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Questions and answers => General discussions (Q&As) => Topic started by: lvelve0901 on May 15, 2017, 02:30:20 pm

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Title: Definition of gauche and trans for gamma torsion angles
Post by: lvelve0901 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

Title: Re: Definition of gauche and trans for gamma torsion angles
Post by: xiangjun 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

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University