[phenixbb] phenix.pdbtools - renumber specific chains

Pavel Afonine pafonine at lbl.gov
Mon Nov 12 20:24:05 PST 2012

Hi Oliver,

it's not implemented but it's trivial to add. I will do it tomorrow. I 
would say that this is rather a bug (the fact that "selection" is 
ignored). So yes I will fix it tomorrow and it will be available in a 
nightly build then.


On 11/12/12 8:17 AM, Nathaniel Echols wrote:
> On Mon, Nov 12, 2012 at 5:08 AM, Antony Oliver 
> <Antony.Oliver at sussex.ac.uk <mailto: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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