[Chimera-users] Apply rotation with precision

Elaine Meng meng at cgl.ucsf.edu
Sat Nov 14 21:06:52 PST 2009

I forgot to mention that the command "reset" without any position  
specified, or equivalently, "reset default" will remove the  
translations/rotations of all models so that they are in the  
laboratory frame of reference (described at the bottom of my previous  

That can only be applied to all models, not just specific ones.  To  
remove the translations/rotations of a specific model, one  
possibility would be to create a matrix file with all zeros and then  
apply it to that model with the command "matrixset".  The command and  
the matrix format, which is pretty simple, are described here:


On Nov 14, 2009, at 12:18 PM, Elaine Meng wrote:

> 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
> <general-axes.bild>
> On Nov 14, 2009, at 3:12 AM, Damien Larivière 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
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