[Chimera-users] Quantify the movement between two domains

[Ahmad Khalifa]

Hi,

I'm looking for a way to quantify the movement between two domains in my
structure. I know I can calculate an RMSD between the same domains in
different conformations. I can also generate a distance matrix between the
two chains in different conformations.

I tried to measure the distance between the two centers of mass of
my domains, but the change doesn't really capture the magnitude of the
movement, also the same domains are not identical in the two conformations
in the sense that one domain is missing so many loops, which will affect
the com calculation.

What other ways to quantify the distance between two different domains?

Thank you.
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