[PyMOL] Protein-ligand interactions

[James S. <jms...@gm...>]

Dear PyMol users!


I've decided create new topic about representation of the protein-ligand
interactions via Pymol because of alot of questions wich have been emerged
during last month.

Commonly I use the PyMol built-in command a-> present->ligands sites->
cartoon for the representation of the polar contacts between protein and
ligand


1- Some of my proteins consist of ligand wich include some of amino acids
from sequence of my protein ( e.g fluorophores in GFP). So I'd like to
assign some residue motif as the ligand group ( e.g Ser Tyr Gly motif in
GFP). How I could do it?


2- In some cases there are relatively long distances between polar ligand
groups and protein's polar residues where H-bond must be formed ( eg in
some cases up to 3.5-3.7 A ). So the default  a-> present->ligands sites->
cartoon  does not recognize that long H-bonds. How I could set the H-bond
cutoff distance in the above method?



3- Is there any way to represent tight packing contacts beetween non-polar
groups in my protein (or protein\ ligand sites) besides common
representation of the Vdv radii ?


Thank for help,


James