Netiquette · Download · News · Gallery · Homepage · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · DSSR Licensing · Video Overview· RNA Covers

Author Topic: how x3DNA locates the base-pairs for calculating the helical parameters  (Read 4736 times)

Offline bratarajghosh

  • with-posts
  • *
  • Posts: 6
    • View Profile
Dear All,
I wanted to understand how x3DNA locates the base-pairs for calculating the helical parameters from a PDB coordinate file. Specifically, does it find the corresponding base pairs from the same residue number, or, does it find the right base-pair that is spatially closest?
For example, one may have a n-length sequence which is -(AT)- . For, say, the 10th base (A), will it locate the corresponding 10th (T) nucleotide?
How can I interpret it from the generated output file?
Your help is greatly appreciated.

Offline xiangjun

  • Administrator
  • with-posts
  • *****
  • Posts: 1640
    • View Profile
    • 3DNA homepage
As explained in the 2003 3DNA NAR paper, and more explicitly in the 2015 DSSR paper (Fig. 1), 3DNA/DSSR uses a geometric appoach to find any pair in 3D space that fulfill a set of criteria. Since 3DNA v2.3 is open source, you can dig into the details in find_pair on how it works. If you could provide a PDB coordinate file, we can work through a concrete example to make the point clear.

HTH,

Xiang-Jun

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.