**From:** Norman Geist (*norman.geist_at_uni-greifswald.de*)

**Date:** Mon Jun 20 2011 - 09:30:02 CDT

**Next message:**Ajasja Ljubetič: "Re: aligning two molecules by principal axes of inertia using measure.c"**Previous message:**Wang Yi: "Re: restraining groups of atoms"**In reply to:**Ada Sedova: "aligning two molecules by principal axes of inertia using measure.c"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag

von Ada Sedova

Gesendet: Montag, 20. Juni 2011 15:19

An: namd-l_at_ks.uiuc.edu

Betreff: namd-l: aligning two molecules by principal axes of inertia using

measure.c

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:**Ajasja Ljubetič: "Re: aligning two molecules by principal axes of inertia using measure.c"**Previous message:**Wang Yi: "Re: restraining groups of atoms"**In reply to:**Ada Sedova: "aligning two molecules by principal axes of inertia using measure.c"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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