Messages

1

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

« on: October 14, 2018, 04:57:03 pm »

Thank you for the quick response Xiang-Jun.

As described in the 2003 3DNA paper (https://www.ncbi.nlm.nih.gov/pubmed/12930962), since this is a Watson-Crick base pair (M-N), and the faces of the base pairs are opposite each other (M is up, N is down), it is convention to have the frame of N rotated 180 on its x-axis, so that the frame's z-axis faces down. Thus the scalar product between the z-axis of each frame would be negative.

I have attached a picture below to show the difference between F2c (green) and F2 (blue). F2 and F2c share the same x-axis. The yellow dots are the origins of the atoms of base M, and the red dots are the origins of the atoms of base N. Rotating F2c 180 degrees about its x-axis would make it equivalent to F2.

Calculating the base pair parameters between F1c and F2c returned the same result as DSSR. This means that to calculate the base pair parameters, F2 needs to be rotated 180 degrees about its x-axis before base pair parameters are calculated.

2

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