The molecule/atom information is organized as in the CHARMM/CHARMm program(s). All atoms in a molecule system can be defined/identified through a segment name, residue name and/or residue number and an atom name. This arrangement is very flexible and can be used to define quite complicated commands.
The line commands, when they want to be applied on a set of atoms, must be give as:
Segment_name Residue_name/number Atom_name/number
The segment, residue and atom name can be 1-4 characters long. The names are assigned when one reads a coordinate file. For a command the data is supplied as three fields separated by ':'. Example set atom colour S1 * CA yellow sets all CA atoms in all residues in segment S1 to the colour yellow. The general identifier looks like segment residue atom where the segment name is always a character string. The wild character '*' and the '?' characters can be used. The '*' character matches all strings and '?' matches any character at it's position. In the residue and atom field residue numbers and atom numbers can be used or a combination of characters and integer numbers. Example: set atom colour S1 TYR,1,10,30-45 CA,N,C blue command sets all CA,N and C atoms in all tyrosine residues and residues 1,10 and range 30-45 in segment S1 to the colour blue.
Please note:
The interpreter for gOpenMol interprets the lower and upper case letters as different. This applies for both commands and segment/residue/atom names.
This is not really useful for more than me (so far).