[Chimera-users] Request for axes measurements

Elaine Meng meng at cgl.ucsf.edu
Tue Jun 9 09:52:46 PDT 2015


Hi,
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.

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes>

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
----------
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. 
> Thanks.



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