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Author Topic: What do numbers in *.inp files mean?  (Read 5530 times)

Offline mikeshelk

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What do numbers in *.inp files mean?
« on: August 25, 2010, 07:05:00 am »
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?

Mikhail Schelkunov

Offline xiangjun

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Re: What do numbers in *.inp files mean?
« Reply #1 on: August 26, 2010, 12:06:32 am »
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". 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.




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The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.