Standardize a PDB

In many applications you need to constrain PDB files to certain chains. You can do it using this program.

A. What does it do?

Given a pdb file, write out the ATOM and HETATM entries for the supplied chain(s), put them on a single chain with the name provided by the user.

PDB_standardize needs four arguments:

  1. PDB file to constrain.
  2. Chains from the pdb file to constrain.
  3. Output file.
  4. Name of the new chain

B. Requirements:

Biopython – should be installed on your machines but in case you want to use it locally, download the latest version into the PDB_constrain.py’s directory (don’t need to build).

C. Example use:

C.1 Constrain 1A2Y.pdb to chains A and B, placed on a single chain C – write results in constr.pdb

python PDB_standardize.py -f 1A2Y.pdb -c AB -o const.pdb -s C

 

C.2 Constrain 1ACY to chain L, with a new chain name F, write results in const.pdb – this example shows that the constrainer works well with ‘insertion’ residue numbering as in antibodies where you have 27A, 27B etc.

python PDB_standardize.py -f 1ACY.pdb -c L -o const.pdb -s F

 

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