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