Ab inito particle limit

ab inito, asking for 1 class, has repeatedly stopped early.
with ~1M particles input, only 262,800 are used in the abinitio.
we are not happy with our output and would like to force it to
use more/all of the particles.

we have seen related threads (ie)

but have not gotten around this.

we have tried entering the “number of particles to use in optimization”
but this is ignored. We would like to get some control of this parameter.

John Donohue

Don’t have a direct solution for you re the original question, but are you 100% sure you need 1M particles for a single class ab initio?

Modifying parameters, cleaning up the stack first or using multiple classes in ab initio may be faster ways to get a better initial model.

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If you must force all particles in a single Ab-initio class try increasing Maximum resolution (Angstroms) to something high and also Initial resolution could go up. For 1M particles you are better off using multi class or really cleaning them up. 3DVA, 3D Class, etc are all great but probably should clean up with other jobs before this.

I think 262K are going into a class for a reason. What happens if you take the input of 1M particles for Ab-initio with 4-6 classes (maybe set class similarity to 0.8 if you think they are very similar) and send it to heterogeneous refinement ? Would the volumes be the same in the end or will these jobs filter out some junk ?

It could be worth putting the micrographs and particles together in the curate exposure job before any of this to see if the 1M are coming from good micrographs.