[BioPython] PDBParser -> structure not loaded

[Omid Khalouei]

Hi Brad, Yes actually Thomas had sent me an e-mail and let me know that I 
had to download the PDB file on my computer first. Now my problem is 
resolved.
Originally I was expecting it to also go there and get the file, since I've 
myself written a python code that gets the PDB id from user and then gets it 
from PDB and stores it on the user's computer, so I thought such a feature 
was also implemented in PDBParser. But PDBParser is already a great program 
and I think I should lower my expectations! :)

Thanks for your help,
Sam



>From: Brad Chapman <chapmanb at uga.edu>
>To: biopython at biopython.org
>Subject: Re: [BioPython] PDBParser -> structure not loaded
>Date: Thu, 4 Dec 2003 17:00:20 -0500
>
>Hi Sam;
>I can jump in and help as well. I don't really use the PDB parser
>and Thomas in the authority but I can provide my amateur opinion
>which will hopefully help.
>
> > Hi Thomas, Thanks for the help. Actually it seems that the structure is 
>not
> > retrieved from PDB.
> >
> > After the following lines
> >
> > >>>from Bio.PDB.PDBParser import PDBParser
> > >>>p=PDBParser(PERMISSIVE=1)
> > >>>structure_id="1fat"
> > >>>structure=p.get_structure(structure_id, "filename")
> > >>>model=structure[0]
> >
> > I tried to print the model and chain by the following lines,
> >
> > >>>print structure.child_list
> > [<Model id=0>]
> > >>>print model.child_list
> > []
> >
> > but from the results it seems that 1FAT is not being retrieved from PDB
> > site. I have an established connection to the Internet. I would 
>appreciate
> > your help on this.
>
>The PDBParser doesn't do any internet retrieval at all, at least as
>far as I can see. It is meant to parse a PDB file that you have
>retrieved.
>
>So, if you want to parse out the 1fat structure and deal with it you
>should download the PDB file:
>
>http://www.rcsb.org/pdb/cgi/explore.cgi?job=download;pdbId=1FAT;page=0;pid=293101070575263&opt=show&format=PDB&pre=1
>
>Then, if you saved it to "1FAT.pdb" you can parse it with:
>
> >>> from Bio.PDB.PDBParser import PDBParser
> >>> p = PDBParser(PERMISSIVE=1)
> >>> structure = p.get_structure("1fat", "1FAT.pdb")
> >>> print structure.child_list
>[<Model id=0>]
> >>> model = structure[0]
> >>> model.child_list
>[<Chain id=A>, <Chain id=B>, <Chain id=C>, <Chain id=D>, <Chain id= >]
>
>Hopefully this helps!
>Brad
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