[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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