[Biopython] Help for PDBParser

[Mikael Trellet]

The second argument you give to the get_structure function has to be the
path of your PDB file. You will certainly find this PDB file in the PDB
database : http://www.rcsb.org/pdb/home/home.do

Moreover, your "print structure" will return only the structure object like
that : "<Structure id=Tripsina>"
You will have to iterate on it to print models, chains, residues and/or
atoms to have something understandable !

Don't hesitate to read the Biopython wiki to have more details and
informations : http://biopython.org/wiki/Biopython


Cordially,


On Wed, Sep 21, 2011 at 4:34 PM, Nana Trapnest <nanatrapnest at hotmail.it>wrote:

>
> Hello,I'd like to know how to print structure of a protein using Biopython,
> I istalled Python and Biopython, but where I get the proteins? I use this
> from Bio.PDB import
> *parser=PDBParser()structure=parser.get_structure("Tripsina",
> "2PTC.pdb")print structure
> but there is an error...
> Traceback (most recent call last):  File "C:/Documents and
> Settings/Stefania/Desktop/PITON/prova", line 4, in <module>
>  structure=parser.get_structure("Tripsina", "2PTC.pdb")  File
> "C:\Python27\lib\site-packages\Bio\PDB\PDBParser.py", line 77, in
> get_structure    file=open(file)IOError: [Errno 2] No such file or
> directory: '2PTC.pdb'
> Can you help me please???  Where I find 2PTC.pdb??? Thanks
> _______________________________________________
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> http://lists.open-bio.org/mailman/listinfo/biopython
>



-- 
Mikael TRELLET,
Computational structural biology group, Utrecht University
Bijvoet Center,
The Netherlands