[phenixbb] GUI admin issues

Nathaniel Echols nechols at lbl.gov
Mon Jul 8 18:29:50 PDT 2013

On Mon, Jul 8, 2013 at 3:49 PM, Yarrow Madrona <amadrona at uci.edu> wrote:
> 2. Is there a quick way to specify which ligand or amino acid to remove in
> the GUI with doing simmulated annealing or better to do manually?

Okay, the next build (1426 or newer, as always depending on whether
anything breaks tonight) will have an "Omit map" button in the Output
tab, which lets you specify atoms which will have occupancies set to
zero before refinement.  On the command-line the equivalent parameter
is omit_selection.  The bulk solvent mask will not be extended to

For composite omit maps, or iterative-build omit maps, you should
still use AutoBuild (i.e. the separate omit map GUI).


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