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Dr. Xiang-Jun, hello!
I would like to ask about the find_pair output
Consider a string "
194 239 0 # 5 | -:...5_:[..T]T-----A[..A]:..23_:- 0.32 0.17 17.11 8.91 -0.83
"
Could you please tell me what all five numbers in "0.32 0.17 17.11 8.91 -0.83" exactly mean?
Thanks
Mikhail Schelkunov
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Well, this is a clearly defined question with a concrete example and I am in a unique position to answer it :) .
Could you please tell me what all five numbers in "0.32 0.17 17.11 8.91 -0.83" exactly mean?
The content after the # sign is not documented because it was initially used for debugging purpose only. Since you asked, here is a brief account of what the five numbers mean, using your specified example with unit in () at the end:
- the distance between origins of the two base reference frames (0.32 Å).
- the vertical distance between the base planes, i.e., |stagger| (0.17 Å).
- the angle between the two base normals (17.11°).
- distance between RN9 and YN1 of the pair (8.91 Å).
- an empirical measure combining a few other quantities; for deciding if a pair should be included in a double helix (-0.83).
Overall, the first four numbers are for identifying a base pair, while the fifth number is for checking its inclusion/exclusion in a duplex.
Over the years, [mono:3bemt574]find_pair[/mono:3bemt574] has turned out to be an essential 3DNA application that makes analyzing nucleic acid structure straightforward. See my blog post "What find_pair in 3DNA can do (http://http://xiang-jun.blogspot.com/2010/03/what-findpair-in-3dna-can-do.html)". As I've mentioned in several occasions, a detailed account of the underlying algorithm of [mono:3bemt574]find_pair[/mono:3bemt574] has still to be written. I've been continuously refining [mono:3bemt574]find_pair[/mono:3bemt574] internally, and hopefully I will be able to write a paper on it in the not too distant future.
HTH,
Xiang-Jun
Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids
Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University