[phenixbb] Option to select array from mtz in phenix.real_space_refine?

Pavel Afonine pafonine at lbl.gov
Thu Oct 6 08:07:46 PDT 2016


For the record: the answer is in the documentation, see

https://www.phenix-online.org/version_docs/1.11rc3-2553/reference/real_space_refine.html

-> Usage examples, #4.

Pavel


On 10/5/16 14:27, Billy Poon wrote:
> Hi Oliver,
>
> 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
> Web: https://phenix-online.org
>
> On Wed, Oct 5, 2016 at 2:21 PM, Billy Poon <bkpoon at lbl.gov 
> <mailto: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 work.
>
>     --
>     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 <tel:%28510%29%20486-5709>
>     Fax: (510) 486-5909 <tel:%28510%29%20486-5909>
>     Web: https://phenix-online.org
>
>     On Wed, Oct 5, 2016 at 2:16 PM, Oliver Clarke
>     <olibclarke at gmail.com <mailto: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).
>
>         Cheers
>         Oli
>
>>         On Oct 5, 2016, at 5:12 PM, Billy Poon <bkpoon at lbl.gov
>>         <mailto: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 <tel:%28510%29%20486-5709>
>>         Fax: (510) 486-5909 <tel:%28510%29%20486-5909>
>>         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:
>>
>>             Hi,
>>
>>             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.
>>
>>             Cheers
>>             Oli
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>>
>
>
>
>
>
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