.PU
.TH RASMOL 1 "October 1994"
.SH NAME
rasmol \- Molecular Graphics Visualisation Tool v2.5

.SH SYNOPSIS
.B rasmol
.RB "[\|" \-nodiplay "\|]"
.RB "[\|\&[\|" "\-"\c
.I "format"\c
.RB "\|]"
.I filename\c
\&\|]
.RB "[\|" "\-script "\c
.I scriptfile\c
\&\|]

.SH FORMATS
.PD 0
.TP 12
.B \-pdb
Brookhaven Protein Databank
.TP
.B \-mdl
MDL's MOL File Format
.TP
.B \-mol2
Tripos' Sybyl MOL2 Format
.TP
.B \-xyz
MSC's XYZ (XMol) Format
.TP
.B \-alchemy
Alchemy File Format
.TP
.B \-charmm
CHARMm File Format
.PD
.SH 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.

.SH COMMANDS
RasMol allows the execution of interactive commands typed at the
.B 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.

.TP
.B Backbone
The RasMol
.B 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
.B wireframe
command. The command
.B backbone off
turns off the selected `bonds', and
.B 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
.B colour backbone
command.

.TP
.B Background
The RasMol
.B 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
.B 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
.B background
command is synonymous with the RasMol
.B set background
command.

.TP
.B Centre
The RasMol
.B centre
command defines the point about which the
.B 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
.B help expression
for more information on RasMol atom expressions.

.TP
.B Clipboard
The RasMol
.B 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
.B write
command.

.TP
.B 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
.B help colours
will give a list of all the predefined colour names recognised
by RasMol.

Allowed objects are
.B atoms,
.B bonds,
.B backbone,
.B ribbons
.B labels
.B dots,
.B hbonds,
and
.B ssbonds.
If no object is specified, the default keyword
.B atom
is assumed.
Some colour schemes are defined for certain object types. The colour scheme
.B 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).
.B Atom
objects can also be coloured by
.B cpk,
.B amino,
.B chain,
.B group,
.B shapely,
.B structure,
.B temperature
.B charge
and
.B user. Hydrogen bonds can also be coloured by
.B type
and dot surfaces can also be coloured by
.B electrostatic potential.
For more information type
.B help colour .

.TP
.B Connect
The RasMol
.B 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
.B 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
.B 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
.B load
command.

.TP
.B Define
The RasMol
.B 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.

.TP
.B Dots
The RasMol
.B 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
.B 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
.B 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
.B colour dots
command.

.TP
.B Echo
The RasMol
.B 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
.B echo
command displays a blank line. This command is particularly useful
for displaying text from within a RasMol
.B script
file.

.TP
.B HBonds
The RasMol
.B 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
.B 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
.B hbonds on
displays the selected `bonds' as dotted lines, and the
.B hbonds off
turns off their display. The colour of hbond objects may be changed
by the
.B 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
.B 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.

.TP
.B Help
The RasMol
.B help
command provides on-line help on the given topic.

.TP
.B Label
The RasMol
.B 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
.B 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
.B 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
.B set fontsize
command.

.TP
.B Load
Load a molecule co-ordinate file into RasMol2. Valid molecule file
formats are
.B pdb
(Brookhaven Protein Databank),
.B mdl
(Molecular Design Limited's MOL file format),
.B alchemy
(Tripos' Alchemy file format),
.B mol2
(Tripos' Sybyl Mol2 file format),
.B charmm
(CHARMm file format) or
.B xyz
(MSC's XMol XYZ file format). If no file format is specified,
.B 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
.B zap
command.

The
.B 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
.B connect
command.

.TP
.B Print
The RasMol
.B 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
.B write ps
or
.B write vectps
commands and printing that or generating a raster image file and using a
utility to dump that to the local printer.

.TP
.B Quit
Exit from the RasMol program. The RasMol commands
.B exit
and
.B quit
are synonymous.

.TP
.B Renumber
The RasMol
.B 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.

.TP
.B Reset
The RasMol
.B reset
command restores the original viewing transformation
and centre of rotation. The scale is set to it default value,
.B zoom 100,
the centre of rotation is set to the geometric centre of the currently
loaded molecule,
.B 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
.B zap
command which deletes the currently stored molecule, returning the
program to its initial state.

.TP
.B Restrict
The RasMol
.B 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
.B 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
.B select
command, except restrict disables the
.B wireframe,
.B spacefill
and
.B backbone
representations in the non-selected region.

Type "help expression" for more information on RasMol atom expressions.

