[Chimera-users] Apply rotation with precision

[Elaine Meng]

Hi Damien,
I attached a file that you can open directly in Chimera (File...  
Open) to show red, yellow, and blue arrows pointing along the X, Y,  
and Z axes, respectively.

The file simply contains the following 9 lines of text:
.translate 0.0 0.0 0.0
.scale 5
.sphere 0 0 0 0.5
.color red
.arrow 0 0 0 5 0 0
.color yellow
.arrow 0 0 0 0 5 0
.color blue
.arrow 0 0 0 0 0 5

You could change the origin in the ".translate" line and the scale in  
the ".scale" line.  This simple format for describing geometric  
objects is described here:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html>

You can apply the rotation/translation of one model to another (put  
one model in the reference frame of another) with the command  
"matrixcopy":
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html>

So, if you have opened the arrows as model 6 and you want them to  
show the frame of reference of model 3, you would use the command:  
matrixcopy 3 6

You would use the same approach to put any type of model (not just  
the arrows model) in the same frame of reference as another model.

I don't think there is a default reference frame of Chimera -- it may  
depend on the command.  (Others, please correct me if I'm wrong!)   
For some commands, the default is the "laboratory" frame of  
reference, where X is horizontal in the plane of the screen, Y  
vertical in the plane of the screen, Z perpendicular to the screen.

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

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On Nov 14, 2009, at 3:12 AM, Damien Larivi?re wrote:

> Hi Tom,
> Thank you very very much for this solution! It works perfectly.
> I have two other questions:
>
> Is is possible in Chimera to display a reference frame? if yes, can  
> we display the default one of the software or the one of a 3D  
> structure?
>
> Also, can we modify the reference frame attached to a 3D structure  
> so that it possible to align it with the default reference frame of  
> the software?
>
> My best regards
> Damien