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Hi xiangjun,
I have obtained helical parameters for damaged DNA from trajectory by using 3DNA, there are three mismatched T:T pairs and a bend in the DNA. However when I calculated the averages have got large deviations in the damaged regions. Would you please check my plot and suggest me whether these kind of deviations are allowed or not. Where shall we find the basic definitions of all these parameters ?
Thanks in Advance.
Kartheek Joshua .

Hi Kartheek,
Thanks for your followup questions on the analysis of DNA structures with nonWC base pairs. For the definition of 3DNA basepair parameters, please see:
 A standard reference frame for the description of nucleic acid basepair geometry (http://ndbserver.rutgers.edu/ndbmodule/archives/reports/tsukuba/tsukuba.pdf)
 3DNA: a software package for the analysis, rebuilding and visualization of three‐dimensional nucleic acid structures (http://nar.oxfordjournals.org/content/31/17/5108.full)
The standard base reference frame is based on an idealized WatsonCrick base pair. There are numerous nonWC pairs, each diverting from the WC pairs in a unique way that can be rigorously characterized by the six basepair parameters (see the 3DNA 2003 NAR paper). However, the basepair frame derived from nonWC pairs can have a big impact on the step parameters, often leading unintuitive numerical values, as in your case. That's where the new set of 'simple' basepair and step parameters in 3DNA 2.3 comes in. See my blog post "Details on the simple basepair parameters (http://x3dna.org/highlights/detailsonthesimplebasepairparameters)" and links therein.
With the 3DNA v2.3 distribution, there is a PDF doc "techdetails.pdf", which gives stepbystep worked examples on how the parameters are calculated. Since 3DNA v2.3 is now open source, you can dig into the bottom as to how all the parameters are defined. As with any tools, it is up to the user to decide how to make best use of them.
HTH,
XiangJun

Dear xiangjun,
Thanks for your reply, I have observed rise value ve for one particular base pair. As far as I know, rise is just distance between two adjacent base pairs, how can be this rise value be ve ??

A negative value of "rise" is unexpected in a intuitive sense, but it comes "naturally" in 3DNA based strictly on its definition of the six step parameters as described in the docs I referred to you previously. To verify, simply "rebuild" the structure using the derived parameters, and you should get virtually same structure as the original one as far as basepair geometry goes. You could further "analyze" the rebuilt structure, and you are guaranteed to get back essentially the same basepair parameters.
Also as I mentioned in my previous response, the new set of simple parameters are introduced to give parameters that are sensible. For one thing, the rise value should not be negative. The above statement is general. Please provide a concrete example to illustrate your case step by step. If you have difficulty in the process, I will try my best to help.
Did you know Curves+? Give it a try since it may better fit your needs.
Best regards,
XiangJun
Created and maintained by Dr. XiangJun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.