I tried to convert cs file to star file, and found that the opticsGroup in star file is a little weird.
If I do Import, MotionCor to Particle Extract in Relion, then import the particle star file in CryoSparc. After Class2D and Select2D in CryoSparc, I convert the cs file to star file. I found the OpticsGroup is always 2 and the OpticsGroupName is OpticsGroup2, while the original OpticsGroup in Relion is 1 and and the OpticsGroupName is OpticsGroup1.
Though I can manually revise the star file, I’d like to know whether there is better way to keep the OpticsGroup.
cryoSPARC numbers the groups from 0, Relion numbers them from 1. It can either add one, which will work without any messages for the basic export scenario, or it can not do that which is will give some warnings from Relion and it renumbering them anyway.
So I’ve just had it add one so far. In any event, the particles stay grouped correctly even if the name is adjusted like this.
Thanks for your reply. Now I use offset-optics in star.py to revise the opticsGroup in data_particles, but I need to manually revise the opticsGroup and opticsGroupName in data_optics. If I have a lot of opticsGroups, it’s a little boring to do that manually.
Why to you have to change them? You can just set them once (in cryoSPARC, or in the .star file).
Also, for Relion, only the opticsGroupName matters. The opticsGroupNumbers are just used to associate the particles with a group in one file. So if you have different files with the same optics names, but those names have different numbers, that is fine. (The number maps particles to the optics group table, within one file, the names specify the group properties, potentially across multiple files).