[phenixbb] Option to select array from mtz in phenix.real_space_refine?
olibclarke at gmail.com
Wed Oct 5 14:16:28 PDT 2016
Hi Billy, I should clarify that I typically use real_space_refine on the command line - I have not checked it in the GUI.
On the command line, it provides a list of the available arrays, but no way to input a selected array (and the output of phenix.real_space_refine --help doesn’t provide any promising looking options).
> On Oct 5, 2016, at 5:12 PM, Billy Poon <bkpoon at lbl.gov> wrote:
> Hi Oliver,
> When you provide a MTZ file with map coefficients to the phenix.real_space_refine GUI, the widget labeled "Map coefficients label" should refresh and provide a list of available arrays. It should behave the same way as the "Data labels" and "Phase labels" widgets in the phenix.refine GUI. If the "Map coefficients label" widget is not displaying the arrays in your MTZ file, can you provide your file so that I can take a closer look? Thanks!
> Billy K. Poon
> Research Scientist, Molecular Biophysics and Integrated Bioimaging
> Lawrence Berkeley National Laboratory
> 1 Cyclotron Road, M/S 33R0345
> Berkeley, CA 94720
> Tel: (510) 486-5709
> Fax: (510) 486-5909
> Web: https://phenix-online.org <https://phenix-online.org/>
> On Wed, Oct 5, 2016 at 2:02 PM, Oliver Clarke <olibclarke at gmail.com <mailto:olibclarke at gmail.com>> wrote:
> I find phenix.real_space refine very effective for initial refinement of a model against a density modified map after molecular replacement (with morphing and reference restraints etc enabled).
> However, when I do this it seems like if there is more than one array of map coefficients in the file there is no way to select which columns to use, unlike for phenix.refine - would it be possible to add such an option? Currently I just use cad in ccp4 to make a file with the desired columns, but it would be a smoother process if the desired column labels could be specified directly at run time.
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