Is there a pre-existing tool which will tidy up the numbering of a PDB file?
Firstly, I would like to re-number the residues on inserts to make the icode an actual residue in the chain (by that I mean it's own number, shifting everything after it, so 45A becomes 46).
Secondly, I would also like to re-number so that each residue is one after another, as there are skips in the numbering, in spite of the two residues being physically next to each other.
I could do this in-house with a python script, but I thought I would ask specifically if there is a library or pre-existing tool?
Worst case scenario I have found this Perl script that does similar.