**From:** Ada Sedova (*aasedova_at_unca.edu*)

**Date:** Mon Jun 20 2011 - 08:18:41 CDT

**Next message:**Wang Yi: "Re: restraining groups of atoms"**Previous message:**Jérôme Hénin: "Re: restraining groups of atoms"**Next in thread:**Norman Geist: "AW: aligning two molecules by principal axes of inertia using measure.c"**Reply:**Norman Geist: "AW: aligning two molecules by principal axes of inertia using measure.c"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hi,

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?

Thanks

**Next message:**Wang Yi: "Re: restraining groups of atoms"**Previous message:**Jérôme Hénin: "Re: restraining groups of atoms"**Next in thread:**Norman Geist: "AW: aligning two molecules by principal axes of inertia using measure.c"**Reply:**Norman Geist: "AW: aligning two molecules by principal axes of inertia using measure.c"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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