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Command Reference
RasMol allows the execution of interactive commands typed at the "RasMol>" prompt in the command-line window (a window separate from the graphics 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 recognized by RasMol are given below.

*Note that the Set command includes a large number of important options, including, for example, set picking which allows the measurement of distances, angles and torsion angles among other things.

Backbone
Syntax:  backbone {<boolean>}
             backbone <value>
             backbone dash
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 parameter 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 �) or above results in a "Parameter value too large" error. Backbone objects may be colored using the RasMol color backbone command.
The reserved word backbone is also used as a predefined set and as a parameter to the set hbond and set ssbond commands. The RasMol command trace renders a smoothed backbone, in contrast to backbone which connects alpha carbons with straight lines. Wireframe, backbone, and strands representations may be displayed with dashed (dotted) lines. This is enabled by allowing the dash or dashes parameter to the wireframe, backbone, and strands commands.
Background
                                 Syntax:   background <color>
The RasMol background command is used to set the color of the "canvas" background. The color may be given as either a color name or a comma-separated triple of Red, Green and Blue (RGB) components enclosed in square brackets. Typing the command help colors will give a list of the predefined colors recognized by RasMol. When running under X Windows, RasMol also recognizes colors in the X server's color name database.
The background command is synonymous with the RasMol set background command.






Cartoon
                         Syntax:   cartoon <number>
The ribbons representation in RasMol has been extended to allow the display of Richardson (MolScript) style protein cartoons. They are currently implemented as thick (deep) ribbons. The easiest way to obtain a cartoon representation of a protein is to use the new Cartoons option on the Display menu. The cartoon <number> or cartoons <number> command on the RasMol command line represents the currently selected residues as a deep ribbon with width specified by the command's argument. Using the command cartoons without a parameter results in the ribbon's width being taken from the protein's secondary structure, as described in the ribbons command. By default, the C-termini of beta-sheets are displayed as arrow heads. This may be enabled and disabled using the set cartoons <boolean> command. The depth of the cartoon may be adjusted using the set cartoons <number> command. The set cartoons command without any parameters returns these two options to their default values.
Center
Syntax:  center {<expression>}
             centre {<expression>}
The RasMol center (or 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
Syntax:  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.

Color
Syntax:  color {<object>} <color>
             colour   {<object>} <colour>
             color   {<object>} <[RGB triplet]>
Color the atoms (or other objects) of the selected zone. The color may be given as either a color name or a comma-separated triple of Red, Green and Blue (RGB) components enclosed in square brackets. A typical RGB triplet is [255,255,255], which is the color white. Typing the command, help colors, will give a list of all the predefined colors recognized by RasMol.
Allowed objects are atoms, bonds, backbone, ribbons, labels, dots, hbonds, and ssbonds. If no object is specified, the default keyword atom is assumed. Some color schemes are defined for certain object types.
The color scheme none can be applied to all objects except atoms and dots, stating that the selected objects have no color of their own, but use the color of their associated atoms (i.e. the atoms they connect). This command is especially useful in script files.
Atom objects can also be colored by cpk, amino, chain, group, shapely, structure, temperature, charge, and user. Hydrogen bonds can also be colored by type and dot surfaces can also be colored by electrostatic potential.
For more information, see Colors and Color Schemes.


Connect
                           Syntax:   connect {<boolean>}
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.
CPK
             The RasMol command cpk is synonymous with spacefill.
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