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Author Topic: Calculate base step parameters manually  (Read 570 times)

Offline m.bruist

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Calculate base step parameters manually
« on: February 22, 2020, 02:54:32 pm »
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

Offline xiangjun

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Re: Calculate base step parameters manually
« Reply #1 on: February 22, 2020, 06:52:57 pm »
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
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.