PDB-matching

Before we calculate RMSD, it is often a good pratice to make sure the ref.pdb and model.pdb files have the same chain IDs and the same residue numbering.

Prerequisite

1. install pdb-tools by HADDOCK: https://github.com/haddocking/pdb-tools
2. Add this line to ~/.bashrc:

       export PATH="$PATH:YOUR_DIR/PDB-matching"
   

   Replace YOUR_DIR with your local folder for PDB-matching. Then in your terminal run: source ~/.bashrc

Two main scripts

• Step 1. pdb_match_chn_batch.py: match chain IDs of pdb files to ref.pdb. Output _newChnID.pdb files.

  Note: This step can be skipped if model.pdb files have already matched chain IDs.

• Step 2. pdb_renum_batch.py: align and renumber pdb files to ref.pdb. Output _renum.pdb files.

  Note: Update file.list to _newChnID.pdb files.

Step 1: Match chain IDs to ref.pdb

For two PDB files

• pdb_match_chn.py:

  -> match chain IDs for two PDB files (Does not always work well. Need to manually check the results!)

• pdb_rename_chain.py:

  -> rename chain IDs of a pdb file according to the ref.pdb (the chain ID map file generated by pdb_match_chn.py)

For a list of pdb files

• pdb_match_chn_batch.py

Step 2: Renumber pdb files to ref.pdb

For two PDB files

• pdb-pdbalign ref.pdb chainID model.pdb chainID:

  -> align and renumber model.pdb according to ref.pdb. Output: new model.pdb

  -> If model.pdb has a residue that is not in ref.pdb, new_model.pdb will use X to denote this residue: e.g., ATOM 1447 N GLN X 1 ....

• pdb_renumber_onepair_EXMPL.sh:

  -> an example code

For a list of pdb files

• pdb_renum_batch.py file.list 'A,C,D,E', where 'A,C,D,E' are matched chain IDs