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Questions and answers => General discussions (Q&As) => Topic started by: Abermebo on October 16, 2026, 04:04:10 am

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Title: Questions about 3DNA
Post by: Abermebo on October 16, 2026, 04:04:10 am

Dear Dr. Xiang-Jun Lu,

First, of all thank you for accepting me in the forum and for your work. Could you please tell me where I can download the 3DNA v2.4 to perform structural analysis of nucleic acids? (academic research)

I would also like to ask you a more specific question. I am analyzing a modified base pair (completely different from WC bp), and when trying to determine the base-step parameters using nastruct, I obtain some artifacts (especially in the twist) due to the structural flexibility of the pair. I belive the best option would be to use the so-called simple helical parameters, based on consecutive C1'-C1' vectors. However, the problem is how to make the program recognize these non-natural bases. Is there any way to force the program to recognize them?

Thank you very much in advance for your help  :)

Title: Re: Questions about 3DNA
Post by: xiangjun on October 19, 2026, 11:08:09 am

Hi Abermebo,

Thanks for your interest in 3DNA and for posting your question on the Forum.

You should now be able to access the Downloads page to download 3DNA v2.4. Regarding your specific question, please provide a concrete example so others can reproduce your problem.

Best regards,

Xiang-Jun

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