[phenixbb] Option to select array from mtz in phenix.real_space_refine?
bkpoon at lbl.gov
Wed Oct 5 14:21:51 PDT 2016
Oops, the keyword for the command-line would be "map_coefficients_label". I
think you have to wrap the label in quotes. Let us know if that doesn't
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
On Wed, Oct 5, 2016 at 2:16 PM, Oliver Clarke <olibclarke at gmail.com> wrote:
> 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
> On Wed, Oct 5, 2016 at 2:02 PM, Oliver Clarke <olibclarke at gmail.com>
>> 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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>> phenixbb at phenix-online.org
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