[phenixbb] Option to select array from mtz in phenix.real_space_refine?
bkpoon at lbl.gov
Wed Oct 5 14:27:12 PDT 2016
Actually, I think it's just "label"
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 2:21 PM, Billy Poon <bkpoon at lbl.gov> wrote:
> Hi Oliver,
> 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
> Web: https://phenix-online.org
> On Wed, Oct 5, 2016 at 2:16 PM, Oliver Clarke <olibclarke at gmail.com>
>> 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.
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
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