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Topics - Damien

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w3DNA -- web interface to 3DNA / Structural quality
« on: January 11, 2013, 12:00:39 pm »
Dear Xiang-Jun,

Could you look at the attached cyclized DNA structure and give your opinion about its structural quality by using Web 3DNA? It seems that many covalent bond angles like for example N1-C2-O2 or C3'-C4'-C5' are not correct. Do you confirm?

Many thanks


w3DNA -- web interface to 3DNA / misshapen base ring
« on: January 07, 2013, 10:25:54 am »
Dear all,

I have a long DNA 3D structure that contains 4 bases with misshapen rings. I detected them thanks to visual inspection.

How can I identify these structural deficiencies in a more automatic manner with Web 3DNA? From the list of numbers resulting from "Analysis", can I detect these misshapen bases?

Thanks for your help,


Dear Xiangjun,

I analyzed the DNA molecule contained in PDB 2AOR from Web 3DNA. I then downloaded the parameter file. And I performed a reconstruction from the parameter file.

The resulting structure build.pdb contains many O3'-P bonds having a too long length, up to 4 A.

May you tell me what I made wrong ?

Many thanks for your help


General discussions (Q&As) / Rebuild DNA from C trace
« on: April 15, 2011, 03:16:49 am »
Dear Xiang-Jun,

I have a PDB file of a DNA portion. It only contains the carbon trace (the C4 atoms). I would like to know whether it is possible to rebuild the whole structure from this trace with 3DNA? If not, do you know a way to do so?

Many thanks for your help


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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.