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Label

Syntax:  label {<string>}
         label <boolean>

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

Load

Syntax:  load {<format>} <filename>
         load {<format>} inline 

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>}

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

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

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    Command Reference:   A-C     D-H     I-P     Q-Se     Se-St     T-Z