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Author Topic: Rebuilding protonated RNAs with non-canonical basepairs  (Read 6731 times)

Offline ramon989

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Rebuilding protonated RNAs with non-canonical basepairs
« on: July 23, 2008, 07:50:16 am »
Hi all,

I am using 3DNA to rebuild RNA helices which are protonated.
To do so, I first build a DNA helix:
fiber -a pdbfile.pdb
subsequently analyze:
find_pair pdbfile.pdb stdout|analyze
Then replace in the parameter files the thymidines by Urdines, and subsequently rebuild using protonated nucleotides to do so.
[Probably there is a fastre way to do so]

My question is the following:
I found 3DNA can handle all basepairs (canonical and non-canonical), the one flaw I discovered is that it cannot handle U-U basepairs.
Can I fix this problem by modifying some file(s) ? Or is it hard-coded into 3DNA ?

Kind regards,
Ramon van der Werf

Offline xiangjun

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Re: Rebuilding protonated RNAs with non-canonical basepairs
« Reply #1 on: July 23, 2008, 10:27:15 pm »
There is nothing special about U-U pair in rebuilding. Could you please provide a minimal reproducible example? You could take advantage of the attachment functionality.

Xiang-Jun

Offline ramon989

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Re: Rebuilding protonated RNAs with non-canonical basepairs
« Reply #2 on: July 28, 2008, 10:21:13 am »
Dear Xiang-Ju,

Sorry, I mis-formulated... I meant:
I can rebuild a U-U basepair, but analyzing does not work.

Attached is the bp_helical.par file, from which I rebuilt the structure RNA.pdb (protonated).
If subsequently I type:
find_pair rna.pdb stdout|analyze, the bp_helical.par does not contain the U-U basepair.

If you want to, I can tar all Atomic_*.pdb files I use together with the bp_helical.par and so on.

Kind regards,
Ramon

Offline xiangjun

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Re: Rebuilding protonated RNAs with non-canonical basepairs
« Reply #3 on: July 30, 2008, 11:25:21 pm »
Quote
Sorry, I mis-formulated... I meant:
I can rebuild a U-U basepair, but analyzing does not work.
Well, it is not a problem of the 'analyze' program either. As a side note, how many such misunderstandings exist in literature?

Check FAQ #6 carefully: you should be able to get the answer. For your own understanding of the issue and to the benefit of other users, I am hoping that you would summarize your solution and post it back  :) . Otherwise, I will have no incentives on follow-up questions  :(  

HTH,

Xiang-Jun

Offline ramon989

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Re: Rebuilding protonated RNAs with non-canonical basepairs
« Reply #4 on: July 31, 2008, 12:23:40 pm »
Dear Xiang-Ju (and other readers),

Thanks....
I have to read the FAQ... sorry I forgot.

Solution to this problem.
If an A-T basepair is replaced by a U-U basepair in bp_helical.par, the distance between the atoms in the H-bond is too large.

The solution was to be found in FAQ#6, and is the following....
In the X3DNA/BASEPARS/misc_3dna.par

there is a line:
Quote
4.0 0.0 ON A1 # upper H-bond length limits/atoms, alternative location

I increased the upper H-bond length t0 5.0. So this line looks in my file:
Quote
5.0 0.0 ON A1 # upper H-bond length limits/atoms, alternative location

Now the basepair is detected, and the problem is solved.

Kind regards,
Ramon

 

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.