Command Language

Spock's command language is divided into two categories, ``actions'' and ``selections''. Actions are commands you want spock to carry out, such as coloring bonds, or rotating the molecule. Selections specify which objects (atoms, ribbons, and surfaces, for example) you want the command to apply to. In order to keep from introducing yet another command language, spock's command language is based in part on GRASP by Anthony Nichols [11], and RasMol by Roger Sayle. In spock's syntax, the action is always specified first, optionally followed by a selection. For example, if you wanted to color all bonds red, you would type bc=$red, but if you only wanted to color the bonds in residue 23 red, you would type bc=$red,rn=23. (Throughout this document, things in Text Type font indicate commands you would type on spock's command line. Also, for the nucleic acid aficionados out there, don't feel slighted, but I'll use the term ``residue'' to refer to either an amino acid residue or a nucleic acid nucleotide.) Note that any trailing colon in the descriptions and examples is not a part of the command.