[cctbxbb] MTZ object creation bug or feature?

Robert Oeffner rdo20 at cam.ac.uk
Tue Mar 30 02:58:07 PDT 2021


Thank you, Huw, for your enlightening explanation of this behaviour. 
I'll make sure not to have adjacent F,SIGF and DANO,SIGDANO columns when 
creating mtz objects with cctbx.
It always amazes me how such problems have been highlighted in the past 
on the bulletin boards.

Rob


On 30-03-2021 09:33, Huw Jenkins wrote:
> Hi Rob,
>
>> On 30 Mar 2021, at 01:27, Robert Oeffner <rdo20 at cam.ac.uk> wrote:
>>
>> Is this a bug, a well known feature or am I simply doing something wrong?
> This is certainly known (http://phenix-online.org/pipermail/phenixbb/2011-October/017772.html) - it's because when F,SIGF and DANO,SIGDANO are adjacent columns they are converted to F+/SIGF+,F-/SIGF- with Observation type: xray.reconstructed_amplitude
>
> Adding:
>
> for a in mtz1.mtz_object().as_miller_arrays():
>    if a.observation_type().__str__() == 'xray.reconstructed_amplitude':
>      for i,hkl in enumerate(a.indices()):
>        print('{:4d}{:4d}{:4d} {:0.2f} {:0.2f}'.format(hkl[0], hkl[1], hkl[2], a.data()[i], a.sigmas()[i]))
>
> to your example code shows this:
>
>     1  -2   3 12.30 4.02
>    -1   2  -3 4.10 4.02
>     0   0  -3 39.45 85.31
>     0   0   3 13.15 85.31
>     1   2   3 3.15 3.24
>    -1  -2  -3 1.05 3.24
>     0   1   2 7.35 68.42
>     0  -1  -2 2.45 68.42
>     1   0   2 48.60 1.23
>    -1   0  -2 16.20 1.23
>
>
> Best regards,
>
>
> Huw
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-- 
Robert Oeffner, Ph.D.
Research Associate, The Read Group
Department of Haematology,
Cambridge Institute for Medical Research
University of Cambridge
Cambridge Biomedical Campus
The Keith Peters Building
Hills Road
Cambridge CB2 0XY
www.cimr.cam.ac.uk/investigators/read/index.html
tel: +44(0)1223 763234


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