Hello,
I've been using 'super' to align the C-alphas within one domain of two
different models of the same protein while leaving the second domain
to move freely. I can do this using:
super (A and resid 1-100 and name ca), (B and resid 1-100 and name ca)
What I would like to do is determine the rotation and translation of
model B's second domain as it moves away from A's second domain.
I can output a matrix after running super using:
print cmd.get_object_matrix("A")
How do I go from the matrix to an angle and distance?
Thanks for any thoughts,
Jon
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