How to use Enable higher-order CTF in Nonuniform Refinement

3D Refinement
1

Hi,

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?

Thanks!

2

Hi Feng10, this should work as it will use those new values.

3

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:

  1. Homogeneous Refinement (new) with CTF refinement on
  2. Non-uniform refinement with higher order CTF on
  3. standalone local and global CTF refinement using the volume output of 2.
  4. non-uniform refinement with the output of 3, with higher order CTF on
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