Tony, I'll answer the easy questions, and leave the tough ones to the real gurus...
> 1) I would like to show certain residues and have no problem getting the > ones I want selected and displayed as sticks or whatever. The problem is > color. When I change the color of the selection, it changes the color of > the associated section of the ribbon. I would like to leave the ribbon, say > green, and show the residues in yellow. The easiest way is to use two objects. Say you already have your protein object (my_protein) and the selection of required objects (my_sel): hide everything create copy, my_protein show ribbon, my_protein color green, ribbon show sticks, my_sel color yellow, my_sel > 2) When selecting specific sidechains, it is often preferable to choose > only the sidechain atoms instead of the sidechain+backbone. In the good ol' > molscript days you would say select and not c or n or o but if you do that > in pymol it thinks you mean all carbon, nitrogen, and oxygen atoms instead > of their id in the PDB file. I'm sure this is worked out but I don't see it > in the example scripts I've found on line. PyMOL distinguished between element types and PDB atom names. For example, select all_oxygen, (e;o) select backbone_oxygen, (n;o) So to select sidechain atoms of an existing selection my_sel: select sidechain_of_my_sel, (my_sel & !n;n,c,o) Gareth -- ------------------------------------------------------------------------------- Gareth Stockwell EMBL - European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD gar...@ebi.ac.uk Tel 01223 492548 http://www.ebi.ac.uk/~gareth
