aligning two molecules by principal axes of inertia using measure.c

From: Ada Sedova (
Date: Mon Jun 20 2011 - 08:18:41 CDT

I would like to align two molecules by their principle axes of inertia
rather than by backbone or weighted "all atoms." If I use measure inertia to
obtain the principle axes of inertia for two molecules (say, frame one and
two of a trajectory), could I still use measure fit to find the matrix of
rotation that superimposes one set of axes onto another? Obviously, I would
not need to least-squares-fit the two, so there really is no need to use the
Kabsch algorithm. Is there a way to access just the part of measure.c from
the Tcl window that performs the simple rotation, or should I write a script
to do that?

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