gawells/pdb_renumber

Python scripts for renumbering PDB files according to primary sequence (or whichever sequence makes sense)

My attempt to make a robust script for renumbering PDB files according to their primary sequence. Requires ProDy (http://www.csb.pitt.edu/prody/), EMBOSS (http://emboss.sourceforge.net/) and Biopython (http://biopython.org/wiki/Main_Page). Seems to be robust so far for handling multiple chains, chain breaks/gaps, modified residues and ligand/solvent renumbering that may clash with the new numbers

This can be run in two ways:

- Given a .pdb structure file, reference alignment in .fasta format and chain selections using the VMD selection algebra, it'll create a global alignment using needle from EMBOSS to use for renumbering.
  - e.g.:
  renumber_pdb -s structure.pdb -r sequence.fasta -v "chain A","chain B",... -o structure.r.pdb

-  Alternitavely you can supply a pre-existing multiple alignment in .fasta format including the reference sequnce and the entry corresponing to the pdb chain to be renumbered.
  - e.g.:
  renumber_pdb -s structure.pdb -a alignment.fasta -r refseqid -p pdbseqid -v "chain A",.... -o structure.r.pdb


usage: renumber_pdb.py [-h] [-s STRUCTURE] [-a ALIGNMENT] -r REFSEQ
                       [-p PDBSEQ] [-v SELECTIONS] [-o OUTFILE] [-n NEWRES]

optional arguments:
  -h, --help            show this help message and exit
  -s STRUCTURE, --structure STRUCTURE
                        PDB file to be renumbered. Defaults to <pdbseq>.pdb
                        when used with '-a'
  -a ALIGNMENT, --alignment ALIGNMENT
                        Multiple alignment to use for renumbering (fasta
                        format)
  -r REFSEQ, --refseq REFSEQ
                        Reference sequence id (for multiple alginment) or
                        .fasta file of reference sequence according to which
                        to renumber. Required.
  -p PDBSEQ, --pdbseq PDBSEQ
                        Sequence id to renumber if using an existing multiple
                        alignment.
  -v SELECTIONS, --selections SELECTIONS
                        Comma separated list of vmd atomselections in double
                        quotes. Each selection will be renumbered according to
                        the alignment
  -o OUTFILE, --outfile OUTFILE
                        Output .pdb filename
  -n NEWRES, --newres NEWRES
                        Add a new residue to the table of non-standard amino
                        acids: XXXYZ[Z]. XXX = three-letter abbreviation, Y =
                        one-letter abbreviation, Z[Z] = atom to relabel as CA
                        (if needed)