3DNA Forum

Questions and answers => w3DNA -- web interface to 3DNA => Topic started by: Damien on January 11, 2013, 12:00:39 pm

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Title: Structural quality
Post by: Damien 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

Damien

Title: Re: Structural quality
Post by: xiangjun on January 11, 2013, 12:26:12 pm

Hi Damien,

Please note that 3DNA works 'mechanically' -- it calculates a set of parameters for your input structure, without checking if it is reasonable at all. However, since an erroneous structure often gives some bizarre parameters, 3DNA can give a careful user some hint on possible issues.

A quick check using Jmol (or RasMol) shows one region of your model is displayed differently from the rest, signaling some problems. For a detailed report regarding the quality of your model, please try MolProbity (http://molprobity.biochem.duke.edu/).

Xiang-Jun

Title: Re: Structural quality
Post by: Damien on January 11, 2013, 12:36:11 pm

Thanks for the reply Xiang-Jun! I'm going to test the structure with MolProbity.

This DNA is in fact 1BNA prologated with a model DNA and made cyclized.

Thanks for your help!

Damien

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.