# [Chimera-users] Orientation and quaternion

Thomas Goddard goddard at cgl.ucsf.edu
Thu Aug 6 18:27:51 PDT 2009

```Hi Damien,

You can measure the relative orientation of the two models with the
"measure rotation" command:

measure rot #0 #1

which produces output in the reply log (Favorites / Reply Log) like

Position of 2gbp.pdb (#1) relative to 1a0m.pdb (#0) coordinates:
Matrix rotation and translation
0.90028335   0.21178251  -0.38031310  38.41870000
0.30675800   0.31121759   0.89946825 -28.00030000
0.30885177  -0.92644038   0.21521804  53.80560000
Axis  -0.93447169  -0.35270388   0.04860698
Axis point   0.00000000  15.26078714  51.99569332
Rotation angle (degrees)  77.68070000
Shift along axis -23.41004496

Also it draws the rotation axis on the screen (append "show false" to
suppress that).

The rotation is shown as a matrix and as axis/angle in the output.  You
can compute the quaternion equivalent of the rotation if you need that:

(sin(a/2)*axis, cos(a/2))

where a is the angle.

The "measure" command is only in Chimera 1.4 so get a daily build to use it.

http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation

Tom

-------- Original Message --------
Subject: [Chimera-users] Orientation and quaternion
From: Damien Larivière <damien.lariviere at fourmentinguilbert.org>
To: chimera-users at cgl.ucsf.edu
Date: 8/6/09 11:11 AM

> Dear all,
>
> In the attached image, two copies of the FtsZ protein (pdb 1FSZ) are
> displayed in Chimera.
>
> I would like to know the orientation of one copy with respect to the
> other one. Is there a way to get this information ? Is it possible to
> get a quaternion instead of a set of Euler angles ?
>
> My best regards
>
> Damien
>
>
>
> ------------------------------------------------------------------------
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

```