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