3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: pqtak on October 28, 2008, 01:16:53 pm

Title: 3DNA misses one pair of nucleotides
Post by: pqtak 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?
Title: Re: 3DNA misses one pair of nucleotides
Post by: pqtak 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
Title: Re: 3DNA misses one pair of nucleotides
Post by: ghzheng 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
Title: Re: 3DNA misses one pair of nucleotides
Post by: pqtak 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.