helical parameters for damged conformation of the DNA

[kartheekpitta]

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 !

[xiangjun]

Hi,

Thanks for using 3DNA. Your attached PDB file is helpful in locating where the 'problem' is.

The 3DNA web server is doing its job since the middle parts are clearly far off from each other for any sensible pairs. To get what you want, please try the command-line version. First, run 'find_pair' to get a list of base pairs. You need to manually edit the list as desired, and then feed your revised list to 'analyze'. This is the trick that has been repeated many time on the Forum, and mentioned in the 2008 3DNA Nature Protocols paper.

HTH,

Xiang-Jun

[kartheekpitta]

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.

[xiangjun]

Please ask the maintainer of the do_x3dna tool for support.

Xiang-Jun