So youre basically looking to do a search match? What inputs do you put into the software? Are these powder diffraction peaks? Laue? On Wed, Nov 14, 2018, 9:18 AM 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 To: Pavel Afonine

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 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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