[BioPython] PDB file - Validation and WebService

[Peter]

On Sun, Nov 9, 2008 at 2:18 PM, Rodrigo faccioli
<rodrigo_faccioli at uol.com.br> wrote:
> Hello,
>
> I am a very new BioPython member and I have listened only good news about
> BioPython project.
>
> So, I have two doubts:
>
>
>   1. The module Bio.PDB checks a PDB file like
>   http://deposit.rcsb.org/cgi-bin/validate/adit-session-driver . If not,
>   are there others possibilities in software ?

Bio.PDB can do some validation (it has an optional strict mode for
parsing).  I don't know if this checks the same things as ADIT.

Have you looked at downloading ADIT itself?
http://sw-tools.pdb.org/apps/ADIT/index.html

>   2. I read about PDB webservice from pdb website. The BioPython project is
>   there supports for it? Because I read in
>   http://www.rcsb.org/robohelp/webservices/summary.htm and there is a
>   option with Python.

I've not looked at that before - all it seems to be at the moment is a
way to run BLAST against the PDB database.  Assuming their XML BLAST
output is compatible with the NCBI's you should be able to use the
Bio.Blast.NCBIXML parser on the results.

I just tried their python example on Linux with Python 2.4.3 but it
failed - perhaps my version of SOAP is out of date?  Note they have a
stray semi colon at the end of the call which shouldn't be there.  See
http://www.rcsb.org/robohelp/webservices/samples/python_samples.htm

On the other hand, you could just use the NCBI's qblast (via Biopython
if you like) to run an online BLAST search against the PDB database.
So I don't see what benefit using the PDB's server offers - unless
they plan additional functionality in future.

Peter