Run refinement for each frame and corresponding particles directly

3D Variability Analysis
1

Hi- I ran 3dva display using intermediate mode and some frames, let say 10 frames are of interest among those 20 frames. How to run refine jobs using those frames and corresponding particles without manually importing each frame from unzip series file.
Thanks for your suggestions.

BTW, Is’t ok to do such kind of a refinement after 3dva?

2

Hi @Verdandy! There is certainly nothing wrong with refining the outputs of a 3DVA job. I’ll provide a CryoSPARC Tools script for you automate this below. However, I’ll point out a few potential pitfalls and alternate options.

3DVA Display parameters

First, I want to make sure you know that by default, the Intermediates mode of 3DVA outputs frames which have overlapping particles. That is, the same particle may be in several frames. To avoid this, you can change the Intermediates: window (frames) parameter:

  • Setting this parameter to 0 creates frames of the same width with no shared particles
  • Setting this parameter to -1 creates frames which contain approximately the same number of particles, with no shared particles

For this analysis, I also recommend you turn Intermediates: output particle subsets on so that you can easily connect the particles and volumes together.

3D Classification

You may want to consider using the volumes from your 3DVA job to a 3D Classification job (see this example). In some cases, this may give better classification.

Automated refinement

To automate the refinement of your frames, you can use the script found here. This will load volumes and particles from the frames of interest in a 3DVA Display job and launch a Non-Uniform refinement for each.

I hope that’s helpful!

1 Like
3

Thanks @rposert, I’ll give it a try!