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Topics - wolson

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According to their 3DNA output files, all four of the attached structures have the same positive rise (+3.4 A), the PP and MM files have the same positive twist (+36 deg), and the PM and MP files have the same negative twist (-36 deg). The structures should have all four possible combinations of the signs for rise and twist, i.e., (+3.4, +36) for PP, (–3.4, -36) for MM, (+3.4, -36) for PM, and (-3.4, +36) for MP.

The error is related to the implementation of the Cambridge Convention in the computation of base-pair step parameters in 3DNA. Users interested in structures like these are interested in rigid-body parameters that reproduce the input structures rather than adhering to the Convention.

A useful option for such users would be the option NOT to follow the Cambridge Convention.

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.