Thanks Thomas

I've just one extra question about ligand sites.

As I've said previously I can obtain information about polar contacts between ligand and its surrounding residues via Present- ligand sites.

On the next step I mask all other non relevant parts of the protein ( wich are represented as the cartoon) by

hide cartoon

so as the consequence I have only ligand and its environment ( other residues and some water)

How I could select all this visible (relevant) part and save it in the separate pdb?
I've not found such simple selection by the visible part in the selection algebra :(


2012/1/20 Thomas Holder <>
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 to find settings) For example:

set h_bond_cutoff_center, 5.0
set h_bond_cutoff_edge, 4.0


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