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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
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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
Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.
