Hi! I am currently working on a protein where I have selected residues within 10A of its bound ligand in pymol. However, I can not find a way to print out what residues are contained in that group of residues that are within 10A. So far, I have tried this:
https://stackoverflow.com/questions/60049266/print-or-output-the-selected-residues-in-pymol
However, after cross-referencing the residues printed with those that I can see selected in the pdb file sequence, this method omits many of the residues.
Does anyone have a pymol command line they have used to accomplish this!
Thank you,
Kat Myers
Basically, what you want to do is to list all residues that contain at least one atom within 10Å of the ligand. However, you do not want to list all these atoms, but list each contact residues only once. So you first select all atoms within 10Å, then expand the selection to the entire residue using br., then contract the selection to an atom type which occurs only once in each residue, e.g. CA:
select contactRes, name CA and br. (receptor within 10.0 of ligand)
list=[]
iterate (contactRes), list.append(chain,resi,resn)
print list
(replace receptor and ligand by the selectors appropriate to your object)
See Presentation Intermediate PyMOL
, page 7- Badges
- Science topic