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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