I just imported a volume series from a 3DVA job and superimposed it onto a previously solved structure, upon which I noticed that it is a mirror image of my volume. I typically use the Volume Tools job on CryoSPARC to flip the volume, but since it doesn’t accept zipped files straight from the 3DVA display job, I’m wondering if there is a more straighforward alternative to flip the volume series. I tried the ‘volume flip # axis z’ command on ChimeraX, but it ended up separating the volume series into individual volumes, and I’m not sure if there’s a fix for that either. Any help would be appreciated!
If you still have access to the 3DVA Display job that generated the volume series that you imported, you can also re-run that job and turn on the Flip hand of outputs parameter to flip the series’s hand.
This would correct the hand, but with just flipping (here or via external software) there’s no guarantee that the series will then be rotationally aligned with the volume that you’d like to superimpose it on. You could use Align 3D Maps for that purpose, although you’d also need to use Volume Tools to flip the hand of the consensus that went into the original 3DVA job, then import that flipped consensus map, and use it as the “Reference map” input in Align 3D Maps. The “Maps to align” would have to contain the previously solved structure that you’d like to superimpose the series on.
