- 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 determine the cylinder radius of the representation in 0.004 angstrom
units. Backbone objects may be coloured using the RasMol
colour backbone
command. A parameter value of 500 (2 angstroms) or above results in an
"Integer argument too large" error.
- 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.
- 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.
- Colour
-
Colour the atoms (or other objects) of the selected zone. 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,
hbonds,
ribbons
and
ssbonds.
If no object is specified, the default keyword
atom
is assumed.
Some colour schemes are defined for certain object types. The colour scheme
none
can be applied all objects accept atoms, 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
amino,
cpk,
chain,
group,
shapely,
structure,
temperature
and
user
and hydrogen bond objects can also be coloured by
type.
For more information type
help colour <colour>.
- 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.
- Load
-
Load either a Brookhaven Protein Databank (PDB) file or Alchemy(tm) format
file into RasMol2. Only a single PDB file may be loaded at a time. This
command selects all the atoms in the molecule, and sets the default
representation to be a cpk coloured wireframe model.
- Quit
-
Exit from the RasMol program.
- Renumber
-
The RasMol
renumber
command sequentially numbers the residues in a macromolecular chain.
The optional parameter specifies the value of the first residue in the
sequence. By default, this value is one. For proteins,
each amino acid is numbered consecutively from the N terminus to the C
terminus. For nucleic acids, each base is numbered from the 5' terminus
to 3' terminus. All chains in the current database are renumbered and gaps
in the original sequence are ignored. The starting value for numbering may
be negative.
- Reset
-
The RasMol
reset
command restores the original viewing transformation
and centre of rotation. The scale is set to it default value,
zoom 100,
the centre of rotation is set to the geometric centre of the currently
loaded molecule,
centre all,
this centre is translated to the middle of the screen and
the viewpoint set to the default orientation.
This command should not be mistaken for the RasMol
zap
command which deletes the currently stored molecule, returning the
program to its initial state.
- Restrict
-
The RasMol
restrict
command both defines the currently active zone 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
zone. 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-active zone.
Type "help expression" for more information on RasMol atom expressions.
- Ribbons
-
The RasMol
ribbons
command displays the currently loaded protein 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 width of the ribbon at each position is determined by the optional
parameter in the usual RasMol units. By default this value is 380, which
produces a ribbon 1.52 Angstroms wide. The number of strands in the
ribbon may be altered using the RasMol
set strands
command. The rendering of the ribbon may also be changed using the
set ribbons
command.
- 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. This command should not be
confused with the RasMol
write
command which generates either image or script files.
- Script
-
The RasMol
script
command reads a set of commands sequentially from a
text file and executes them. This allows sequences of commonly used
commands to be stored and performed by a 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.
- Select
-
Define the currently active zone of the molecule. All subsequent RasMol
commands that manipulate a molecule or modify its colour or representation,
only effects the currently selected zone. The parameter of a
select
command is a RasMol expression that is evaluated for every atom of the
current molecule. The currently selected (active) zone of the molecule
are those atoms that cause the expression to evaluate true. To select
the whole molecule use the RasMol command
select all.
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. For more information on each
internal parameter type
help set <parameter>.
- 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.
Integer 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
-
Represent the currently selected zone as a spacefilling union of spheres
model. An integer parameter may be used to specify the radius of each
atom given in 4nm units. If no parameter is given, each atom is drawn as
a sphere of its Van der Waals radius.
The
temperature
option is used to set the radius of each selected sphere
to the value in the temperature field of the molecule file. A zero or
negative value causes no change in the selected atom. Temperature values
greater than 2.00 are truncated to 2.00 Angstrom radius.
The
user
option allows the radius of the selected spheres to be determined
by matching each atom against optional lines in the input data file. Details
of the wildcard pattern matching used by Raster3D's COLOR records is given
in the manual.
- 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.
- Structure
-
The RasMol
structure
command calculates secondary structure assignments
for the currently loaded protein. If the original PDB file contained
structural assignment records (HELIX and SHEET) these are discarded.
Initially, the hydrogen bonds of the current molecule are found, if this
hasn't been done already. The secondary structure is the determined using
Kabsch and Sander's DSSP algorithm. Once finished the program reports the
number of helices and ladders 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
-
Represent each bond within the selected zone of the molecule as either
a cylinder or depth-cued vector. If no parameter is given, RasMol draws
each bond as a hither-and-yon shaded narrow vector. An integer parameter
specifies the radius of a cylinder, given in 4nm units, to be used as a
stick bond.
- Write
-
Write the current image to a file in a standard raster format. Currently
supported file formats include
gif
(Compuserve GIF),
ppm
(Portable Pixmap),
ras
(Sun rasterfile),
ps
and
epsf
(Encapsulated PostScript),
monops
(Monochrome Encapsulated PostScript) and
bmp
(Microsoft bitmap). This command should not be confused with the RasMol
save
command which save the currently selected portion of the molecule.
- 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.
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.
- Example Expressions
-
The following table gives some useful examples of RasMol
atom expressions.
- Primitive Expressions
-
RasMol primitive expressions are the fundamental building blocks
of atom expressions. There a two basic 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,
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.
- 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
RasMol 0.004 Angstrom units. 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(800,backbone)
selects any atom within a 3.2 Angstrom radius of any atom in a
protein or nucleic acid backbone.
Within
expressions are particularly usefull for selecting the atoms
around an active site.
- Predefined Sets
-
RasMol atom expressions may contain predefined sets. Thsese 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 predfined sets
is given below.