[cctbxbb] unmerged data as mtz object

Daniel Paley dwpaley at lbl.gov
Tue Aug 4 11:28:02 PDT 2020


Rob, I'll also mention that phenix.reflection_file_converter (alias
iotbx.reflection_file_converter) has a new option --write_unmerged. It
won't write an mtz file, but I believe it will write any format that
accepts unmerged data.
-Dan



On Tue, Aug 4, 2020 at 10:54 AM Robert Oeffner <rdo20 at cam.ac.uk> wrote:

> Thank you David. That looks useful to me.
>
> Rob
> On 04-08-2020 18:49, David Waterman wrote:
>
> You might like to look at the MTZ export functionality in DIALS
> https://github.com/dials/dials/blob/master/util/export_mtz.py
>
> -- David
>
>
> On Tue, 4 Aug 2020 at 18:45, Robert Oeffner <rdo20 at cam.ac.uk> wrote:
>
>> Thanks Aaron, I was aware of the  merge_equivalents function. My interest
>> is just for doing some testing on my code which involves reading and
>> writing unmerged data. I guess I could always use the iotbx.mtz functions
>> and write individual mtz columns including separate HKL indices to a file.
>>
>> Rob
>>
>>
>> On 04-08-2020 18:03, Aaron Brewster wrote:
>>
>> Hi Rob, I don't know how to create an unmerged mtz file, but if you want
>> to merge the data you can use the cctbx miller array function
>> merge_equivalents:
>>
>> mtzobj = millarr.merge_equivalents().as_mtz_dataset(column_
>> root_label="I")
>>
>> I believe it does simple weighted averaging of the data using the sigmas.
>>
>> -Aaron
>>
>> On Tue, Aug 4, 2020 at 6:16 AM Robert Oeffner <rdo20 at cam.ac.uk> wrote:
>>
>>> Hi,
>>>
>>> Does anybody know how to convert a miller array of unmerged data to an
>>> mtz object? For merged data I do something like this:
>>>
>>> mtzobj = millarr.as_mtz_dataset(column_root_label="I")
>>>
>>> But if millarr contains multiple observations with the same hkl index.
>>> Then the above code fails with the exception
>>>
>>> cctbx Error: Duplicate entries in miller_indices array.
>>>
>>> Any suggestions?
>>>
>>> Many thanks,
>>>
>>> Rob
>>>
>>
>
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-- 
Daniel W. Paley
Project Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
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