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... 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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