Thank you for this pearl.
Em ter., 7 de jul. de 2020 às 11:23, Thomas Holder <
thomas.hol...@schrodinger.com> escreveu:
> Hi Pedro,
>
> I would probably just count CA atoms. Something like this:
>
> # Check nearby peptides
> tmpsele = pm.get_unused_name("_tmp")
> pm.select(tmpsele, f"({sim_pdb} a
Hi Pedro,
I would probably just count CA atoms. Something like this:
# Check nearby peptides
tmpsele = pm.get_unused_name("_tmp")
pm.select(tmpsele, f"({sim_pdb} and polymer) within 5 of "
f"({entry.pdb_id} and (bysegi resid {entry.ligand_resid} "
f"and chain {entry.ligand_chain}))")
for
I used the function to check if the fasta is smaller than 25 characters. If
it is then it is a peptide:
https://github.com/pslacerda/pymol-labimm/blob/master/scripts/peptbase/create.py#L186
There is another way to check for peptides using only selection?
Em seg., 6 de jul. de 2020 às 02:47, Thoma
Hi Pedro,
cmd.get_fastastr() always returned a FASTA formatted string. What changed in
PyMOL 2.2 is that it now creates a record for every chain, not just for every
object. There is a new "key" argument, you get the old behavior with
key="model".
print(cmd.get_fastastr(key="model"))
If you ac
