[Chimera-users] Measure rotation

Dan Asarnow asarnow at msg.ucsf.edu
Mon Apr 16 18:33:55 PDT 2018

Thanks, I'm all straightened out.

For anyone else, if you want the translation *before* the rotation it's:

u = r.T.dot(o - v) - o

Where r is the rotation matrix, v is the translation from Chimera, and o is
the desired origin.


On Mon, Apr 16, 2018 at 10:30 AM, Tom Goddard <goddard at sonic.net> wrote:

> Hi Daniel,
>   The origin of a map can be any point in the map.  It is set with volume
> command (e.g. "volume #0 originIndex 75,75,75”) or with Volume Viewer menu
> Features / Coordinates.  The “measure rotation” command reports the
> transformation matrix using that origin, so the 4th column giving the shift
> will be the shift of that origin to the origin of the target model.  The
> “measure rotation” command also specifies "an axis of rotation (a unit
> vector), point on the axis, rotation angle, and shift parallel to the axis”
> as described in the documentation
> https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/
> measure.html#rotation
> The axis of rotation is not the z axis.  This is the axis, rotation and
> shift along axis that takes one coordinate system to the other.  The axis
> doesn’t in general go through the origin so the point on the axis positions
> the axis in space.
> Tom
> On Apr 13, 2018, at 11:19 AM, Daniel Asarnow <asarnow at msg.ucsf.edu> wrote:
> Hello!
> I was wondering how the transformations from measure rotation are
> calculated.
> In particular, for my case, the translation reported with the rotation
> matrix is very long - much longer than the reported shift, and outside the
> box. Is the origin really 0,0,0 in the map frame? (I.e. box corner).
> Also, is the axis reported the new Z after rotation, or something else? Is
> that axis times the reported angle a correct axis-angle representation?
> Finally, what is the axis point?
> Thanks & best,
> -da
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