Netiquette · Download · News · Gallery · Homepage · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · DSSR Licensing · Video Overview· RNA Covers

Author Topic: about "curavture" and "tangent" in dnaMD  (Read 16134 times)

Offline xroxzero

  • with-posts
  • *
  • Posts: 2
    • View Profile
about "curavture" and "tangent" in dnaMD
« on: November 08, 2017, 11:14:05 am »

I have a question about the unit of "curavture" and "tangent" in dnaMD. 

In dnaMD, my dna contains 24bp, and I type " dnaMD vsTime -i 24bp_dna.h5 -tbp 24 -bs 1 -be 24 -p "curvature" -mm sum -o curvature.dat ".

An error occur, "The requested end bp 24 is out side of 1-23 range" , why the range is 1-23?

This error occur on "tangent" ,too.

Also,I concern the unit of "curavture" and "tangent" ?

Thank you very much for your help,

Offline Rajendra Kumar

  • with-posts
  • *
  • Posts: 10
    • View Profile
    • 3DNA and dnaMD for MD trajectory analysis
Re: about "curavture" and "tangent" in dnaMD
« Reply #1 on: November 08, 2017, 12:02:40 pm »

As written in tutorial (, axis coordinate is determined using two base-pairs (one base-step) by 3DNA. Therefore, number of helical-axis coordinates is less than one of total number of base-pairs.

Unit of helical-axis is A, therefore, curvature unit is (1/A). Tangents are a list of vectors with same as helical-axis unit.

With regards,


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