[Chimera-users] trigonometry

Thomas Goddard goddard at cgl.ucsf.edu
Mon Apr 3 11:05:48 PDT 2006

Hi Jean-Francois,

  The Chimera matrixget command writes out a 3 by 4 matrix to a file like:

Model 0.0
	0.440056 0.454627 0.774381 -31.4343
	0.0100309 0.859825 -0.51049 20.8174
	-0.897914 0.232412 0.373811 25.777

The first 3 columns are a 3 by 3 rotation matrix and the 4th column is
an amount to translate.  This matrix tells how to rotate and translate
the original data set to its current position in the Chimera coordinate
system.  Another way to look at it is that the data set x-axis is pointed
in the direction of the first column of this matrix in the Chimera
coordinate system.  In the above case the data set x-axis is oriented
in direction (0.440056, 0.0100309, -0.897914) in  Chimera coordinates,
so pointed roughly in the -z direction which is into the screen.

  I'm not sure what angles you want.  We don't have a routine to produce
Euler angles from the rotation matrix although the formulas could be
found in a textbook.  If you want Euler angles, I can probably look it
up and give you some Python code that will report those directly from
Chimera.  Another possibility is to get the axis and amount of rotation
for the above rotation matrix.  That is can also easily be done using
Python in Chimera.  Let me know if you are interested in those details.


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