[Chimera-users] Measure rotation

[Tom Goddard]

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 <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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