We are just starting to test out 3D-Flex, very exciting!
A couple of queries:
Is 3D-Flex compatible with prior local refinement? E.g. can I take the output of a local refinement, and look at residual flexibility/heterogeneity in the domain afterwards using 3D-Flex?
What is the recommended way to handle symmetric systems? Symmetry expansion and local refinement? Or refine with higher symmetry, but then treat in C1 for the purposes of 3D-Flex?
So far seems to be working with symmetry expanded particles (and improved resolution/detail after flex-reconstruct vs C1); Flex-refine jobs after local refinement have so far only yielded latent coordinates that seem to correspond to rigid rotations of the entire masked region. Perhaps parameter tweaking is required.
Relatedly - how does Flex Data Prep handle data that has been treated with Volume Alignment Tools? In this case, the center of the local reconstruction is not at the center of the particle image. Does Flex data prep crop around the sub-particle (as would happen if one re-extracted with re-centering) or around the center of the particle image? I think probably the latter, but presume that means 3D-flex is not compatible with data treated in this way?
I can comment on your second question: 3D Flex Prep does the latter – it doesn’t crop around the sub-particle, it takes the particle images as they are on disk and crops around the center of the images, then downsamples. For treating data that has been aligned to a sub-particle via Volume Alignment Tools, you could re-extract particles with re-centering enabled, and with a large enough box size to ensure that none of the original protein is “cut off” if any of the particles. (This way the center of the re-extracted images would coincide with the center of the sub-particles.) Note that since the sub-particle is likely not centered at the COM of the protein, this means that slightly larger box sizes are probably needed to do this.