On Tue, Jul 6, 2010 at 3:51 AM, Vellieux Frederic <span dir="ltr"><<a href="mailto:Frederic.Vellieux@ibs.fr">Frederic.Vellieux@ibs.fr</a>></span> wrote:<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Refinement with minimization (selected part of model):<br>
% phenix.refine data.hkl model.pdb strategy=individual_sites sites.individual="chain A"<br>
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This will refine the coordinates of atoms in chain A while keeping fixed the atomic coordinates in chain B.<br>
<br>
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.<br>
</blockquote><div><br></div><div>In general, anything possible on the command line should be possible in the GUI as well.</div><div><br></div><div>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.</div>
<div><br></div><div>-Nat</div></div>