The problems on pdb renumbering

[Anonymous]

Hello everyone,

I am learning to do antibody-antigen docking with snugdock. The antigen I am working on has two chains (chain A and . Before the antigen pdb file can be used for docking, it must be renumbered (changing it to a single A chain and numbering all residues continuously), am I right? There is some renumbering scripts in the Rosetta package. I have tried some of them, but none can work. 

(1)  The pdb_renumber.py script in the /app/rosetta_src_2017.08.59291_bundle/tools/protein_tools/scripts directory. The command:

/app/rosetta_src_2017.08.59291_bundle/tools/protein_tools/scripts/pdb_renumber.py input.pdb output.pdb

gives the following error:

value= (‘ ‘, 1, ‘ ‘)

Traceback (most recent call last):

  File “/app/rosetta_src_2017.08.59291_bundle/tools/protein_tools/scripts/pdb_renumber_new.py”, line 36, in <module>

    residue.id=(‘ ‘,residue_id,’ ‘)

  File “/usr/lib/python2.7/site-packages/biopython-1.69-py2.7-linux-x86_64.egg/Bio/PDB/Entity.py”, line 92, in id

    ” this entity.”.format(self._id, value, value))

ValueError: Cannot change id from `(‘ ‘, 1, ‘ ‘)` to `(‘ ‘, 1, ‘ ‘)`. The id `(‘ ‘, 1, ‘ ‘)` is already used for a sibling of this entity.

(2) The renumber_pdb.py script in the  /app/rosetta_src_2017.08.59291_bundle/tools/ directory. The command:

python /app/rosetta_src_2017.08.59291_bundle/tools/renumber_pdb.py input.pdb output.pdb

gives the error:

Traceback (most recent call last):

  File “/app/rosetta_src_2017.08.59291_bundle/tools/renumber_pdb.py”, line 35, in <module>

    pdblines = open( options.pdbname ).readlines()

TypeError: coercing to Unicode: need string or buffer, NoneType found

 

(3) The enumber_pdb.py script in the /app/rosetta_src_2017.08.59291_bundle/demos/protocol_capture/replica_docking/csrosetta3/com directory. The command:

/app/rosetta_src_2017.08.59291_bundle/demos/protocol_capture/replica_docking/csrosetta3/com/renumber_pdb.py input.pdb output.pdb

doesn’t give any error, but the chain mode in new pdb file it produces is just the same with the input pdb file: there are still two chain identifiers (A and and the residues of the two chain is still numbered seperately.

Could anyone tell me how to fix these pdb renumbering scripts and do you know which script can properly work?

Yeping Sun

 

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