Re: [PyMOL] Protein-ligand interactions

[Thomas H. <sp...@us...>]

Hi James,

> 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?

The preset selects hetatoms as ligands, so you could do:

select motif, (pepseq SYG) and not (name C+N+O)
alter motif, type="HETATM"

> 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?

there are several h_bond_* settings that control this. (I recommend 
http://pymolwiki.org/index.php/Grepset to find settings) For example:

set h_bond_cutoff_center, 5.0
set h_bond_cutoff_edge, 4.0


Cheers,
   Thomas

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen