-------- Forwarded Message --------

Subject:	Re: indexing diffraction pattern
Date:	Sat, 10 Nov 2018 09:30:53 -0500
From:	Wen Jiang <[email protected]>
To:	Pavel Afonine <[email protected]>

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 <[email protected]> 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