Symmetry alignment query


Does symmetry alignment in volume alignment tools search offsets (coordinates), or only orientations?

This is important when aligning using local symmetry (where the center of the mask one chooses initially may not be perfectly aligned to the molecular symmetry axis).


EDIT: Looking at the volume alignment tools log, I think I answered my own query - there is an entry for both rotation matrix & shift, good to know

Just confirming that volume alignment tools’s symmetry alignment feature does search over shifts. There are two advanced parameters that can be tweaked if it is missing the optima or if the volume is far away from the center of the box:

  • Initial shift extent (voxels): This is the radius of the sphere of shifts that the job will search over. It may be increased to search over a wider range of shifts.
  • Initial shift grid sampling: This controls the initial number of shifts that are searched over (multiple iterations of alignment are done, and the sampling gets progressively finer; this controls the number of sampling points at the first iteration). Increasing this will take more time but will result in a more conservative search.