Combining the volumes generated by Heterogeneous refinement

I generated over 10 volumes from my heterogeneous refinement step. But I don’t know how to combine them into one. I understand that they are individual 3D models, however, I am interested in combining them all. Is there such a function on cryosparc?

I would appreciate your help and guidance!

Stay well.

Hi @Arya,
I am assuming you performed a 10-class heterogeneous refinement to explore heterogeneity in the dataset. If this is the case, you should examine the volumes visually and inspect the orientation distribution plots for each class as well as the number of particles, to inform whether there are in fact distinct conformations/states/etc.

To obtain a single volume from all the particles, you can run an Ab-Initio Reconstruction job using the default 1 class, and then take all the particles from the Ab-Initio Reconstruction along with the volume that was generated, and put those into a Homogeneous Refinement (NEW) job to generate a single refined structure.

Please let us know if there are other specific considerations. Thanks!

Were orientation distribution plots added to het. refine output in 2.16? Up to 2.15 they haven’t been shown.

Hi @Arya, @DanielAsarnow, I mis-wrote, you’re right that we do not have orientation distribution/viewing direction plots in Heterogeneous Refinement right now - adding this as something for the next release!

@Arya Also, if you think that some of your 10 classes are actually the same structure, you can try combining multiple particles_class_n outputs from heterogeneous refinement, to the ‘particles’ input in a Homogeneous Refinement job, along with a single volume in the volume input, if you want to combine those particles and generate a single refined volume representative of that “class”.

It would be really great to have this, I’ve been missing this for a while. It would be particularly useful to diagnose when heterogeneous refinement is separating by view rather than 3D conformation, which happens on occasion.

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And while you have your hands in that code, a bar graph, or even better a line plot over iterations, showing the class size would be amazing.

even better, a chord diagram showing flow between classes while we’re at it :slight_smile:

the homogeneous refinement (NEW) does not allow multiple (in this case 10) volumes to be added. So I am stuck once again.

Hi @Arya, sorry about the confusion; you will need to create separate Homogeneous Refinement (NEW) jobs for each of the 10 volumes.