[cctbxbb] Fwd: Re: indexing diffraction pattern

Abbey Garant abbey.garant at gmail.com
Wed Nov 14 08:35:40 PST 2018


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 <pafonine at lbl.gov wrote:

> 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> <jiang12 at purdue.edu>
> To: Pavel Afonine <pafonine at lbl.gov> <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> 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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> cctbxbb at phenix-online.org
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>
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