I autopicked and did multiple rounds of 2D classifications with CTF estimated with CTFFIND4 job in cryosparc. Since I had some gold subtract in lots of images, GCTF gave a different defocus estimation and I wanted to switch to the GCTF values. But I want to use the particles picked from CTFFIND4. However, when I used GCTF as micrograph exposure group and particles selected after rounds of 2D as particle input, the Extract from Micrographs job said "Particles already have CTF estimates: these will not be modified’’. I know I can export the particles to relion star and import them back again without ctf information. But I am wondering that is there an easier way to do within cryosparc? Thank you so much!
Edited 2022-03-30: Overriding “low level inputs” for an Extract from Micrographs job, which I proposed earlier, may not produce a particle stack with the desired GCTF estimates. Investigating…
Thank you for the suggestions! I have not found the ‘input override’ option in ‘Extract from Microgrpahs’ Advance mode. I used the GCTF micrographs & particles picked on CTFFIND as inputs before but the results did not use the ctf from GCTF but used ctf from particles. Could you explain a little bit more about how I can have the override option interface in the Extraction job? Thank you so much!
@Lige_uw At the moment, I have no suggestion for replacing particle CTF parameters more easily than using the method you have already described. We are looking into making this easier with a future software patch or release.
Thank you, wtemple. Looking forward to the new feature.
@Lige_uw Release 3.3.2 introduces the Force re-extract CTFs from micrographs option for the Extract from Micrographs job.
@wtempel Awesome! I will give it a try. Thank you so much!