[BioPython] Getting protein structure names from primary IDs

[Nick Matzke]

Hi again -- Esummary was what I needed, so nevermind!

Sorry for the trouble,
Nick


Nick Matzke wrote:
> 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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