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Author Topic: Reading the BPS File  (Read 2165 times)

Offline ashay

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Reading the BPS File
« on: February 07, 2017, 02:34:45 pm »
Hi Dr. Lu,

When reading the BPS file, what do each of the five numbers on rightmost side represent?

1   24  0 #    1 | ....>A:...1_:[.DC]C-----G[.DG]:..24_:B<....  0.50  0.06 14.47  8.89 -3.65
2   23  0 #    2 | ....>A:...2_:[.DG]G-----C[.DC]:..23_:B<....  0.37  0.25 11.73  8.90 -3.55

In the case of 1BNA and the resulting 1BNA.bps file, the numbers read: 0.50  0.06 14.47  8.89 -3.65
 
Thanks,

Ashay

Offline xiangjun

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Re: Reading the BPS File
« Reply #1 on: February 07, 2017, 06:57:51 pm »
Hi Ashay,

The fiver numbers are some technical details users may generally ignore. Since you asked, here they are, using first line as an example:

  • 0.50 is the distance (in Å) between origins of the base references frames in the pair.
  • 0.06 is the vertical distance (in Å) of base planes, i.e. |stagger|.
  • 14.47 is inter-plane angle (in degrees) of the two bases.
  • 8.89 is the distance (in Å) between RN9/YN1 of the two bases.
  • -3.65 is a mixed measure, combining the first three items.

Since 3DNA v2.3 is open source, you can dig into the bottom of how the numbers are calculated (see find_pair.c).

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.