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General discussions (Q&As) / Clarification on Rebuilding Reference Frames from the Middle Frame

« on: October 09, 2018, 03:51:32 pm »

Dear Xiang-Jun,

I have been having trouble rebuilding the base reference frames from the middle frame and base pair parameters outputted by x3DNA/DSSR.

Middle Frame: [[0.825, 0.565, 0.001], [-0.565, 0.824, -0.032], [-0.018, 0.026, 1.0]]
Base Pair Parameters: [-0.176, -0.054, 0.306, -0.548, -9.232, -3.527]

I am implementing the method from the x3DNA user manual (attached below). It seems that one of the frames I am calculating (labeled F2) has its y and z axes reflected.

Reference Frames calculated by me:
F1c: [[ 0.838,  0.54   ,  0.082], [-0.539,  0.841, -0.034], [-0.087, -0.016,  0.996]]
*F2c: [[ 0.806,  0.586, -0.0802], [-0.59,  0.807, -0.025], [ 0.051 ,  0.067,  0.996]]

*y and z axes are reflected

Reference Frames outputted by DSSR:
F1: [[0.838, 0.54, 0.082], [-0.539, 0.841, -0.034], [-0.087, -0.016, 0.996]]
F2: [[0.806, 0.587, -0.081], [0.59, -0.807, 0.024], [-0.051, -0.067, -0.996]]

I can just multiply the frame by this matrix: [[ 1,  0,  0], [ 0, -1,  0], [ 0,  0, -1]], but I was wondering what might be wrong with my implementation.

I have attached the formulas I am using, as well as the pdb I am analyzing and DSSR json file output. Let me know if I should attach anything else that may be helpful.

Edit: The bases I am analyzing in the pdb file are the modified 8OG-C pair (Base numbers 2 and 5).

Thank you for your time,
Nil