[BioPython] Getting protein structure names from primary IDs

[Nick Matzke]

Hi all,

This has got to be trivial, but I can't find a hint about the solution 
online.

I want to:

1. Search NCBI's structure database for structures from a certain group

from Bio import Entrez
handle = Entrez.einfo()
record = Entrez.read(handle)
print "Search the structure database on Organism = Drosophila"
Entrez.email = "A.N.Other at example.com"     # Always tell NCBI who you are
#handle = Entrez.esearch(db="structure", term="Drosophila")
handle = Entrez.esearch(db="structure", term="Drosophila[Orgn]")

pdb_record = Entrez.read(handle)
print pdb_record	#["IdList"]

pdblist = pdb_record["IdList"]



OK, now I have a list of primary IDs for the protein structures from 
Drosophila.



2. Download those structures.  Apparently I have to do this from RSCB 
and not NCBI? (NCBI efetch has no information on efetching from the 
structure database, and I tried a few obvious methods on analogy to 
other databases without result)

This will download from RSCB, but apparently you need the structure 
name, not the NCBI primary ID.


from Bio.PDB import *
pdbl=PDBList()
pdbl.retrieve_pdb_file('1FAT')


So, how do I get from primary ID to structure name?  I'm sure I'm 
missing something obvious.

Cheers,
Nick




-- 
====================================================
Nicholas J. Matzke
Ph.D. student, Graduate Student Researcher
Huelsenbeck Lab
Center for Theoretical Evolutionary Genomics
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Department of Integrative Biology
University of California, Berkeley

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Mailing address:
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