Volume Tools - Revert Recentering

Utilities
1

Hello!

I used the Volume Tools job to recenter a volume, mask, and its particles based on the center of mass of the mask. The volume, mask and particles come from a local refinement job.

After running another local refinement using the recentered particles, I obtained an improvement in resolution.

I would now like to revert the map and mask to their original coordinates, effectively undoing the recentering. I tried applying the negative values of the center-of-mass coordinates reported by the Volume Tools job, but this does not seem to work.

What is the correct procedure for reverting the recentering and restoring the map and mask to their original coordinates?

Thank you!

2

Hi @Knight!

When you recenter a volume with Volume Alignment Tools (which I assume is the job you’re referring to, since Volume Tools cannot recenter volumes), you pick a new center, not a shift. So instead of applying the negative of your original input, you’ll need to choose the location in the shifted volume which used to be the center.

  1. Box size: 256 px (center coordinate is 128, 128, 128 px)
  2. Use Volume Tools to recenter on 150, 128, 128 px
  3. To undo step 2, you must recenter on 106, 128, 128 px

Another way of thinking about this is that you need to first calculate the shift and then subtract that shift from the box’s center

  1. Box size: 256 px
  2. Recenter on 150, 128, 128 px. Shift = 22, 0, 0 px
  3. To undo, subtract shift from box’s center: (128, 128, 128) - (22, 0, 0) = 106, 128, 128 px.

Instead of calculating this yourself you could use Align 3D Maps to find the optimal shift automatically.

I hope that helps!

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3

Hello @rwaldo,

Thank you very much for the detailed reply!

Now I understand how to do it correctly.

Using the Align 3D maps is also a cool way to do it. But I suppose it is better to do it manually with the initial shifts. As locally refined maps, or 3D classified ones, might have offsets that would end up mixing the calculation of Align 3D maps job.

THANKS

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