Messages

1

General discussions (Q&As) / Re: helical parameters for damged conformation of the DNA

« on: November 10, 2016, 08:14:37 am »

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 ??

2

General discussions (Q&As) / helical parameters for damged conformation of the DNA

« on: November 02, 2016, 08:12:11 am »

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 .

3

w3DNA -- web interface to 3DNA / Re: helical parameters for damged conformation of the DNA from trajectory

« on: October 06, 2016, 07:55:10 am »

Hi,
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.

4

w3DNA -- web interface to 3DNA / helical parameters for damged conformation of the DNA

« on: October 03, 2016, 01:18:31 pm »

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 !