[phenixbb] phenix.pdbtools - renumber specific chains

Nathaniel Echols nechols at lbl.gov
Mon Nov 12 08:17:12 PST 2012

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:


(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

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