I am working on a project aimed at compiling papillomavirus sequence information. I will gladly share the link if people are interested, but I do not want to spam. Anyway, as part of the effort we want to show alignments between pdb structure files and HPV sequences.
We noticed that several PDB files were not numbered according to the actual genome. E.g. assume the C-terminal domain of protein x was crystallized, the numbering should be residue 250 to residue 500, however, the crystallographer numbered the PDB file according to the peptide crystallized. Does anyone have any suggestions for a program that may be able to accomplish the renumbering? Thanks!
EDIT: I think I may have found a solution.
I think I can write a tool pdbsws using and a perl file I found here: http://www.canoz.com/sdh/renumberpdbchain.pl