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

From: Norman Geist (
Date: Mon Jun 20 2011 - 09:30:02 CDT

Hi Ade,
I don't know exactly what you try to do, but I wrote a program some time ago
which aligns to molecules by their density centers and some binding points
to bind them to each other at the right points and make one molecule out of
two. For the alignment I just used some binding points(or one) and a mean of
all coordinates which gives a density center, so you have to points and are
able to adjust the molecules in the right way.
Best wishes
Norman Geist.
Von: [] Im Auftrag
von Ada Sedova
Gesendet: Montag, 20. Juni 2011 15:19
Betreff: namd-l: aligning two molecules by principal axes of inertia using
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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