Volume alignment tool

I am moving a map (200px) together with its particles into the center of the box. So I used the volume alignment tool and input the center of map as “100,100,100”. But the aligned map seems to deviate greatly from the center in Z direction shown as below.

Is there anything wrong with my input center?

Hi @rainfieldcn! What did the map look like before recentering?

But in this case you would want to specify the center as something like 100,120,130, no? You want to specify the coords in the starting reference frame - which will then be translated to the center of the box (this doesn’t explain your observation, as if you input the existing center as the position to translate to it shouldn’t do anything).

If you have a mask matching your density, there is an option in volume alignment tools to recenter on the mask - that is probably the easiest way to get the result you seek.


I am using v4.4.1. The input field is “3D Coordinates of new center (voxels)” , so I input the center of box.
And there is no “center on mask center” option.
Is this function available in the newer v4.5.1 ?

Yes I can see how it is confusingly worded - but it means the new center in the reference frame of the old box - so where you want the new center to be. In this case, it looks like you want to move the density at 100,120,130 to the center of the box (100,100,100), correct?

Yes, I believe the center on mask option was added in 4.5

I understand it now. I’ll update to v4.5 when I get a chance.
Thank you very much!