Error generating .star from .cs

Hi, I have a small error in the 3D classification, Heterogeneous Refinement and AbInitio when converting the .cs to a .star and it has come with the latest version of the software(v4.5.1). When the jobs finish, the class to which each particle belongs is not specified. I convert the .cs to a .star with pyem and what I said is verified in this file. On the other hand, I have taken the .cs and loaded it as a numpy array and also confirmed that the class number isn’t especify. Finally, I downgraded CS and with version 4.4.1 it works fine.

Hey @cfonseca

In v4.5, we’ve introduced a new low-level output called alignments3D_multi which will cause the current version (as of May 16, 2024) of to break. I just now submitted a PR for this but I’m sure it’ll take a bit of time for @DanielAsarnow to test/merge.

In the mean time, if you’re willing, you can try manually implementing the necessary code addition in your version of pyem/metadata/ (it’s a relatively simple addition) which should fix things while keeping everything as-is for cs files produced by v4.4.1 and earlier.


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I merged Valentin’s PR into the pyem master branch, afaict it is a good patch. Let us know if any edge cases come up!

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Thank you very much for the effort. Everything is going well now

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