In Cryosparc CTF refinement tutorial for Nonuniform Refinement, it mentions:
On-the-fly CTF refinement cannot be done during a Non-uniform Refinement , so particles should be processed through the standalone Local CTF Refinement then Global CTF Refinement jobs first.
I am wondering if I did Optimize per-particle defocus and Optimize per-group CTF params on-the-fly in Homogeneous Refinement (NEW!)) already, can I just use those particles from Homogeneous Refinement to do Non-uniform Refinement with Enable higher-order CTF on? Or still do I have to do standalone Local CTF Refinement then Global CTF Refinement jobs first?
Hi @Feng10, @user123 is correct:
You can use particles directly from Homogeneous refinement (NEW) where you had optimized CTF parameters. If you connect these to non-uniform refinement and then turn on the “Enable higher-order CTF” switch, the job will use the refined CTF parameters.
However, there is a possibility that you could get slightly better CTF refinements by doing the following:
Homogeneous Refinement (new) with CTF refinement on
Non-uniform refinement with higher order CTF on
standalone local and global CTF refinement using the volume output of 2.
non-uniform refinement with the output of 3, with higher order CTF on