.TP
.B Ribbons
The RasMol
.B 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
.B colour ribbon
command. If the current ribbon colour is
.B 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
.B structure
command. This command is similar to the RasMol command
.B strands
which renders the biomolecular ribbon as parallel depth-cued curves.

.TP
.B 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.

.TP
.B 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
.B write
command has been dropped. The only difference is that without a format
specifier the
.B save
command generates a
.B PDB
file and the
.B write
command generates a
.B GIF
image.

.TP
.B Script
The RasMol
.B 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
.B echo
command.

The most common way to generate a RasMol script file is to use the
.B write script
or
.B 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
.B source
is synonymous with the
.B script
command.

.TP
.B 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
.B 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
.B select all.
The behaviour of the
.B select
command without any parameters is determined by the RasMol
.B hetero
and
.B hydrogen
parameters.

Type "help expression" for more information on RasMol atom expressions.

.TP
.B Set
The RasMol
.B 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.

.TP
.B Show
The RasMol
.B show
command display details of the status of the currently
loaded molecule. The command
.B 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
.B show sequence
lists the residues that compose each chain of the molecule.

.TP
.B Slab
The RasMol
.B 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.

.TP
.B Spacefill
The RasMol
.B 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,
.B spacefilll true,
the default, represents each atom as a sphere of Van der Waals radius.
The command
.B 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
.B 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
.B 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
.B cpk
is synonymous with the
.B spacefill
command.

.TP
.B SSBonds
The RasMol
.B 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
.B 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
.B ssbonds on
displays the selected `bonds' as dotted lines, and the command
.B 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
.B set bondmode
command. The colour of disulphide bonds may be changed using the
.B 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
.B set ssbonds
command the position of the cysteine's alpha carbons may be used instead.

.TP
.B Strands
The RasMol
.B 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
.B colour ribbon
command. If the current ribbon colour is
.B 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
.B colour ribbon1
and
.B colour ribbon2
commands respectively. The number of strands in the ribbon may be
altered using the RasMol
.B 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
.B structure
command. This command is similar to the RasMol command
.B ribbons
which renders the biomolecular ribbon as a smooth shaded surface.

.TP
.B Structure
The RasMol
.B 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.

.TP
.B Translate
The RasMol
.B 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
.B translate x 0
and
.B translate y 0
centres the molecule on the screen.

.TP
.B Wireframe
The RasMol
.B 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
.B wireframe
or
.B 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
.B colour bonds
command.

.TP
.B Write
Write the current image to a file in a standard raster format. Currently
supported image file formats include
.B gif
(Compuserve GIF),
.B ppm
(Portable Pixmap),
.B ras
(Sun rasterfile),
.B ps
and
.B epsf
(Encapsulated PostScript),
.B monops
(Monochrome Encapsulated PostScript),
.B bmp
(Microsoft bitmap) and
.B pict
(Apple PICT). The
.B write
command may also be used to generate command scripts for other graphics
programs. The format
.B script
writes out a file containing the RasMol
.B script
commands to reproduce the current image. The format
.B molscript
writes out the commands required to render the current view of the
molecule as ribbons in Per Kraulis' Molscript program and the format
.B kinemage
the commands for David Richardson's program Mage.

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

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

.TP
.B 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.

.SH SET PARAMETERS
RasMol has a number of internal parameters that may be modified using the
.B set
command. These parameters control a number of program options such as
rendering options and mouse button mappings.

.TP
.B Set Ambient
The RasMol
.B ambient
parameter is used to control the amount of ambient (or surrounding)
light in the scene. The
.B 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.

.TP
.B Set Axes
The RasMol
.B 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
.B set axes
command is similar the the commands
.B set boundbox
and
.B set unitcell
that display the bounding box and the crystallographic unit cell
respectively.

.TP
.B Set Background
The RasMol
.B 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
.B 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
.B set background
is synonymous with the RasMol command
.B background.

.TP
.B Set BondMode
The RasMol
.B set bondmode
command controls the mechanism used to select individual bonds. When
using the
.B select
and
.B restrict
commands, a given bond will be selected if i) the bondmode is
.B or
and either of the connected atoms is selected, or ii) the bondmode is
.B and
and both atoms connected by the bond are selected. Hence an individual
bond may be uniquely identified by using the command
.B set bondmode and
and then uniquely selecting the atoms at both ends.

.TP
.B Set BoundBox
The RasMol
.B 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
.B set boundbox
command is similar the the commands
.B set axes
and
.B set unitcell
that display orthogonal co-ordinate axes and the bounding box
respectively.

.TP
.B Set Display
This command controls the display mode within RasMol. By default,
.B set display normal,
RasMol displays the molecule in the representation specified by the
user. The command
.B 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).

