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

Author Topic: About DNA contour length  (Read 8936 times)

Offline candery

  • with-posts
  • *
  • Posts: 1
    • View Profile
About DNA contour length
« on: October 29, 2009, 03:06:04 am »
I have a question when calculating the DNA contour length. Can I use the sum of Rise as the contour length and use the sum of h-Rise as the end-to-end distance? So DNA bending is measured by the ratio of the end-to-end distance and the contour length?
The other question is how to analyze a pdb file that has a lot of frames in it?
 
Thank you very much.

Offline xiangjun

  • Administrator
  • with-posts
  • *****
  • Posts: 1642
    • View Profile
    • 3DNA homepage
Re: About DNA contour length
« Reply #1 on: October 30, 2009, 08:57:38 pm »
Quote
I have a question when calculating the DNA contour length. Can I use the sum of Rise as the contour length and use the sum of h-Rise as the end-to-end distance? So DNA bending is measured by the ratio of the end-to-end distance and the contour length?

3DNA does not calculate DNA contour length. As far as if it is appropriate to use sum of Rise as contour length, and sum of h-rise as end-to-end distance, why not you try some examples? Using ribosomal DNA superhelix, for example, would the numbers make sense? For quantify DNA bending, there are already discussions in the 3DNA forum. You could also try Curves/Curves+ from Lavery et al.

Quote
The other question is how to analyze a pdb file that has a lot of frames in it?

I do not think I understand your point here. Could you be more specific?

Xiang-Jun

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.