@olibclarke thanks a lot and sorry for the late reply! I have been testing the script, and got strange results
I have converted a set of particles from csv file back to star file and tried the following with RELION:
- Displaying particles seems to be alright (nothing strange at first sight)
- 2D classification with alignment: seems to work fine, although surprisingly the resulting classes seem to have a different contrast/birghtness (the white intensity of the resulting images seems very high when displaying at a sigma of 3). Interestingly, if I display the particles corresponding to the classes they look normal
- 2D classification without alignment: simmilar problem with the contrast of the classes
- 3D classification with alignment into 1 model (I know this set of particles is homogeneous): comes up with a very strange elongated model
- 3D classification without alignment into 1 model: even more elongated model
I was wondering if you had found similar problems?
Best wishes,
Rafa