What does the “Volume Alignment Tools” job do when given a symmetry string? For example if I give this job a map and input C2 as the symmetry string what does this job do? How does it find the correct symmetry axis?
Thanks for the question. When running Volume Alignment Tools with a symmetry string and activating symmetry alignment, the job will attempt to re-orient the volume so that the actual symmetry axes in the density (which may be arbitrarily oriented, if the density is from Ab-initio for example) match that of CryoSPARC’s convention. Under the hood, this happens by rotating the volume by many different rotations, and testing which of these brings the volume closest to the true symmetry axes convention (this is done by calculating the difference between the volume after rotating around the symmetry axes, and the original volume, which should be ~0 for a truly symmetric structure, up to interpolation error). FYI, CryoSPARC currently uses the z-axis as the symmetry axis for C symmetries, and the y axis as the dyad symmetry axis for D symmetry.
Let me know if this answers your question!