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 Tom Goddard a écrit :

Hi Damien,

The Chimera 1.4 turn command can do a precise rotation for you. For example,

turn -0.00376406,0.97263698,-0.23229967 0.5 model #0 coordinateSystem #1

Here is the manual page:

http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html

Tom

-------- Original Message -------- Subject: [Chimera-users] Apply rotation with precision From: Damien Larivière To: chimera-users Date: 11/12/09 9:48 AM

...

Dear Chimera team,

Once two pdb structures are opened, the command measure rot #1 #0 give the orientation of one structure with respect to the other one under the form of:

Position of 1Wxx_chB1.pdb (#0) relative to 1Wxx_chB1.pdb (#1) coordinates: Matrix rotation and translation 0.99727151 0.01713873 0.07180395 46.50921950 -0.01715871 0.99985272 -0.00033862 3.66357812 -0.07179918 -0.00089436 0.99741871 15.01300748 Axis -0.00376406 0.97263698 -0.23229967 Axis point 231.74603365 0.00000000 -638.91369622 Rotation angle (degrees) 4.23351417 Shift along axis -0.09924878

Let's suppose that I want to decrease the rotation angle from 4.233° to 0.5°: I can use "Movement" and select the model to be rotated in order to do that with the mouse but I will not be accurate. Is there way to do such rotation with precision?

Thank for your help

Damien

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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