.TP
.B Set HBonds
The RasMol
.B hbonds
parameter determines whether hydrogen bonds are drawn between
the donor and acceptor atoms of the hydrogen bond,
.B set hbonds sidechain
or between the alpha carbon atoms of the protein backbone and between
the phosphorous atoms of the nucleic acid backbone,
.B set hbonds backbone.
The actual display of hydrogen bonds is controlled by the
.B 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
.B backbone,
.B ribbons
or
.B strands.
his parameter is similar to the RasMol
.B ssbonds
parameter.

.TP
.B Set FontSize
The RasMol
.B 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
.B fontsize
is 32 pixels, and the default value is 8 pixels high. To
display atom labels on the screen use the RasMol
.B label
command and to change the colour of displayed labels, use
the
.B colour labels
command.

.TP
.B Set Hetero
The RasMol
.B hetero
parameter is used to modify the `default' behaviour of the RasMol
.B select
command, i.e. the behaviour of
.B select
without any parameters. When this value is
.B false,
the default
.B select
region does not include an heterogenous atoms (refer to the
predefined set
.B hetero
). When this value is
.B true,
the default
.B select
region may contain hetero atoms. This parameter is similar to
the RasMol
.B hydrogen
parameter which determines whether hydrogen atoms should be
included in the default set. If both
.B hetero
and
.B hydrogen
are
.B true,
.B select
without any parameters is equivalent to
.B select all.

.TP
.B Set HourGlass
The RasMol
.B 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
.B set hourglass on
enable the indicator, whilst
.B 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.

.TP
.B Set Hydrogen
The RasMol
.B hydrogen
parameter is used to modify the `default' behaviour of the RasMol
.B select
command, i.e. the behaviour of
.B select
without any parameters. When this value is
.B false,
the default
.B select
region does not include any hydrogen or deuterium atoms (refer
to the predefined set
.B hydrogen
). When this value is
.B true,
the default
.B select
region may contain hydrogen atoms. This parameter is similar to
the RasMol
.B hetero
parameter which determines whether heterogenous atoms should be
included in the default set. If both
.B hydrogen
and
.B hetero
are
.B true,
.B select
without any parameters is equivalent to
.B select all.

.TP
.B Set Kinemage
The RasMol
.B set kinemage
command controls the amount of detail stored in a Kinemage output
file generated by the RasMol
.B write kinemage
command. The output kinemage files are intended to be displayed by
David Richardson's Mage program.
.B set kinemage false,
the default, only stores the currently displayed representation in
the generated output file. The command
.B 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.

.TP
.B Set Menus
The RasMol
.B 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.

.TP
.B Set Mouse
The RasMol
.B set mouse
command sets the rotation, translation, scaling and zooming mouse
bindings. The default value is
.B 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
.B insight
and
.B quanta
provide the same mouse bindings as other packages for experienced
users.

.TP
.B Set Radius
The RasMol
.B set radius
command is used to alter the behaviour of the RasMol
.B dots
command depending upon the value of the
.B solvent
parameter.
When
.B solvent
is
.B true,
the
.B radius
parameter controls whether a true Van der Waal's surface
is generated by the
.B dots
command. If the value of
.B 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
.B solvent
is
.B 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
.B solvent
and changing
.B solvent
resets
.B radius
to its new default value.

.TP
.B Set Shadow
The RasMol
.B 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
.B 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.

.TP
.B Set SlabMode
The RasMol
.B 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".

.TP
.B Set Solvent
The RasMol
.B set solvent
command is used to control the behaviour of the RasMol
.B dots
command. Depending upon the value of the
.B solvent
parameter, the
.B 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
.B radius
parameter.
The command
.B set solvent false,
the default value, indicates that a Van der Waal's surface
should be generated and resets the value of
.B radius
to zero. The command
.B set solvent true
indicates that a `Connolly' or `Richards' solvent
accessible surface should be drawn and sets the
.B radius
parameter, the solvent radius, to 1.2 Angstroms (or 300
RasMol units).

.TP
.B Set Specular
The RasMol
.B 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
.B set specpower
command.

.TP
.B Set SpecPower
The
.B 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
.B 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.

.TP
.B Set SSBonds
The RasMol
.B 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
.B 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
.B backbone,
.B ribbons
or
.B strands.
his parameter is similar to the RasMol
.B hbonds
parameter.

.TP
.B Set Strands
The RasMol
.B 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
.B ribbons
command.

.TP
.B Set UnitCell
The RasMol
.B 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
.B show symmetry
display details of the crystal's space group and unit cell axes. The
.B set unitcell
command is similar the the commands
.B set axes
and
.B set boundbox
that display orthogonal co-ordinate axes and the bounding box
respectively.

