Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Support for STOPGAP motivelists in STAR format #4

Open
rdrighetto opened this issue Aug 23, 2022 · 0 comments
Open

Support for STOPGAP motivelists in STAR format #4

rdrighetto opened this issue Aug 23, 2022 · 0 comments

Comments

@rdrighetto
Copy link

rdrighetto commented Aug 23, 2022

First of all, thanks a lot for this really useful ChimeraX plugin!

I've added support for reading STOPGAP v0.7.1 (https://github.com/williamnwan/STOPGAP) motivelists in STAR format:

rdrighetto@eb6d353

Known issues:

  • Currently only works if "STOPGAP star files" is explicitly selected as the file type in the "Open File..." dialog for particle lists. Otherwise, it tries to open it as a RELION .star format, since both use the same extension (and strictly speaking it's the same STAR file format, but obviously the fields are different for each package). Would be nice to resolve this ambiguity in a more elegant and automated way.

  • Writing as STOPGAP .star motivelist currently not supported, for two reasons:
    -- One is that I was not able yet to correct the coordinates offset by 1 voxel as in the Artiatomi motivelist format i.e. .em/.av3 format), when writing;
    -- Second, the starfile module is currently writing out a RELION .star file header and I don't know how to change that.
    Help implementing write_file() in STOPGAPParticleData.py would be very much appreciated!

I would be happy to make a pull request if the ArtiaX developers agree, please let me know if you have any questions.

Best wishes,
Ricardo

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant