Calculate base step parameters manually

[m.bruist]

Hi,

I am getting an unexpected dichotomy in my measurements of twist for two stacked noncanonical base pairs from molecular dynamics data. The twist values fall in two distributions separated by ~120°. See attached pdf.  When I view the frames, I do not see discontinuities.  I would like to superimpose the reference coordinate axes on my frames and visualize the twist angle that is being reported.  I have not found a place that tells me exactly how to create the appropriate axes and vectors to see this angle. Can you direct me to a paper or site that will help?

Mike Bruist

[xiangjun]

Hi,

The "unexpected dichotomy" of twist in your MD data is sort of understandable based on my experience: they could be due to a flip of base-pair reference frame. However, given the limited information provided, it is impossible to decipher where the issue is. As always, it helps to provide a minimum example that can reproduce the reported issue.

For details on how 3DNA parameters are calculated, please see $X3DNA/doc/tech-details.pdf and the 3DNA 2.4 source code. Check also the supplementary PDF of the paper "Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures": http://docs.x3dna.org/w3DNA2.0/w3DNA2.0-supp.pdf.

Best regards,

Xiang-Jun