.TP
.B Set VectPS
The RasMol
.B vectps
parameter is use to control the way in which the RasMol
.B write
command generates vector PostScript output files. The command
.B 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
.B set vectps off

.SH 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,
.B 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
.B and, or
and
.B 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
.B protein and backbone
selects protein bacbone atoms, not the protein and [nucleic] acid
backbone atoms!

.TP
.B 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
.B select 5,6,7,8
is also
.B 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.

.TP
.B 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
.B atomno
for the atom serial number,
.B elemno
for the atom's atomic number (element),
.B resno
for the residue number,
.B radius
for the spacefill radius in RasMol units (or zero if not represented
as a sphere) and
.B 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.

.TP
.B Within Expressions
A RasMol
.B within
expression allows atoms to be selected on their proximity to
another set of atoms. A
.B 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
.B within
expressions.

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

.TP
.B 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
.B select oxygen
is equivalent to the command
.B select elemno=8.

.SH Predefined Sets
.TP
.B 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
.B at
or the set
.B cg
This set is equivalent to the RasMol atom expressions
.B a,t
and
.B nucleic and not cg

.TP
.B Acidic Set
The set of acidic amino acids.
These are the residue types Asp and Glu.
All amino acids are classified as either
.B acidic,
.B basic
.B or
.B neutral.
This set is equivalent to the RasMol atom expressions
.B asp, glu
and
.B amino and not (basic or neutral)

.TP
.B Acyclic Set
The set of atoms in amino acids not containing a cycle or
ring. All amino acids are classified as either
.B cyclic
or
.B acyclic.
This set is equivalent to the RasMol atom expression
.B amino and not cyclic

.TP
.B 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
.B ala, gly, ile, leu, val

.TP
.B Alpha Set
The set of alpha carbons in the protein molecule. This set is
approximately equivalent to the RasMol atom expression
.B *.CA
This command should not be confused with the predefined set
.B helix
which contains the atoms in the amino acids of the protein's
alpha helices.

.TP
.B 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.

.TP
.B 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
.B cyclic.
This set is equivalent to the RasMol atom expressions
.B his, phe, trp, tyr
and
.B cyclic and not pro

.TP
.B 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
.B protein
and
.B nucleic
to distinguish between the two forms of backbone.
Atoms in nucleic acids and proteins are either
.B backbone
or
.B sidechain.
This set is equivalent to the RasMol expression
.B (protein or nucleic) and not sidechain

The predefined set
.B mainchain
is synonymous with the set
.B backbone.

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

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

.TP
.B 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
.B surface
or
.B buried.
This set is equivalent to the RasMol atom expression
.B amino and not surface

.TP
.B 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
.B at
or the set
.B cg
This set is equivalent to the RasMol atom expressions
.B c,g
and
.B nucleic and not at

.TP
.B Charged Set
This set contains the charged amino acids. These are the amino
acids that are either
.B acidic
or
.B basic.
Amino acids are classified as being either
.B charged
or
.B neutral.
This set is equivalent to the RasMol atom expressions
.B acidic or basic
and
.B amino and not neutral

.TP
.B Cyclic Set
The set of atoms in amino acids containing a cycle or rings.
All amino acids are classified as either
.B cyclic
or
.B acyclic.
This set consists of the amino acids His, Phe, Pro, Trp and Tyr.
The members of the predefined set
.B 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
.B his, phe, pro, trp, tyr
and
.B aromatic or pro
and
.B amino and not acyclic

.TP
.B 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
.B cystine
nor the RasMol
.B ssbonds
command have been used since the molecule was loaded. The set of
free cysteines may be determined using the RasMol atom expression
.B cys and not cystine

.TP
.B 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
.B structure
command.

This predefined set should not be confused with the predefined set
.B alpha
which contains the alpha carbon atoms of a protein.

.TP
.B 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
.B hetero
atoms are classified as either
.B ligand
or
.B solvent
atoms. These heterogenous
.B solvent
atoms are further classified as either
.B water
or
.B ions.

.TP
.B 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
.B elemno=1

.TP
.B 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
.B hydrophobic
or
.B polar.
This set is equivalent to the RasMol atom expressions
.B ala, leu, val, ile, pro, phe, met, trp
and
.B amino and not polar

.TP
.B 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
.B hetero
atoms are classified as either
.B ligand
or
.B solvent
atoms. All
.B solvent
atoms are classified as either
.B water
or
.B ions.

