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

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Mon Jun 20 2011 - 09:40:20 CDT

You might find this script useful.
http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/orient/

Best regards,
Ajasja

On Mon, Jun 20, 2011 at 16:30, Norman Geist
<norman.geist_at_uni-greifswald.de>wrote:

> Hi Ade,****
>
> ** **
>
> I dont 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****
>

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