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Author Topic: Definition of gauche and trans for gamma torsion angles  (Read 446 times)

Offline lvelve0901

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Definition of gauche and trans for gamma torsion angles
« on: May 15, 2017, 02:30:20 pm »
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





Offline xiangjun

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Re: Definition of gauche and trans for gamma torsion angles
« Reply #1 on: May 15, 2017, 03:09:26 pm »
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
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.