Katherine,

 

not sure if that is what you are looking for but you can select for non-polymer residues with:

 

select lig, prot and organic

 

That will select any non polymer (protein and R(D)NA) residues present in the pdb. You then would need to break the selection further into the individual constituents, by either chain Id and resid.

 

Hope this helps a bit.

 

Carsten

 

From: Katherine Sippel [mailto:katherine.sippel@gmail.com]
Sent: Friday, December 13, 2013 10:28 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Selection algebra issue

 

Hi all,

I'm trying to write a script to data mine the pdb. I'm want to look at the ligands in a pdb file and fish out those that meet a certain criteria. I've got a script that can look at the ligands all at once but I need to assess each ligand individually. Since I'm looking at 40,000+ pdbs I need a way to define them individually. I've tried variations on "%s' % (resi)" and "bymolec" but I can't seem to figure out how to get them parsed separately without specifying a number. I've also tried using index to create a tuples list and iterating from that but I keep hitting the same issue. I've attached a couple of the attempted scripts so you can laugh at my google derived python skills.

I've been trying to figure this out for a week now and I'm completely stumped. If anyone could nudge me in the right direction, even if it's some Pymolwiki article I missed, I would appreciate it immensely.

Thanks for your time,
Katherine


--

"Nil illegitimo carborundum" - Didactylos