[Biopython] Error in pdb superimposer: global name Bio not defined

Sanjeev Sariya s.sariya_work at ymail.com
Fri Nov 7 14:55:49 UTC 2014


Hi Team,
I am trying to align 2 pdb files..When I try to create an object for Bio.PDB.Superimposer(), I get a strange error.
Langauge specs:
Python version - 2.7Bio.__version__ - 1.61 ## bio python versionMy code looks like:
from Bio.PDB import * 
def alignPDB_file(refPDB, samplePDB): # function to align pdb file
     ref_atoms,sample_atoms=[],[]

     ref_model=PDBParser(QUIET=True).get_structure("reference",refPDB)[0] # get the 0th model
     sam_model=PDBParser(QUIET=True).get_structure("sample",samplePDB)[0] # get the 0th model

     for ref_chain in ref_model:
          for ref_res in ref_chain:
               if not "CA" in ref_res:continue
               else:  ref_atoms.append(ref_res['CA']) 

     for sam_chain in sam_model:
          for sam_res in sam_chain:
               if not "CA" in sam_res: continue
               else: sample_atoms.append(sam_res['CA'])

     #super_imposer=Bio.PDB.Superimposer()
     super_imposer = Bio.PDB.Superimposer()


Error:    super_imposer = Bio.PDB.Superimposer()
NameError: global name 'Bio' is not defined

Kindly advise.
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