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

[Mooers, Blaine H.M. (HSC)]

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
>
> _______________________________________________
> cctbxbb mailing list
> cctbxbb at phenix-online.org
> https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mailman_listinfo_cctbxbb&d=DwIDaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=wysWRjTnlpkcS7AX5EQA5s_aXLBMBSAq7euZ1zI8J6I&s=Zkw5Au452TkeMi_7sqcMtJEaek8Q9liXZLYMVy0h9oI&e=