[cctbxbb] How to extract I(+) and I(-) from miller array?

Pavel Afonine pafonine at lbl.gov
Tue Jun 9 16:58:57 PDT 2020


You are welcome, Blaine!
Pavel

On 6/9/20 16:56, Mooers, Blaine H.M. (HSC) wrote:
> Hi Pavel,
>
> Thank you very much for the leads.
> They were very helpful.
> I was able to make the desired plot.
>
> Best regards,
>
> Blaine
>
> ________________________________________
> From: Pavel Afonine [pafonine at lbl.gov]
> Sent: Tuesday, June 09, 2020 2:07 PM
> To: Mooers, Blaine H.M.  (HSC); cctbx mailing list
> Subject: [EXTERNAL] Re: [cctbxbb] How to extract I(+) and I(-) from miller array?
>
> Hi Blaine,
>
> this is correct, this is how anomalous data are read in and stored in an
> instance of miller.array class. In this case I(+) and I(-) will be
> stored in one miller_array, anomalous_flag will be set to True, and
> .indices() will contain 'plus' and 'minus' mates as well as singletons.
>
> Now, if you want to get separate I(+) and I(-), for an example look in
>
>     def anomalous_signal(self, use_binning=False):
>     def anomalous_differences(self, enforce_positive_sigmas=False):
>     def hemisphere_acentrics(self, plus_or_minus):
>     def hemispheres_acentrics(self):
>     def convert_to_non_anomalous_if_ratio_pairs_lone_less_than(self,
> threshold):
>
> in cctbx/miller/https://urldefense.proofpoint.com/v2/url?u=http-3A__-5F-5Finit-5F-5F.py&d=DwIDaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=wysWRjTnlpkcS7AX5EQA5s_aXLBMBSAq7euZ1zI8J6I&s=Z89gPpuGtxEJFRbpBhg8EyWuOGixW13wNgllafUKGjA&e= .
>
> Pavel
>
>
> On 6/9/20 07:55, Mooers, Blaine H.M. (HSC) wrote:
>> Dear CCTBX experts,
>>
>> The diffraction data for 3hz7 from RC Researcher's question includes one dataset with column labels of 'I(+)', 'SIGI(+)', 'I(-)', 'SIGI(-)'.
>> When the diffraction data of 3hz7 data are read from a mtz file into miller arrays,
>> it would appear that the I(+) and I(-) are stored in a single column of intensities rather than two parallel columns.
>>
>> from iotbx.reflection_file_reader import any_reflection_file
>>
>> hkl_file = any_reflection_file('3hz7.mtz')
>> miller_arrays = hkl_file.as_miller_arrays(merge_equivalents=False)
>> Iobs = miller_arrays[1]
>> list(Iobs[100:105])
>>
>> [((7, 4, 38), 84.0, 52.20000076293945),
>>    ((-7, -4, -38), 112.80000305175781, 48.20000076293945),
>>    ((8, 4, 38), 119.69999694824219, 57.400001525878906),
>>    ((-8, -4, -38), 152.10000610351562, 65.9000015258789),
>>    ((6, 5, 38), 732.5, 57.5)]
>>
>> How would I extract the I(+) and I(-) into lists to plot against each other in a scatter plot in matplotlib?
>>
>>
>> Best regards,
>>
>> Blaine
>>
>> Blaine Mooers, Ph.D.
>> Associate Professor
>> Department of Biochemistry and Molecular Biology
>> College of Medicine
>> University of Oklahoma Health Sciences Center
>> S.L. Young Biomedical Research Center (BRC) Rm. 466
>> 975 NE 10th Street, BRC 466
>> Oklahoma City, OK 73104-5419
>>
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>
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