Messages

1

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

« on: April 27, 2009, 04:10:43 pm »

By the way, I find that dna residues numbering is not very convenient in the rebuilt dna; chain B continues the numbering from chain A. So, I have to change the numbering manually.

2

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

« on: April 27, 2009, 03:38:09 pm »

Hi Xiangjun,
this DNA came from a protein-DNA complex, but the initial parameters were not good. So, I rebuilt it with your program, but before I put it back in the structure of the complex for the refinement, I want to connect all O3'-P linkages. Some distances are >2.5 A.

3

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

« on: April 27, 2009, 03:30:07 pm »

Hi,
Here what you say in one example:

"Please note that in the rebuilt bdl084_3dna.pdb file, some O3'(i-1) to P(i) linkages can be quite long (broken). This structure can be easily minimized to obtain a better backbone linkage."

I got some long O3'(i-1) to P(i) bonds and would like to minimize the structure to fix it.

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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.

5

General discussions (Q&As) / Re: 3DNA misses one pair of nucleotides

« 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.

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General discussions (Q&As) / Re: 3DNA misses one pair of nucleotides

« 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

7

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?

8

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?

9

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

« on: September 13, 2008, 07:42:01 pm »

Dear Xiang-Jun,
You clearly have the ability to avoid answers to the questions.  You lecture me how to pose a question, I recommend you learn how to answer a question. I read your answers to other questions and the pattern is the same: to give as little help as possible. Still I like your program better than the other programs, so please, try to be more helpful. Do you think Wilma knows how to use this program? Maybe I should write to her?

10

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

« on: September 13, 2008, 02:26:54 pm »

Hi,
I built an ideal DNA with the same sequence in coot and I analysed it with 3dna. I compared results with the DNA from the protein-DNA complex. Strangely, the deviation of the global helical axis was the same??? I was looking for a parameter to measure the DNA bending caused by protein interaction and I thought that this deviation was the right parameter. Now I see that I was wrong. Could you explain to me why the deviation from the regular axis for the ideal DNA is the same as in perturbed DNA?

11

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

« on: September 11, 2008, 01:09:50 pm »

I used coot for building DNA with a given sequence. I guess, the "fiber" is doing the same thing.
I would like to know how can I use rebuild in my work? I would like to learn how to use it

12

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

« on: September 11, 2008, 09:49:23 am »

Hi, Xiang-Jun
if I only knew how to do things that you recommended. Could you please send me a manuel, because on your site there is only one instruction how to do find_pair, so I can run only this command. I have no idea how to use fiber or how to do rebuild. I need more help from you. Anyway, please, answer my question, as I need to answer reviewers comments as soon as possible. I still need to learn more about your program, as I have another structure with DNA in the refinement stage.

13

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

« on: September 09, 2008, 07:03:17 pm »

Hi, Xiangjun
1. A reviewer of my paper asked if the "deviation of the global helical axis from a regular linear axis" refer to the maximum deviation of the two axes. Could you please answer that question for me.

2. Parts of my DNA in a protein-DNA complex has bad angles. Can I improve the geometry of my DNA using your program.
Is "rebuild " option allows you to do that?

14

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?