[cctbxbb] bin data by a Miller index

Pavel Afonine pafonine at lbl.gov
Fri Apr 24 12:55:44 PDT 2015


Hi Blaine,

I would be surprised if there is no better way of doing this, but here 
is what I could type in 5 minutes:

***
from cctbx.development import random_structure
from cctbx import sgtbx
from cctbx.array_family import flex

def exercise():
   # generate random structure
   xrs = random_structure.xray_structure(
     space_group_info = sgtbx.space_group_info("P212121"),
     elements         = ["N","C","O"]*10)
   # compute structure factors up to given resolution
   f_calc = xrs.structure_factors(d_min=1.5).f_calc()
   # obtain selection for miller indices you are interested in
   selection = flex.bool()
   for mi in f_calc.indices():
     h,k,l = mi
     if(h==1 or h==3): selection.append(True)
     else:     selection.append(False)
   print "Number of reflections selected %d out of total %d"%(
     selection.count(True), selection.size())
   # apply obtained selection
   f_calc_selected = f_calc.select(selection)
   # do binning
   f_calc_selected.setup_binner(reflections_per_bin = 50)
   for i_bin in f_calc_selected.binner().range_used():
     sel_i_bin = f_calc_selected.binner().selection(i_bin)
     d_range = f_calc_selected.binner().bin_legend(
       i_bin=i_bin, show_bin_number=True, show_counts=True)
     print d_range

if(__name__ == "__main__"):
   exercise()
***

Hope this does the job for you!

Pavel


On 4/24/15 10:22 AM, Mooers, Blaine H.M. (HSC) wrote:
> Dear cctbxbb:
>
> I have a simple question.
>
> I have a data set with a strong off origin Patterson peak (0,0,0.11). 
> I want to
> plot the average I/sig per zone l = n. I expect to see enhanced values 
> at l=9n.
> How do you bin data by the L Miller index in iotbx?
>
> Best regards,
>
> Blaine
>
> Blaine Mooers, Ph.D.
> Assistant Professor
> Director of the Laboratory of Biomolecular Structure and Function
> Department of Biochemistry and Molecular Biology
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center Rm. 466
>
> Shipping address:
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
>
> Letter address:
> P.O. Box 26901, BRC 466
> Oklahoma City, OK 73190
>
> office: (405) 271-8300   lab: (405) 271-8313  fax: (405) 271-3910
> e-mail:  blaine-mooers at ouhsc.edu
>
> Faculty webpage: 
> http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/faculty/blaine-mooers-ph-d-
>
> Small Angle Scattering webpage: 
> http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/small-angle-scattering-links-27aug2014.html?sfvrsn=0
>
> X-ray lab webpage: 
> http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/department-facilities/macromolecular-crystallography-laboratory
>
>
>
> _______________________________________________
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