[phenixbb] Super: Rotation and translation

J. Fleming moloch525 at gmail.com
Fri May 28 16:56:42 PDT 2010


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,

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