[Chimera-users] Euler angles in "Transform coordinates" tool

Tom Goddard goddard at sonic.net
Mon Jul 15 13:08:06 PDT 2013


Hi Dany,

  Since Chimera and IMP use different Euler angle definitions you might be better off trying to use a representation of rotations that both IMP and Chimera support.  I don't know what IMP offers, but if you could get a rotation axis (vector) and a rotation angle from IMP then you could use the Chimera "turn" command to perform that rotation.

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

  I believe the Chimera "Transform Coordinates" is correctly applying the Euler rotations and the description in the Chimera manual is unambiguous about what convention is being used.

"Euler angles [φ θ ψ] - rotations defined by the χ-convention, where the first rotation is by an angle φ about the Z-axis, the second is by an angle θ (potentially ranging from 0 to π) about the new X-axis, and the third is by an angle ψ about the new Z-axis. "

	http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/transform/transform.html

	Tom


On Jul 15, 2013, at 7:03 AM, Dan Cohen wrote:

> Hello all,
> 
> I have been wrecking my mind in trying to use the "Transform coordinates" tool to apply a rotation to a PDB file based on Euler angles taken from IMP. I focused my problem to the following :
> 
> According to IMP, they use the ZXZ notation in the original (lab) coordinate system.
> 
> According to my understanding of the chimera docs, you use ZXZ in the self (rotating) coordinate system.
> 
> I have been trying to convert between those two using a python library I found on the net but keep on getting results that either show I'm missing something or a bug in somewhere. (It's called transformations.py by Christoph Gohlke)
> 
> Are you aware of any issues or similar problems? I saw somewhere that someone mentioned a similar problem that was due to PDB header file with weird axis origin, but i wasn't able to get any more info. 
> 
> Will be thankful for any hint,
> Dany
> 
> 
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