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
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