Using PDFgetX3 and PDFGui for TEM diffraction patterns

[Yang Yangz]

Hi all,

I am very very new to the PDF technique, and I am working with TEM data. I was wondering whether I can use PDFgetX3 to calculate an observed PDF, in which I:

- Used imageJ to take a radial integration on a scale of 1/nm

- Generated a tsv file and threw it into PDFgetX3

I also have a .cif file, in which I used PDFGui to generate a calculated PDF. 

The difference between the two plots are pretty large, where the observed PDF had very little peaks, while the calculated PDF has a lot of peaks within the same range. I believe the radial integration may be incorrectly done, but any insights or recommendations to more literature will be very helpful.

Thanks,

Yang

[Simon Billinge]

Thanks for your question Yang.

We have a version of PDFgetX3 for electrons, but unfortunately it is not available for free.  It is licensed by Columbia to Nanomegas who use it in their software product.   If you have sufficient research funds, this program is powerful and easy to use.   Moving forward we are thinking about how to handle these things, especially as I will be leaving Columbia shortly, so this may change in the future, but for now this is the case.  

You can of course use PDFgetX3 itself and it will work ok, biut will not give quantitatively reliable intensities.  The main impact will be incorrect ADPs.   It won't give any extra peaks, so if you have extra peaks this is presumably an issue with your experiment or your integration.

For the integration of electron diffraction data we use pyFai and not imageJ.  A challenge is always the calibration of finding the center of the pattern and any angular offsets.  Unlike with x-rays, with ED, the direct beam can move a bit on the detector, so the measurements and the calibrations have to be done systematically.  We have a couple of papers on this that you can look at:

doi: 10.1107/S1600576715000412

doi: 10.1524/zkri.2012.1510

doi: 10.1017/S1431927614014561

and others have written on this topic also, we are far from being the only ones.

On Thu, Nov 20, 2025 at 4:57 PM Yang Yangz <yangy...@gmail.com> wrote:

Hi all, I am very very new to the PDF technique, and I am working with TEM data. I was wondering whether I can use PDFgetX3 to calculate an observed PDF, in which I: - Used imageJ to take a radial integration on a scale of 1/nm - Generated a

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Simon Billinge

Professor, 

Department of Applied Physics and Applied Mathematics

Columbia University

[Yang Yangz]

Thank you for the detailed answer!

Yang