[Chimera-users] [chimera-dev] Rotation about the axis of symmetry

Elaine Meng meng at cgl.ucsf.edu
Mon Nov 23 09:26:17 PST 2009

On Nov 23, 2009, at 2:06 AM, Liam Browne wrote:

> I want to rotate a model by 90 degrees about the axis of symmetry,  
> but I seem to be having problems setting the axis correctly.
> After two identical models are superimposed I use measure rotation  
> and get the following:
>   Matrix rotation and translation
>     -0.04092271  -0.36724445   0.92922379 -82.20183653
>     -0.91203666   0.39354649   0.11537022 -54.21831923
>     -0.40806183  -0.84276490  -0.35104539  11.47082481
>   Axis  -0.55288898   0.77167664  -0.31437070
>   Axis point -56.22800779   0.00000000  25.47389901
>   Rotation angle (degrees) 119.94780111
>   Shift along axis   0.00338820
> What should I do to rotate the model at the same axis but by 90  
> degrees?
> Many thanks,
> Liam

Hi Liam,
You can just use the reported values -- the tricky part is remembering  
to indicate that they are in the coordinate system of the first model  
in the "measure rotation" command, and also using the reported axis  
point as the center of rotation.

Let's say you used the command "measure rotation #0 #1".  Then the  
values in the Reply Log are for the transformation of #1 relative to  
#0 expressed in the coordinate system of #0.

Now you can use the values in the Reply Log to rotate #1 further.   
Keep in mind that this transformation will be applied on top of any  
existing transformations.  If you want only the new rotation and not  
prior transformations, you would need to "reset default" first.  To  
rotate model #1 90 degrees about the reported axis and use the  
reported axis point as the center, the command would be:

  turn -.55288898,.77167664,-.31437070 90 center  
-56.22800779,0,25.47389901 mod #1 coord #0


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

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