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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
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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
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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
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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
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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:
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:
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
Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids
Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University