Bug #2477
open
Xmipp refine upload fails for icosohedral symmetry
Added by Amber Herold about 11 years ago.
Updated about 11 years ago.
Category:
Python scripting
Affected Version:
Appion/Leginon 2.2.0
Description
The pickle file was storing the symmetry as Xmipp format, but when the file is read, it needs to match with our database entries. So I have changed the Xmipp refine to store icos symmetry as "Icos (2 3 5) Viper/3DEM" in the pickle file so that it is read correctly during the upload step.
- Status changed from Assigned to In Code Review
- Assignee changed from Amber Herold to Anchi Cheng
- Assignee changed from Anchi Cheng to Dmitry Lyumkis
It is more important that Dmitry agrees with the change since he wrote the code for upload.
This sounds fine ... my one concern has to do with the question of when the euler angles get converted. If we store the pickle file as "3DEM / Viper convention" as default for Xmipp, at which point does Appion read the file and know that the Euler angles have to be converted for icosahedral symmetry based on a different (Xmipp) convention? Anchi, do you have an opinion on this?
If I have coded it right. Any model icosahedral orientation is converted into (2 3 5) in the preparation step before running xmipp which is why at upload we can assume (2 3 5) and Euler angle based on that.
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