From: Kumpula, Esa-P. <esa...@he...> - 2022-05-20 14:39:09
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Hi all, I have two issues when importing particles from cryosparc to scipion. I did initial processing steps in cryosparc (using patch motion correction) and have now successfully imported the particles as well as the associated micrographs into scipion (by running csparc2star.py and then importing using the .star file). The issue then is that all the micrographs and particles look very noisy in scipion, but if I reconstruct I get a reasonable map. If I run extract coordinates and look at the micrographs from there, they look as they should so I think they are essentially ok. The issue is that when I run subtract projection, I get negative density for the remaining part, which suggests to me that there is some issue with the particles, possibly normalization. So what I would think to do is to re-extract the particles using relion’s extraction protocol to get the normalization correct. The issue is that I don’t know how to transfer the previously refined ctf parameters of the particles that I imported into these new particles to avoid re-running ctf estimation and later per-particle ctf refinement. The particles I imported have these parameters after import, but they are not a SetOfCtf type that I could use as input for relion particle extraction or assign ctf. Any pointers? I have a slightly older Scipion version (3.0.8) so if this is not an issue with current releases then I’m happy to update. Cheers, EP |