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

Author Topic: Zp/ZpH and depth of DNA  (Read 5605 times)

Nutch [Bot]

  • Guest
Zp/ZpH and depth of DNA
« on: September 24, 2007, 03:52:09 am »
I'm a new user of 3DNA and I have two questions about the following parameters:
 
1) Zp/ZpH: Could you tell me how are they calculated? I can't find any reference about it.

2) Is there a way to calculate the depth of minor/major grooves of DNA from 3DNA? Is there a clear definition of groove depth?

Thanks a lot...

Guillaume

Offline xiangjun

  • Administrator
  • with-posts
  • *****
  • Posts: 1623
    • View Profile
    • 3DNA homepage
(No subject)
« Reply #1 on: September 24, 2007, 09:40:06 pm »
Thanks for using 3DNA!

Please refer to Lu et al A-DNA paper (J. Mol. Biol. 300, 819-840, 2000) on the definition of Zp. ZpH is similarly defined, but w.r.t. to the middle helical frame.

3DNA does not provide groove depth info (yet). Please refer to Curves for it. Also note the "-c" option of "find_pair" in 3DNA to generate input to Curves directly from a PDB file.

In the meantime, if you or anyone know of "a clear definition of groove depth", or better yet, with implementation, please do let me know. I am interested in adding groove depth parameters in future 3DNA release.

HTH,

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.