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General discussions (Q&As) / These distinctly different structures give the same base-pair step parameters.
« on: February 22, 2012, 12:23:05 pm »
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.
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.