[cctbxbb] Fwd: Re: indexing diffraction pattern

[Pavel Afonine]

Perhaps someone can reply Wen..

Pavel


-------- Forwarded Message --------
Subject: 	Re: indexing diffraction pattern
Date: 	Sat, 10 Nov 2018 09:30:53 -0500
From: 	Wen Jiang <jiang12 at purdue.edu>
To: 	Pavel Afonine <pafonine at lbl.gov>



Pavel,
Sorry for insufficient details. The scenario is that I have a numpy 2D 
array of float values that represents an image of "diffraction pattern" 
(generated by an image processing operation, not actual X-ray 
diffraction). I need to determine the peak positions and then find a 2D 
lattice (two 2D vectors) going through these peaks. I have my own simple 
functions that can detect the peaks and find a 2-D lattice to cross the 
peaks but it often fails when the "diffraction pattern" is not very 
clean. Thus, I want to find a more robust method that works well when 
the peaks are relatively weak, not very sharp, and when there are some 
spurious peaks off the lattice. I think these tasks are exactly what 
cctbx has solved for indexing X-ray diffraction images.
Hope that these explanations help clarify the problem.
Thanks,

Wen

Prof. Wen Jiang
Department of Biological Sciences
Department of Chemistry (Courtesy)
Scientific Director, Purdue Cryo-EM Facility
Purdue University
Hockmeyer Hall of Structural Biology
240 S. Martin Jischke Drive
West Lafayette, IN 47907
http://jiang.bio.purdue.edu


On Sat, Nov 10, 2018 at 8:03 AM Pavel Afonine <pafonine at lbl.gov 
<mailto:pafonine at lbl.gov>> wrote:

    Hi Wen,

    I'm not sure I fully understand your question... You say a function
    that takes a numpy array.. Array of what?
    Then, "a list of diffraction spots" -- these are measured in
    diffraction experiment.

    If you could provide more details as to what you are trying to do as
    well as what exactly the inputs are then I will do my best to see
    how to do this in CCTBX or forward your questions to CCTBX mailing
    list so that others can comment.

    All the best,
    Pavel

    On 11/10/18 03:56, Wen Jiang wrote:
>     Hi Pavel,
>     I am looking for a function that takes a numpy array and returns a
>     list of diffraction spots and lattice vectors. I think
>     cctbx should have such a function but I am not familiar with it.
>     Can you point me in the right direction?
>     Thanks,
>
>     Wen
>
>     Prof. Wen Jiang
>     Department of Biological Sciences
>     Department of Chemistry (Courtesy)
>     Scientific Director, Purdue Cryo-EM Facility
>     Purdue University
>     Hockmeyer Hall of Structural Biology
>     240 S. Martin Jischke Drive
>     West Lafayette, IN 47907
>     http://jiang.bio.purdue.edu
>

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