Split output for symmetry expansion

Features and Functionality
#1

Would it be possible to add a “split output” selector for the symmetry expansion job?

This idea is related to but distinct from reversing the expansion. For example, I have a flexible dimer, where I can use subtraction and local refinement to get nice structures of either monomer, and I would like to C2 transform one of these refinements in order to do a single, expanded local refinement with all of the subparticles. One can export the particles and use pyem subparticles.py, but I thought a “split output” feature would be pretty easy to implement and potentially useful for certain classification strategies as well.

1 Like
#2

Hi @DanielAsarnow,

Thanks for the post. To clarify, are you referring to splitting the output by which symmetry operator was applied (e.g. so for a C2 expansion, two particle stacks should be outputted, the first corresponding to the identity operation and the second corresponding to a 180º rotation)? This makes sense, however if you wanted to do a single local refinement with all the sub-particles, wouldn’t you need to merge these two stacks immediately before the refinement? Are there other workflows that would specifically benefit from having each set of transformed particles separated?

Currently, separating particles by symmetry transformation should be possible with the data stored in the particle dataset – the sym_expand/idx field will contain the identity of each rotation applied. (An idx of 0 corresponds to the identity transformation, the others are not in any well-defined order).

Best,
Michael