Hi Carsten,

Thanks for the help. I've tried variants of that selection and it works great if there is only one ligand. Unfortunately it breaks down when there are multiple ligands and they don't all fit the criteria. I'm surveying almost half the PDB so these are all different proteins with different binding sites and ligands. I was hoping for a way to get pymol to recognize each individual ligand automatically by grouping common resids within the non-solvent hetatm selection. Using the %s %(resi) seems to require an explicit input.

I might be able to extract an explicit chain/resi designation for each file from the het portion of the pdb header, though I'm not sure how to automate this. I suppose it's back to the script repository for me.


On Fri, Dec 13, 2013 at 2:50 PM, Schubert, Carsten [JRDUS] <CSCHUBER@its.jnj.com> wrote:



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.




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,


"Nil illegitimo carborundum" - Didactylos

"Nil illegitimo carborundum" - Didactylos