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Define
                    Syntax:   define <identifier> <expression>
The RasMol 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.
Dots
Syntax:  dots {<boolean>}
             dots <value>
The RasMol 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 Waal's radius about each selected atom. Dots that are 'buried' within the Van der Waal's radius of any other atom (selected or not) are not displayed. The command 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 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 color of each point on a dot surface is the color of its closest atom at the time the surface is generated. The color of the whole dot surface may be changed using the color dots command.
Echo
                   Syntax:   echo {<string>}
The RasMol 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 echo command displays a blank line.
This command, combined with pause, is particularly useful for displaying text from within a RasMol script file.
Exit
                          Syntax:   exit
The RasMol exit command is used to terminate execution of a script (returning to the command line, or the calling script), or of inter-process communication (IPC), closing the link between programs.
The quit command, in contrast, terminates the execution of RasMol itself.
HBonds
Syntax:  hbonds {<boolean>}
             hbonds <value>
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 color of hbond objects may be changed by the color hbond command. Initially, each hydrogen bond has the colors 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
Syntax: help {<topic> {<subtopic>}}
                 ? {<topic> {<subtopic>}}
The RasMol help command provides on-line help on the given topic.
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