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Hi Xiangjun,
I have a general question about the definition of gamma torsion angles in 3DNA.
I read some paper about gamma torsion angles and it seems the angular space for the angles are from -360 ~ 360 degree.
For example, in paper titled "Sequence-specific transitions of the torsion angle gamma change the polar-hydrophobic profile of the DNA grooves" The paper defined
Values of γ angle were classified according to
classical three-fold pattern into: gauche + (60° ± 30°),
trans (180° ± 30°), gauche – (300° ± 30°) conformations.
However, in 3DNA, the angular space of gamma is from -180 --> 180. So I am wondering whether there is any degeneracy in the angular space defined in 3DNA?
Best,
Honglue
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There are two conventions to report torsion angles: [-180, +180] or [0, 360]. As noted clearly in 'analyze' output, 3DNA adopts the former. For conversion to the later, simply add 360 to a negative value from 3DNA.
HTH,
Xiang-Jun
Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.