Hi Julien, In Chimera 1.4 daily builds since January 7 there is a command called "measure" that can report the relative orientation of two models: measure rotation #0 #1 prints in the reply log (menu Favorites / Reply Log) Matrix rotation and translation 0.22612416 0.31146762 -0.92296034 15.49596646 0.00745874 0.94692067 0.32138080 -1.29273361 0.97406993 -0.07955609 0.21179848 -13.27353380 Axis -0.20428607 -0.96657822 -0.15489914 Axis point 16.21434627 0.00000000 3.22513422 Rotation angle (degrees) 78.90585699 Shift along axis 0.13997704 giving the 3 by 4 transformation (3 by 3 rotation matrix plus translation in last column) or in a different format the rotation axis vector, a point on the rotation axis, a rotation angle and a shift along the axis. These numbers refer to the orientation of model #1 using the coordinate system of model #0. The command also makes a graphical depiction of the rotation axis. That becomes a new model which can be closed with Model Panel. I added a new optional parameter to "measure rotation" today to not show the graphical depiction: "measure rotation #0 #1 showAxis false". We do not use or provide Euler angles in Chimera. As you note there are problems with conventions and degeneracy with Euler angles. Tom julien(GWDG) wrote:
Dear all,
thank you for the very nice software. I continuously like it.
I have the following problem.
For different molecules, I would like to know what are the transformation that link them. I can do for example match #0 #1 matrixget -
From this matrix I have the rotation information and the translation information. I would like to extract the angles. For that I need to know what convention you used. I guess those are Euler angles (?), but I need to know what is the order of rotation xyz, xzy... Finally how do you get ride of the gimbal lock problem if you use Euler angles.
Thank you for your constant help. (Sorry if this question is a duplicate)
many greetings
julien
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