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OF CONTENTSCommand Reference: A-C D-H I-P Q-Se Se-St
T-Z
Quit
Syntax: quit
Exit from the RasMol program. The RasMol command exit
has a different function.
Refresh
Syntax: refresh
The RasMol refresh command is used in script files to redraw the local
image.
Renumber
Syntax: renumber {{-} <value>}
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
Syntax: reset
The RasMol reset command restores the original viewing transformation and
center of rotation. When the scale is set to its default value, zoom 100, the center of rotation is set
to the geometric center of the currently loaded molecule; with center all, this center is translated
to the middle of the screen and the viewpoint is 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
Syntax: restrict {<expression>}
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 color or
representation affect 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 that restrict disables the wireframe,spacefill and backbone representations in the
non-selected region.
The restrict command now turns off the display of ribbons,
strands, cartoons, and backbones outside of the given
atom expression.
Type help expression for more
information on RasMol atom expressions.
Ribbons
Syntax: ribbons {<boolean>}
ribbons <value>
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 color of the ribbon is changed by the RasMol color ribbon command. If the current ribbon color is none
(the default), the color 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 Å)
for nucleic acids. The default width of protein alpha helices and beta sheets is
380 (1.52 Å) and 100 (0.4 Å)
for turns and random coil. The secondary structure assignment is either from the
PDB file or calculated using the DSSP algorithm as used by the structure command. This command is
similar to the RasMol command strands,
which renders the biomolecular ribbon as parallel depth-cued curves.
Rotate
Syntax: rotate <axis> {-} <value>
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
Syntax: save {pdb} <filename>
save alchemy
<filename>
save mdl
<filename>
Save the currently selected set of atoms in either a Brookhaven Protein Database
(PDB) or AlchemyTM 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
Syntax: script <filename>
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 complicated 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 also often annotated using the RasMol echo command.
A RasMol script file can be generated with the write script or write rasmol commands to output the
sequence of commands that are needed to regenerate the current view, representation and
coloring of the currently displayed molecule. Such automatically-generated scripts
generate only a single image.
RasMol script files can also be created manually with a text editor. Such scripts, through
use of the pause and refresh commands, can generate "movies".
Detailed guides to script
creation are available.
The RasMol command source is synonymous with the script
command.
Select
Syntax: select {<expression>}
Defines the currently selected region of the molecule. All subsequent RasMol commands that
manipulate a molecule or modify its color or representation, only affect the currently
selected region. The parameter of a select command is a RasMol atom
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 behavior of the select command without any parameters is determined by
the RasMol hetero and hydrogen parameters.
Type help expression for more
information on RasMol atom expressions.
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