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Messages - kartheekpitta

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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 ??

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 .

I am able to generate helical parameters successfully for 1PDB file.  I have observed damaged residues part has been excluded by do_x3dna  by default. Is there a way to produce helical parameters for damaged DNA from d0_x3dna.  I mean where do we edit that input file for analyze as it generates all the results in one step.

Dear experts,
I am trying to get helical parameters for a DNA model. It has two missing residues in the middle and are modelled in VMD. When I have uploaded the structure in the server it is showing block representation properly. But while generating parameters,  It is giving for only properly paired bases i.e due to model construction problem newly added residues are bit far when compared other paired base. Is there any way that I can obtain parameters for all the bases in the structure.
Thanks in advance !

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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.