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@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.