[Chimera-users] about model coordinates

Tat Cheung Cheng tc2595 at bu.edu
Fri Feb 20 14:54:20 PST 2015


I recently got a ~4.4A EM map and built a improved model using MDFF. The
map and model is well aligned when loaded in Chimera. But it is off when I
hit "center" in the volume viewer, as the origin is shifted. As I try to
improve the model in Coot, the map and model isn't aligned at all in Coot,
seemingly by the same offset when "center" button was hit.
And also the values in the original index in the volume viewer is different
from the values in the header in the density map. So I wonder what
determines the origin index? and is it possible to find the shift and
transform the coordinates in the model so as to align the model with the
map in coot?

Thanks a lot.

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