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Questions and answers > w3DNA -- web interface to 3DNA

misshapen base ring

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xiangjun:
Hi Damien,

Thanks for your follow-up. Yes, you can certainly use 3DNA to detect anomaly in a structure; that happened a (long) while ago at the NDB.

Thanks for pointing out the "bad" pair involving DT8 on chain F. The issue is due to the very 'generous' distance criteria used, which work well for 'reasonable' cases but apparently fail for your severely distorted structure. I'll fix the issue and update 3DNA shortly.

Xiang-Jun

Damien:
Many thanks for your help Xiang-Jun! I appreciate.

Damien

xiangjun:
Hi Damien,

I've updated 3DNA v2.1 to 2013jan08, with an improved algorithm for nucleotide identification. Specifically, in its default setting, DT8 on chain F is no longer recognized as a nucleotide. For the record, in my yesterday's response with an attached image, I observed the missing pair issue via Jmol using the DT8 as a test case. However, I did not check carefully to notice that previous versions of 3DNA, by virtue of very general distance cutoffs, actually take it as a nucleotide! :-[

Note that the w3DNA web-server hosted at Rutgers is currently not yet updated to the latest version. So your best bet is to download the standard command-line version of 3DNA; it is the most efficient and convenient way to get your job done.

HTH,

Xiang-Jun

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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.