I loaded two forms A and B of the same molecule and aligned domain 1 of A to domain 1 of B. Then I used the rotation command to rotate A, until I was satisfied with the alignment. Now I want to measure distances between A and B, but the distance lines go out into 'space'! Pymol seems to calculate the distance as if A was still in its original position and not the current position. How do I make Pymol calculate the distance between A and B in the current position?
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