[phenixbb] phenix.pdbtools - renumber specific chains

Antony Oliver Antony.Oliver at sussex.ac.uk
Mon Nov 12 08:23:29 PST 2012

Many thanks Nat - very useful indeed.  I would however, definitely like the ability to script it.  I have a series of scripts that help me deal with protein-ligand structures, and would very much like to directly incorporate this feature.

With regards,


Dr Antony W Oliver
Senior Research Fellow
CR-UK DNA Repair Enzymes Group
Genome Damage and Stability Centre
Science Park Road
University of Sussex
Falmer, Brighton, BN1 9RQ

email: antony.oliver at sussex.ac.uk
tel (office): +44 (0)1273 678349
tel (lab): +44 (0)1273 677512

On Nov 12, 2012, at 4:17 PM, Nathaniel Echols wrote:

> On Mon, Nov 12, 2012 at 5:08 AM, Antony Oliver <Antony.Oliver at sussex.ac.uk> wrote:
> Apologies if this has been covered before - but can someone point me to a way of renumbering only specific chains (i.e. F, G, H etc).
> I have tried using phenix.pdbtools with either selection = "chain F or chain G or chain H" or keep "chain A or chain B or chain C or chain D" - but in both cases phenix renumbers every single residue!
> If you don't mind doing it interactively, try this:
> phenix.pdb_editor
> (also in the GUI, of course)  Still in development, but it's meant to be used for situations like this.  The big drawback of course is that you can't script it.
> Otherwise, what you're describing is very easy to code in Python, but it looks like pdbtools is simply not implemented this way.  One of us can change that (and possibly send you a patch, if it doesn't end up being too complex).
> -Nat
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