Calculation of Jtwist, Jroll and Jslide for junctions

[venkadesh]

Dear Sir,
             How to calculate Jtwist, Jslide and Jroll using 3DNA software for junction structure?

[xiangjun]

How to calculate Jtwist, Jslide and Jroll using 3DNA software for junction structure?

I am not familiar with the names Jtwist, Jslide and Jroll, and they are not calculated by 3DNA.

Would you mind sharing more details, e.g., providing a reference?

Xiang-Jun

[venkadesh]

Reference:
"Definitions and analysis of DNA Holliday junction geometry"
  Jeffrey Watson, Franklin A.Hays and P.Shing Ho.
Nucleic Acids research, 2004, Vol.32, No.10, p 3017-3027.

[xiangjun]

Thanks for the reference. While 3DNA is not directly applicable for calculating such parameters, it could help in some ways, e.g., to identify the double helical regions and get the helical axes etc.

Of course, you could always check with the original authors for further technical details (e.g., the program to reproduce their results). If you want to implement their method yourself and would like to share, I am willing to help in a sensible way.

Xiang-Jun