Reading the BPS File

[ashay]

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

[xiangjun]

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