Topics

1

General discussions (Q&As) / how to minimize DNA built with fiber?

« on: April 22, 2009, 08:41:14 pm »

Hi,
I am wondering how to minimize the BDNA built with fiber. Some bonds are broken and I want to improve the DNA by minimization.

2

General discussions (Q&As) / 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?

3

General discussions (Q&As) / sugar puckers in B-DNA

« on: October 25, 2008, 01:09:27 am »

Hi all,
does anybody know why coot and sybil and may be other programs that I don't know generate the C3*-exo puckers in an ideal B-DNA instead of C2*-endo?

4

General discussions (Q&As) / interpretation of output file

« on: August 09, 2008, 12:18:37 pm »

Hi,
1. I am using the 3dna program and I don't understand some of the  results. Could you please tell me "Deviation from regular linear helix: 3.32 (0.37)".
Is it in angstroms or degrees? Is it a big bend or a mild one?
 
2. Is it possible to see "normal" DNA parameters to compare with the results from the output file?
Which parameters  other than the  "Deviation from regular linear helix" indicate if the bend is big or mild?
 
3. In our structure, a protein interacts only with the half of the double-stranded B-DNA. How can I determine that only one half is bent?