[Biopython] Antwort: Re: Antwort: Re: Antwort: Re: PDB parsing

Paul.Czodrowski at merck.de Paul.Czodrowski at merck.de
Tue May 10 11:05:50 UTC 2011


Dear Joao,

thanks for your help and the documentation link!
So far, I was aware of this documentation
http://biopython.org/DIST/docs/tutorial/Tutorial.html

wherein PDB parsing is only briefly covered.

And, yes, progress is faster now!


Cheers,
Paul


> Use PDBIO.
>
> from Bio.PDB import PDBIO
> IO = PDBIO()
> IO.set_structure(your_structure)
> IO.save(output_filename)
>
> You can also control which parts of the structure to output with Select.
>
> Check the documentation<http://www.biopython.
> org/DIST/docs/cookbook/biopdb_faq.pdf>,
> it will make you progress much faster :)
>
> Cheers,
>
> João [...] Rodrigues
> http://nmr.chem.uu.nl/~joao
>
>
>
> On Tue, May 10, 2011 at 11:32 AM, <Paul.Czodrowski at merck.de> wrote:
>
> > Dear João,
> >
> >
> > cool, thank you very much so far!
> >
> > How do I output the newly generated PDBfile?
> >
> > Cheers & thanks,
> > Paul
> >
> >
> >
> > > Hey Paul,
> > >
> > > First of all, you should not call _parse on your own. That is called
> > > already when you call get_structure(). Generally, if a method has an
> > > underscore behind its name it means it shouldn't really be called
> > > unless you really know what you want to do with it.
> > >
> > > What version of Biopython are you using?
> > >
> > > I'd do this:
> >
> > > structure_id = "1234"
> > > PDBFILE = open(filename,'r')
> > > p = PDBParser(PERMISSIVE=1)
> > > pp = p.get_structure(structure_id, PDBFILE)
> > >
> > > for atom in pp.get_atoms():
> > >  atom.bfactor = 10.0
> > >  print atom.bfactor
> > >
> > > It works pretty well here, with version 1.57.
> > >
> > > Cheers,
> > >
> > > João [...] Rodrigues
> > > http://nmr.chem.uu.nl/~joao
> > >
> > >
> >
> > > On Tue, May 10, 2011 at 11:19 AM, <Paul.Czodrowski at merck.de> wrote:
> > > Dear Joao,
> > >
> > > this one does not work:
> > > "
> > >
> > > structure_id = "1234"
> > > PDBFILE = open(filename,'r').read()
> > > p = PDBParser(PERMISSIVE=1)
> > > p._parse(PDBFILE)
> > > pp = p.get_structure(structure_id, PDBFILE)
> > >
> > >
> > > for atom in pp.get_atoms():
> > >  atom.bfactor = 10.0
> > >  print atom.bfactor
> > > "
> > >
> > >
> > > "p.get_structure(structure_id, PDBFILE)" seems to get the structural
> > data,
> > > but setting the bfactor does not give any output.
> > >
> > >
> > >
> > >
> > > Cheers & Thanks,
> > > Paul
> > >
> > >
> > > > Hey Paul,
> > > >
> > > > When you parse a PDB file with PDBParser it automatically retrieves
> > both
> > > > B-factor and occupancy. If it fails to do so for any reason, it
> > defaults
> > > > those values to 0.
> > > >
> > > > After parsing, you can set those values explicitly by modifying the
> > > > corresponding attribute of the Atom object. So, for example, to
change
> > > the
> > > > B-factor of all your atoms to 10.0, you just have to do:
> > > >
> > > > for atom in structure.get_atoms():
> > > > >   atom.bfactor = 10.0
> > > > >
> > > >
> > > > Hope this answered your question.
> > > >
> > > > Cheers,
> > > >
> > > > João [...] Rodrigues
> > > > http://nmr.chem.uu.nl/~joao
> > > >
> > > >
> > > >
> > > > On Tue, May 10, 2011 at 9:50 AM, <Paul.Czodrowski at merck.de> wrote:
> > > >
> > > > >
> > > > > Dear folks,
> > > > >
> > > > > how do I add a B-factor as well as an occupancy column to a PDB
file?
> > > > >
> > > > > I guess Bio.PDB is the appropriate module.
> > > > > But I already fail with regards to a simple PDB load...
> > > > >
> > > > >
> > > > > Cheers,
> > > > > Paul
> > >
> > > This message and any attachment are confidential and may be
privileged or
> > > otherwise protected from disclosure. If you are not the intended
> > recipient,
> > > you must not copy this message or attachment or disclose the contents
to
> > > any other person. If you have received this transmission in error,
please
> > > notify the sender immediately and delete the message and any
attachment
> > > from your system. Merck KGaA, Darmstadt, Germany and any of its
> > > subsidiaries do not accept liability for any omissions or errors in
this
> > > message which may arise as a result of E-Mail-transmission or for
damages
> > > resulting from any unauthorized changes of the content of this
message
> > and
> > > any attachment thereto. Merck KGaA, Darmstadt, Germany and any of its
> > > subsidiaries do not guarantee that this message is free of viruses
and
> > does
> > > not accept liability for any damages caused by any virus transmitted
> > > therewith.
> > >
> > > Click http://disclaimer.merck.de to access the German, French,
Spanish
> > and
> > > Portuguese versions of this disclaimer.
> > >
> > >
> > > _______________________________________________
> > > Biopython mailing list  -  Biopython at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/biopython
> >
> > This message and any attachment are confidential and may be privileged
or
> > otherwise protected from disclosure. If you are not the intended
recipient,
> > you must not copy this message or attachment or disclose the contents
to
> > any other person. If you have received this transmission in error,
please
> > notify the sender immediately and delete the message and any attachment
> > from your system. Merck KGaA, Darmstadt, Germany and any of its
> > subsidiaries do not accept liability for any omissions or errors in
this
> > message which may arise as a result of E-Mail-transmission or for
damages
> > resulting from any unauthorized changes of the content of this message
and
> > any attachment thereto. Merck KGaA, Darmstadt, Germany and any of its
> > subsidiaries do not guarantee that this message is free of viruses and
does
> > not accept liability for any damages caused by any virus transmitted
> > therewith.
> >
> > Click http://disclaimer.merck.de to access the German, French, Spanish
and
> > Portuguese versions of this disclaimer.
> >
> >
> > _______________________________________________
> > Biopython mailing list  -  Biopython at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biopython
> >
>
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython


This message and any attachment are confidential and may be privileged or
otherwise protected from disclosure. If you are not the intended recipient,
you must not copy this message or attachment or disclose the contents to
any other person. If you have received this transmission in error, please
notify the sender immediately and delete the message and any attachment
from your system. Merck KGaA, Darmstadt, Germany and any of its
subsidiaries do not accept liability for any omissions or errors in this
message which may arise as a result of E-Mail-transmission or for damages
resulting from any unauthorized changes of the content of this message and
any attachment thereto. Merck KGaA, Darmstadt, Germany and any of its
subsidiaries do not guarantee that this message is free of viruses and does
not accept liability for any damages caused by any virus transmitted
therewith.

Click http://disclaimer.merck.de to access the German, French, Spanish and
Portuguese versions of this disclaimer.





More information about the Biopython mailing list