Re: [PyMOL] Viewing a binding pocket

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

Hi Jeff,

try this:

# given a ligand within a protein binding pocket
select ligand, resn HEM

# detect nearest neighbors within X distance
select neighbors, polymer within 5.0 of ligand

# select the residue of each neighbor, add a label
label byca neighbors, resn + resi + chain

# set an appropriate clipping plane
zoom neighbors

# shade the rest of the molecular as solid or something otherwise non
# hostile to viewing.
as lines
show sticks, neighbors ligand
show labels

Hope that helps.

Cheers,
   Thomas


Jeff Johns wrote, On 06/09/12 10:51:
> I am sure this has been asked many times before but I can't find the
> answer after much searching...
> 
> Is there a pymol script that, given a ligand within a protein binding
> pocket, will detect nearest neighbors within X distance (not necessarily
> H bonded), select the residue of each neighbor, add a label, set an
> appropriate clipping plane, then shade the rest of the molecular as
> solid or something otherwise non hostile to viewing.
> 
> Something like ligplot but in 3-D.
> 
> Many thanks,
> 
> Dr Jeff Johns
> Melatonin Research Group
> Faculty of Pharmaceutical Sciences
> Khon Kaen University
> Khon Kaen 40002
> Thailand
> Phone: +66 (0)43 202 378
> Email: jj...@kk...
> Alternative email: jef...@ho...

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