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} and polymer) within 5 of "
> f"({entry.pdb_id} and (bysegi resid {entry.ligand_resid} "
> f"and chain {entry.ligand_chain}))")
> for chain in pm.get_chains(tmpsele):
> if pm.count_atoms(f"guide & bs. ({tmpsele} & chain {chain})") <= 25:
> pm.delete(sim_pdb)
> is_apo = False
> break
> pm.delete(tmpsele)
>
>
> Cheers,
> Thomas
>
>
> > On Jul 6, 2020, at 10:59 PM, Pedro Lacerda <pslace...@gmail.com> wrote:
> >
> > 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, Thomas Holder <
> thomas.hol...@schrodinger.com> escreveu:
> > 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 actually want the plain sequence and not the fasta formatted
> string, then I suggest you use a function like this:
> >
> > def get_sequence(selection='all'):
> > return ''.join(L.strip() for L in
> cmd.get_fastastr(selection).splitlines()
> > if not L.startswith('>'))
> >
> >
> > Cheers,
> > Thomas
> >
> >
> > > On Jul 4, 2020, at 5:17 PM, Pedro Lacerda <pslace...@gmail.com> wrote:
> > >
> > > Hi,
> > >
> > > The get_fastastr function changed. Before it returned the aminoacid
> sequence. Now it returns a FASTA formatted string.
> > >
> > > How can I get the old behaviour (ie. get the aminoacid sequence)?
> > >
> > > --
> > > Pedro Sousa Lacerda
> > >
> > > Laboratório de Bioinformática e Modelagem Molecular
> > > Faculdade de Farmácia / UFBA
> > >
> > > @pslacerda
> > > +55 71 9 9981-1856
> > > http://lattes.cnpq.br/8338596525330907
> > > _______________________________________________
> > > PyMOL-users mailing list
> > > Archives:
> http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> > > Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
> >
> > --
> > Thomas Holder
> > PyMOL Principal Developer
> > Schrödinger, Inc.
> >
> >
> >
> > --
> > Pedro Sousa Lacerda
> >
> > Laboratório de Bioinformática e Modelagem Molecular
> > Faculdade de Farmácia / UFBA
> >
> > @pslacerda
> > +55 71 9 9981-1856
> > http://lattes.cnpq.br/8338596525330907
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
--
Pedro Sousa Lacerda
Laboratório de Bioinformática e Modelagem Molecular
Faculdade de Farmácia / UFBA
@pslacerda
+55 71 9 9981-1856
http://lattes.cnpq.br/8338596525330907
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