[Chimera-users] angles after match
goddard at cgl.ucsf.edu
Wed Feb 25 10:24:49 PST 2009
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.
> 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
> 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
> Thank you for your constant help.
> (Sorry if this question is a duplicate)
> many greetings
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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