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Author Topic: interpretation of output file  (Read 9617 times)

Offline pqtak

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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?

Offline xiangjun

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Re: interpretation of output file
« Reply #1 on: August 11, 2008, 09:56:53 pm »
Quote
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?
It is in angstroms. Based purely on the number, I would guess it is a mild one. As always, however, a number is just a number, and you should use a visualization tool (e.g., RasMol) to see/judge for yourself.

Quote
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?
Try use the "fiber" program to build regular B- and A-DNA models and analyze them. What would you get? Check and compare them with the examples directory (analysis/rebuilding) of A-, B- and nucleosome DNA structures adh006/bdl084/pd0001. It would be helpful that you summarize and post back a table of your findings.

Quote
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?
3DNA works on a user-specified PDB file, which could be the whole structure or half of it.

HTH,

Xiang-Jun

Offline pqtak

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Re: interpretation of output file
« Reply #2 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?

Offline xiangjun

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Re: interpretation of output file
« Reply #3 on: September 10, 2008, 10:04:03 pm »
Well, I do not intend to be mean, but have you ever thought of answering the requests/questions in my reply to your initial post? Going through those questions would have clarified your understanding of the issues and helped other 3DNA users as well.

It might help to (re)read the post "Welcome message from Xiang-Jun Lu", and follow the link on "How To Ask Questions The Smart Way?"

Best regards,

Xiang-Jun

Offline pqtak

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Re: interpretation of output file
« Reply #4 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.

Offline pqtak

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Re: interpretation of output file
« Reply #5 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

Offline pqtak

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Re: interpretation of output file
« Reply #6 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?

Offline xiangjun

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Re: interpretation of output file
« Reply #7 on: September 13, 2008, 05:18:27 pm »
Again, as recommended clearly in the guideline, please provide a minimal, reproducible example to help others HELP YOU.

Quote
on your site there is only one instruction how to do find_pair, so I can run only this command.
As the author of "find_pair", I know clearly that it does not produce output on "deviation of the global helical axis from a regular linear axis".

I am certainly not in a position to answer the reviewer's questions to your paper. As a general rule, it is dangerous to use something you do not understand. You should clarify the issues beforehand instead of afterwards.

Overall, if you do not know how to use "fiber" to build fiber models,  not being able to find and follow the instructions in the 3DNA users' manual, clearly 3DNA is not the right tool for you. Curves is an excellent alternative and it is widely used to quantify DNA curvatures.

Good luck!

Xiang-Jun

Offline pqtak

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Re: interpretation of output file
« Reply #8 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?

 

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.