Task 9 - Journal (PKU)

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Renumbering Atoms in PDB file

To compare structures in normal mode analysis, the sequence and atom numbering has to be identical. We used a very simple python script to renumber a PDB file after we deleted an extra residue:

<source lang="python">

  1. !/usr/bin/env python
  2. first argument: the pdb file
  3. second argument: the number of deleted atoms (would be nice if no number means "start with 1", but that's an effort..)

import sys

filename = sys.argv[1] offset = int(sys.argv[2]) for line in open(filename):

   if line.startswith("ATOM"):
       head = line[:11].split()
       at = int(head[1])-offset
       i = 7-len(str(at))
       head = head[0]+" "*i+str(at)
       print head+line[11:],
       print line,