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Hi everyone,
I hope you are all doing ok on these crazy days.
I have performed some molecular dynamics simulations for a DNAprotein system. I am trying to understand the results by analyzing the DNA's structure before and after the protein binds. In particular I'm trying to calculate a parameter called the crookedness (beta) of the DNA which is defined as cosine(beta) = x / y , where x is the endtoend distance of the molecule and y is the sum of the individual basepaircenter distance (PHYSICAL REVIEW LETTERS 122, 048102 (2019)). Reading the x3dna documentation I've found that the distance between two consecutive basepair centers is equal to the square root of (shift^2 + slide² + rise^2), nevertheless I still need to calculate the endtoend distance of the entire DNA (or the centers for the corresponding basepairs). Can anyone please help me to obtain this information with x3dna? I have already run x3dna_ensemble analyze for a list of MD snapshots and can run x3dna_ensemble extract stuff but do not know where to find the information for the coordinates of the basepairs.
Best regards.
Daniel

Hi Daniel,
I still need to calculate the endtoend distance of the entire DNA (or the centers for the corresponding basepairs). Can anyone please help me to obtain this information with x3dna?
Could you please be specific what you mean here, using a concrete example?
XiangJun

Hi Dr. XianJun,
thank you for your response.
I think I've finally understood how to obtain the information I'm looking for, which is the origin of each basepair. I am attaching one snapshot of the simulations I've performed in pdb (and the result of find_pair). In this case, what I'm interpreting as the endtoend distance corresponds to the distance between the origin of the AT base pair at (166.994, 190.835, 4.669) and the GC basepair at (146.156, 129.39, 144.990), does this make sense? Could this be interpreted as the center of a basepair?
Best regards,
Daniel

Hi Daniel,
Thanks for posting an example to make your point clear.
The numerical values you provided for the origins of the two basepairs at the termini are correct.
I've heard of the term "endtoend distance of the entire DNA" many times, but never used it in my own work. I'm just wondering what is the endtoend distance of a circular DNA. Do you have any idea on that?
Best regards,
XiangJun

Hi Dr. XiangJun,
I'm rather used to modeling cows as discs in a 2d space :P , so I can't say I'm uncomfortable with this simplification of the DNA, but I see your point.
Thank you for taking the time to help me. Nice tool by the way, it's been incredibly helpful for analyzing the results of my simulations.
Best regards,
Daniel
Created and maintained by Dr. XiangJun 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.