Hi Harry,

Thanks for posting on the Forum. 3DNA

*per se* does not generate Ramachandran-like plot for DNA or RNA, or any plot of that kind. It calculates various structural parameters that can be plotted using third-party tools. Regarding Ramachandran-like plot for RNA (based on pseudo torsion angles), you may check papers from the

Pyle lab.

3DNA v2.1 has a new option "

`analyze -torsion`" to calculate commonly used torsion angles, including the following section:

`Pseudo (virtual) eta/theta torsion angles:`

Note: eta: C4'(i-1)-P(i)-C4'(i)-P(i+1)

theta: P(i)-C4'(i)-P(i+1)-C4'(i+1)

eta': C1'(i-1)-P(i)-C1'(i)-P(i+1)

theta': P(i)-C1'(i)-P(i+1)-C1'(i+1)

eta": Borg(i-1)-P(i)-Borg(i)-P(i+1)

theta": P(i)-Borg(i)-P(i+1)-Borg(i+1)

To follow DNA conformational changes, you may find our 2000 JMB paper titled "

A-form conformational motifs in ligand-bound DNA structures" relevant. The work examined a variety of parameters, and found Zp to be the most discriminative between A- and B-form DNAs.

Furthermore, 3DNA v2.1 has a Ruby script

`x3dna_ensemble` that makes analysis of MD simulation trajectories straightforward. We have a new 3DNA

JoVE paper in press that provides protocols for such MD analysis.

HTH,

Xiang-Jun