[Chimera-users] Request for axes measurements
meng at cgl.ucsf.edu
Tue Jun 9 09:52:46 PDT 2015
For angle measurement, axes are treated as infinite lines (not vectors, so they don’t have a directionality). You could use any set of atoms to define an axis (or centroid or plane) and they would not necessarily have any relationship to directionality along a peptide backbone.
For example, the N->C direction of a helix axis is not used, so the order in which you specify two helix axes for angle measurement doesn’t matter, the result will be the same either way. A positive angle is reported, but by visual inspection of the helix N->C directionalities you can convert to an equivalent negative angle as needed. It is not automatic, however, so more work.
I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
> On Jun 8, 2015, at 11:35 PM, Jayaraman T <jram at pusan.ac.kr> wrote:
> Hi all,
> I have calculated few helix axes angles and they are all in positives using defined axes in Chimera .
> Could you please explain me why they are all in positives ?
> It would be grateful.
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