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

« previous next »
Pages: [1]   Go Down

Author Topic: 3DNA misses one pair of nucleotides  (Read 17593 times)

Offline pqtak

  • with-posts
  • *
  • Posts: 14
    • View Profile
3DNA misses one pair of nucleotides
« on: October 28, 2008, 01:16:53 pm »
Hi all,
I have three 20-bp identical DNAs in my pdb. 3DNA finds 59 pairs missing a second pair in one DNA. What can cause such thing?
Logged

Offline pqtak

  • with-posts
  • *
  • Posts: 14
    • View Profile
Re: 3DNA misses one pair of nucleotides
« Reply #1 on: October 31, 2008, 06:26:08 pm »
I figured out what happened. A base of the first nucleotide was making a pair with the base of the  second nucleotide.
I fuxed this problem
Logged

Offline ghzheng

  • with-posts
  • *
  • Posts: 23
    • View Profile
Re: 3DNA misses one pair of nucleotides
« Reply #2 on: November 01, 2008, 09:53:17 pm »
Can you please make clear what was your problem and how you fixed it? I don't get it.
Thanks.

Guohui
Logged

Offline pqtak

  • with-posts
  • *
  • Posts: 14
    • View Profile
Re: 3DNA misses one pair of nucleotides
« Reply #3 on: November 02, 2008, 10:55:01 pm »
The problem was that I have 60 nucleotide pairs (double -stranded DNA), but the program found only 59 pairs. Then I realized that a base from one nucleotide makes a Watson-Crick pair with the wrong nucleotide due to low resolution and poor density. So, I restrained the bases so that they are making right pairs and now the program (3DNA) finds all 60 pairs.
Logged
Pages: [1]   Go Up
« previous next »
 

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University