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Label
Syntax:  label {<string>}
             label <boolean>
The RasMol label command allows an arbitrary formatted text string to be associated with each currently selected atom. This string may contain embedded 'expansion specifiers' which display properties of the atom being labelled. An expansion specifier consists of a '%' character followed by a single alphabetic character specifying the property to be displayed (similar to C's printf syntax). An actual '%' character may be displayed by using the expansion specifier '%%'.
Atom labelling for the currently selected atoms may be turned off with the command label off. By default, if no string is given as a parameter RasMol uses labels appropriate for the current molecule. RasMol uses the label "%n%r:%c.%a" if the molecule contains more than one chain; "%e%i" if the molecule has only a single residue (a small molecule); and "%n%r.%a" otherwise.
The color of each label may be changed using the color label command. By default, each label is drawn in the same color as the atom to which it is attached. The size of the displayed text may be changed using the set fontsize command.
The following table lists the current expansion specifiers:
    %a           Atom Name
    %b %t     B-factor/Temperature
    %c %s    Chain Identifier
    %e           Element Atomic Symbol
    %i           Atom Serial Number
    %m          single letter amino acid code
    %n          Residue Name; three letter code
    %r           Residue Number
The syntax of RasMol atom expressions allows the selection of individual molecule conformations if present in an NMR file. The simplest form of the atom expression is the syntax "::25" to select model 25 from the molecule. This is equivalent to the atom expression, "model = 25", as the keyword model may now be used in comparison expressions. The most general form of atom expression is now CYS32:A:25.SG which denotes the gamma sulfur of residue cysteine-32 in chain A of model 25.
Individual chains may be specified by the syntax ":A" for chain A, or ":1" for chain 1 (i.e. the wildcard may be dropped from the expression "*:A"). This may also be extended to NMR models; ":A:4" denotes chain A of model 4, and even more terse, "::4" means all atoms in all chains of NMR model 4.
Load
Syntax:  load {<format>} <filename>
             load {<format>} inline
Load a molecule coordinate file into RasMol. Valid molecule file formats are pdb (Brookhaven Protein Databank), mdl (Molecular Design Limited's MOL file format), alchemy (Tripos' Alchemy file format), mol2 (Tripos' Sybyl Mol2 file format), mopac (mopac file format; either Cartesian or z-matrix format), nmrpdb (nmr multi-pdb file format), charmm (CHARMm file format) or xyz (MSC's XMol XYZ file format). If no file format is specified, pdb is assumed by default. Only a single molecule may be loaded at a time. To delete a molecule prior to loading another, use the RasMol zap command.
The load command selects all the atoms in the molecule, centers it on the screen and renders it as a CPK colored wireframe model. If the molecule contains no bonds (i.e. contains only alpha carbons), it is drawn as an alpha carbon backbone. If the file specifies less bonds than atoms, RasMol determines connectivity using the connect command.
The load inline command also allows the storing of atom coordinates in scripts to allow better integration with WWW browsers. A load command executed inside a script file may now specify the keyword inline instead of a conventional filename. This option specifies that the coordinates of the molecule to load are stored in the same file as the currently executing commands. Typically this is used in the command load pdb inline, which is followed by a number of RasMol commands terminated by the command exit. The exit command terminates execution of the current script and returns control to the command line (or the calling script). This means any lines following exit are never interpreted by RasMol. These may be used to store atomic coordinates in PDB file format. Because in Brookhaven PDB file format, any line not recognized by the parser should be ignored, only lines beginning ATOM, HETATM, TER, etc. are examined. Hence a file may be both a RasMol script and a PDB file simultaneously. This allows both coordinate and representation data to be transmitted as a single file. One possible use is a standard RasMol script prefix that may be concatenated with an appropriate PDB file on-the-fly.
Monitor
Syntax: monitor <number>  <number>
             monitor {<boolean>}
The RasMol monitor command allows the display of distance monitors. A distance monitor is a dashed (dotted) line between an arbitrary pair of atoms, optionally labelled by the distance between them. The RasMol command monitor <number> <number> adds such a distance monitor between the two atoms specified by the atom serial numbers given as parameters.
Distance monitors are turned off with the command monitors off. By default, monitors display the distance between its two end points as a label at the center of the monitor. These distance labels may be turned off with the command set monitors off, and re-enabled with the command set monitors on. Like most other representations, the color of a monitor is taken from the color of its end points unless specified by the color monitors command.
Distance monitors may also be added to a molecule interactively with the mouse, using the set picking monitor command. Clicking on an atom results in its being identified on the rasmol command line. In addition every atom picked increments a modulo counter such that in monitor mode, every second atom displays the distance between this atom and the previous one. The shift key may be used to form distance monitors between a fixed atom and several consecutive positions. A distance monitor may also be removed (toggled) by selecting the appropriate pair of atom end points a second time.
Pause
                    Syntax: pause
The RasMol pause command is used in script files to stop the script file for local manipulation by a mouse, until any key is pushed to restart the script file. Wait is synonymous with pause.
This command may be executed in RasMol script files to suspend the sequential execution of commands and allow the user to examine the current image. When RasMol executes a pause command in a script file, it suspends execution of the rest of the file, refreshes the image on the screen and allows the manipulation of the image using the mouse and scroll bars, or resizing of the graphics window. Once a key is pressed, control returns to the script file at the line following the pause command. While a script is suspended the molecule may be rotated, translated, scaled, slabbed and picked as usual, but all menu commands are disabled. The pause can probably be used most effectively with echo commands in education pre-scripted demonstrations, where a description of the current image is presented to the user/student. Typically the command before a pause should be "echo   Press any key to continue".
Execution of a script can be cancelled by pressing Control-D or Control-Z (on VAX/VMS, Control-C) while standing at a pause. The command set picking none disables picking, which avoids the display of spurious messages whilst a script is suspended at a pause.
Print
                Syntax: print
The RasMol print command sends the currently displayed image to the local default printer using the operating system's native printer driver. Note: this command is not yet supported under UNIX or VMS. It is intended to take advantage of Microsoft Windows and Apple Macintosh printer drivers. For example, allowing images to be printed directly on a dot matrix printer.
When using RasMol on a UNIX or VMS system this functionality may be achieved either by generating a PostScript file using the RasMol write ps or write vectps commands and printing that, or generating a raster image file and using a utility to dump that to the local printer.
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