[phenixbb] hi

Nathaniel Echols nechols at lbl.gov
Tue Jul 6 07:14:01 PDT 2010

On Tue, Jul 6, 2010 at 3:51 AM, Vellieux Frederic
<Frederic.Vellieux at ibs.fr>wrote:

> Refinement with minimization (selected part of model):
> % phenix.refine data.hkl model.pdb strategy=individual_sites
> sites.individual="chain A"
> This will refine the coordinates of atoms in chain A while keeping fixed
> the atomic coordinates in chain B.
> So I think you probably need to have a different chain ID for your ligand,
> and the above should do the trick. Note that here, Phenix is run in command
> line mode, not the GUI. I haven't checked if it's possible to do this with
> the GUI.

In general, anything possible on the command line should be possible in the
GUI as well.

If you right-click on the check-box for "Individual sites" (or any other
strategy) in the GUI, it should pop up a menu that will give you access to
the relevant atom selection(s).  Alternately, go to the Settings menu and
open Atom selections->Individual sites.  The first control isn't labeled
very well (I  think it just says "Atom selection"), but that's what you want
to use - following the example above, just enter "chain A".  If you click
the "view/pick" button, it will let you verify that the atom selection does
exactly what you want, or you can pick selections with the mouse.

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