Patch ctf estimation on particles from relion/ctffind


I have refined maps to ~3.7-4A resolution in cryosparc using imported particles and micrographs from Relion3.1. The micrographs were motion-corrected using MotionCor2 and the CTFs were estimated with ctffind4.1. I have read the tutorial on Local CTF refinement, Patch CTF Estimation and Patch CTF Extraction but unsure if I understand it correctly.

Can I use the following procedure to check if cryosparc CTFs improve my refinement?

  1. Run Patch CTF Estimation using micrographs from the last Particle Extraction in cryosparc as input
  2. Run Patch CTF Extraction using the output from #1 above and particles from NU refinement as input.
  3. Run particles from #2 above as input to a new NU refine job with volume from old NU refine as reference

Hi, I think this is correct. Were you able to try it out?

Thanks for the reply. Yes, I tried it but just wanted to make sure that the new patch CTF values would be written to the particle stack. The refinement using the procedure above gave the same result so if the new ones were indeed used, I guess ctffind did a good job and this is not worth pursuing.

It sounds right as long as your particles going into NU are coming from the patch ctf extraction. Any luck with “optimize per particle defocus?”

No, with optimize per particle defocus the local minima are rather shallow so don’t think it is an option.