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General discussions (Q&As) / Question on base-step parameters calculation in 3DNA

« on: October 18, 2012, 08:48:00 pm »

I am currently trying to repeat the base-stepping calculation in 3DNA. I read the "technical details" document associated with 3DNA and try to follow "5.5 Step parameters" section. I am doing OK until step 4, where the document states that the axes of "middle-frame"  are simply the average between those of R1’ and R2’. When I computed that myself, I got a different Rm compared to the one given in the document. For example the first element of Rm was calculated as (-0.6616 -0.1982)/2 =-0.4299, which was different to the given value -0.4490. Therefore I was unable to follow the rest of the calculation and get the correct base-step parameters myself.

I am wondering if I misunderstood anything or this is an error of the document. I look forward to your response. Thank you very much!