Hi everyone,
I'm trying to do some distance extraction of hetero atoms in pdbs. I've got
for model in pdb_obj.hierarchy.models():
for chain in model.chains():
for rg in chain.residue_groups():
for ag in rg.atom_groups():
for atom in ag.atoms():
if atom.hetero == True:
print atom.distance(atom)
Which prints out 0.0 as expected. But I can't figure out how to, say, measure the distance to an atom in the previous residue (if there is a previous residue).
I also noticed something weird in this tutorial:
They truncate a non-standard amino acid to the beta-carbon but this only works because there's an alternate conformation with a standard amino acid (Cys). So it wouldn't work with a seleno-met for instance (I know there's a convert-to-ala function in mmtbx - I said it was weird, not terrible).
Anyway, I hope someone can explain the distances thing for me. I'm sure there are multiple ways of doing it (should I just do a selection of "hetatm" and iterate over them and try to get some distanes?).
Cheers,
Morten