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Syntax: quit
Exit from the RasMol program. The RasMol command exit has a different function.
Syntax: refreshThe RasMol refresh command is used in script files to redraw the local image.
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.
Syntax: resetThe 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.
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.
Type help expression for more information on RasMol atom expressions.
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.
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.
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.
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.
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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Command Reference:
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