<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><font face="Times"><span style="font-size: 15px;">Hi Dany,</span></font></div><div><font face="Times"><span style="font-size: 15px;"><br></span></font></div><div><font face="Times"><span style="font-size: 15px;"> 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.</span></font></div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span><a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html</a></div><div><br></div><div><font face="Times"><span style="font-size: 15px;"> 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.</span></font></div><div><font face="Times"><span style="font-size: 15px;"><br></span></font></div><div><font face="Times"><span style="font-size: 15px;">"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. "</span></font></div><div><font face="Times"><span style="font-size: 15px;"><br></span></font></div><div><font face="Times"><span style="font-size: 15px;"><span class="Apple-tab-span" style="white-space:pre"> </span><a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/transform/transform.html">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/transform/transform.html</a></span></font></div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div><font face="Times" style="font-size: 15px; "><br></font></div><div><font face="Times" style="font-size: 15px; "><br></font><div style="font-size: 15px; "><div>On Jul 15, 2013, at 7:03 AM, Dan Cohen wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr"><div><div><div><div><div><div>Hello all,<br><br>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 :<br>
<br></div>According to IMP, they use the ZXZ notation in the original (lab) coordinate system.<br><br></div>According to my understanding of the chimera docs, you use ZXZ in the self (rotating) coordinate system.<br><br></div>
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)<br>
<br></div>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. <br><br>
</div>Will be thankful for any hint,<br></div>Dany<br><div><br><div><br></div></div></div>
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