Thanks for the feature request. In the next release, we will be adding a “Volume Alignment Utilities” job that can translate a volume/mask to a specified origin in 3D, while appropriately modifying the particles’ alignments. The same job will also be able to align the masked volume to the desired symmetry axes.
This can be used for the above workflow by:
- Taking the mask to be used by the local refinement, and finding the approximate voxel coordinates of the symmetry center (e.g. if the mask only covers the symmetric homo-oligomer, you could use its center of mass as a guess, from Chimera). This only needs to be approximate because symmetry alignment will search for the optimal residual shift within a specified range.
- Taking the above mask, along with the particles/volume from a global refinement, and passing it to the volume alignment utility, specifying the symmetry group, and the above coordinates as the shift.
This will output a new volume, mask, and stack of particles, that have been shifted to the new origin, then aligned to the symmetry axes. These can be used in local refinement with the enforced symmetry. The only thing to note is that symmetry alignment requires that the sub-region actually does have discern-able symmetry (enough to find the location of the symmetry axes), so if the volume is very low-res/doesn’t have clear symmetry, it might be necessary to manually align it to the axes, then re-refine.