.TP
.B Large Set
All amino acids are classified as either
.B small,
.B medium
or
.B large.
This set is equivalent to the RasMol atom expression
.B amino and not (small or medium)

.TP
.B 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
.B hetero
atoms that are not
.B solvent
atoms. Hence this set is equivalent to the RasMol atom expression
.B hetero and not solvent

.TP
.B Medium Set
All amino acids are classified as either
.B small,
.B medium
or
.B large.
This set is equivalent to the RasMol atom expression
.B amino and not (large or small)

.TP
.B Neutral Set
The set of neutral amino acids.
All amino acids are classified as either
.B acidic,
.B basic
or
.B neutral.
This set is equivalent to the RasMol atom expression
.B amino and not (acidic or basic)

.TP
.B 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
.B purine
or
.B pyrimidine.
This set is equivalent to the RasMol atom expressions
.B a,c,g,t
and
.B purine or pyrimidine

.TP
.B Polar Set
This set contains the polar amino acids.
All amino acids are classified as either
.B hydrophobic
or
.B polar.
This set is equivalent to the RasMol atom expression
.B amino and not hydrophobic

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

.TP
.B Purine Set
The set of purine nucleotides.
These are the bases adenosine and guanosine (A and G respectively).
All nucleotides are either
.B purines
or
.B pyrimidines.
This set is equivalent to the RasMol atom expressions
.B a,g
and
.B nucleic and not purine

.TP
.B Pyrimidine Set
The set of pyrimidine nucleotides.
These are the bases cytidine and thymidine (C and T respectively).
All nucleotides are either
.B purines
or
.B pyrimidines.
This set is equivalent to the RasMol atom expressions
.B c,t
and
.B nucleic and not pyrimidine

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

.TP
.B 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
.B structure
command.

.TP
.B 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
.B protein
and
.B nucleic
to distinguish between the two forms of sidechain.
Atoms in nucleic acids and proteins are either
.B backbone
or
.B sidechain.
This set is equivalent to the RasMol expression
.B (protein or nucleic) and not backbone

.TP
.B Small Set
All amino acids are classified as either
.B small,
.B medium
or
.B large.
This set is equivalent to the RasMol atom expression
.B amino and not (medium or large)

.TP
.B 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
.B hetero
atoms are classified as either
.B ligand
or
.B solvent
atoms. All
.B solvent
atoms are classified as either
.B water
or
.B ions.
This set is equivalent to the RasMol atom expressions
.B hetero and not ligand
and
.B water or ions

.TP
.B 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
.B surface
or
.B buried.
This set is equivalent to the RasMol atom expression
.B amino and not buried

.TP
.B 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
.B structure
command.

.TP
.B 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
.B hetero
atoms are classified as either
.B ligand
or
.B solvent
atoms. The
.B solvent
atoms are further classified as either
.B water
or
.B ions.

.SH COLOUR SCHEMES
The RasMol
.B 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
.B cpk,
.B amino,
.B chain,
.B group,
.B shapely,
.B structure,
.B temperature,
.B charge
and
.B user
colour schemes for atoms, a
.B hbond type
colour scheme for hydrogen bonds and
.B 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.

.TP
.B Amino Colours
The RasMol
.B 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
.B shapely
scheme.

.TP
.B Chain Colours
The RasMol
.B 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.

.TP
.B CPK Colours
The RasMol
.B 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.

.TP
.B Group Colours
The RasMol
.B 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.

.TP
.B Shapely Colours
The RasMol
.B 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
.B shapely
colour scheme is used by David Bacon's Raster3D program. This colour
scheme is similar to the
.B amino
colour scheme.

.TP
.B Structure Colours
The RasMol
.B 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
.B structure
command may be used to force DSSP's structure assignment to be used.

.TP
.B Temperature Colours
The RasMol
.B 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
.B temperature
and
.B charge
colour schemes is that increasing temperature values proceed from blue
to red, whereas increasing charge valuse go from red to blue.

.TP
.B Charge Colours
The RasMol
.B 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
.B charge
and
.B 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
.B colour dots potential
command to colour code a dot surface (generated by the
.B dots
command) by electrostatic potential.

.TP
.B User Colours
The RasMol
.B 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.

.TP
.B HBond Type Colours
The RasMol
.B type
colour scheme applies only to hydrogen bonds, hence is used in the command
.B 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).

.TP
.B Potential Colours
The RasMol
.B potential
colour scheme applies only to dot surfaces, hence is used in the command
.B 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
.B colour charge
command. Like the
.B charge
colour scheme low values are blue/white and high values are red.

.SH SEE ALSO
The RasMol User Manual!

.SH AUTHOR
Copyright (C) 1992-94 by Roger Sayle. All rights reserved.
 (rasmol@ggr.co.uk)