[phenixbb] Heavy atoms outside of molecule

Nathaniel Echols nechols at lbl.gov
Tue Jan 15 12:59:56 PST 2013

On Tue, Jan 15, 2013 at 12:49 PM, Brennan Bonnet
<Brennan.Bonnet at lightsource.ca> wrote:
> Is there an option in Phenix that will fix the heavy atom positions so that they are at their equivalent positions within the molecule?

I hope I'm not misinterpreting the question, but I think this might do
what you want (in the current nightly builds):

phenix.sort_hetatms model.pdb

(Also in the GUI under "Model tools", but you'll need to enable
alpha-test features in the preferences to see it.)


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