[Chimera-users] Apply rotation with precision

[Elaine Meng]

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  
message).
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/reset.html>

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:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matrixset.html>

Elaine

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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