[Chimera-users] Origin of transformation matrices

[Daniel Asarnow]

Hi,
What's the origin for the rotation/translation output by measure rotation
or fit-in-map results? If the origin index is 0, is the transformation
calculated around (0, 0, 0)?

I'm extending my software for transforming single-particle EM alignment
parameters to accept a transformation matrix copy-pasted from Chimera and
am having a slight difficulty. For most EM maps, the origin MRC header is
not set, and the origin appears to be (0,0,0). Thus, if R and V are the
rotation and translation from Chimera, the formula R * O + V - O where O is
the real origin (boxsize / 2, boxsize / 2, boxsize / 2) should give the
correct translation. However, it's exactly one pixel short.

Best,
-da
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