
(rasmol@ggr.co.uk)
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