[Chimera-users] measure rotation command questions

Elaine Meng meng at cgl.ucsf.edu
Fri Aug 12 10:59:57 PDT 2016


Hi Joe,
This command only describes how one model has been moved relative to another, not how they would best superimpose.  I don’t think you can “see” the amount of translation unless you had other knowledge, such as that the two models were originally exactly superimposed.

I can’t really add to the description of the information here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation>

The “showSlabs” option will show both the rotation and the shift, but as I understand it that is a different way of describing the relative transformation than the matrix.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 11, 2016, at 4:47 AM, Joseph Atherton <j.atherton at mail.cryst.bbk.ac.uk> wrote:

> Hi,
> When I use the command 'measure rotation' I get a matrix in the reply log.
> 
> 1) The fourth column is 'translation'. At most the translation I see is 5 Angstrom, so how do I get these numbers (see below)? I also have a shift along axis reported, which seems a more reasonable number, but what if the shift is in a a different vector to the axis?
> 
> 2) I can get depiction of the rotation axis, but can I also get a depiction of the translation vector?
> 
> Cheers,
> Joe
> 
> Position of model2 (#20) relative to model1.pdb (#1) coordinates:
>  Matrix rotation and translation
>     0.98820614  -0.14982292  -0.03165001  43.44553134
>     0.14930460   0.98862441  -0.01816347 -23.90940685
>     0.03401127   0.01322376   0.99933396  -9.65968865
>  Axis   0.10195507  -0.21328736   0.97165512
>  Axis point 180.93496764 275.63881775   0.00000000
>  Rotation angle (degrees)   8.85455905
>  Shift along axis   0.14318049




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