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.
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:
https://github.com/rdrighetto/ArtiaX/commit/eb6d353b5dd118f8995a9938571dc44ebc61853c
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()inSTOPGAPParticleData.pywould 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