What do numbers in *.inp files mean?

[mikeshelk]

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

[xiangjun]

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.

HTH,

Xiang-Jun