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Author Topic: how x3DNA locates the base-pairs for calculating the helical parameters  (Read 1313 times)

Offline bratarajghosh

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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

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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
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.