I am a beginner and still in the learning phase of chimera. 

Here is my question.

I generated the mask from relion (mask creation) and open the mask in chimera.

Using segmentation, I successfully split the mask into three segments and saved them individually.

Then, I found that each mask file changes its box size (smaller than the original mask) and failed to run the multi-body refinement in relion.

Using relion_image_handler (--new_box), I changed the box size but now the origin is shifted and all three masks are overlapping each other by losing their relative position.

Is there a way to save the segmented mask maps by maintaining its original box size and relative position?

Thanks.

Best, Uhnsoo