Recent Posts

11

RNA structures (DSSR) / Re: overlapping area calculation - stacking interactions

« Last post by xiangjun on August 25, 2026, 09:51:06 am »

Hi Agnieszka,

Thanks for reporting this issue. I was able to reproduce it and can confirm that it happens on my end as well. The pre-processed PDB files have the option specified for overlapping area calculation, but the script processing user-uploaded files does not. I have notified Shuxiang (who recently joined our team) about this. It should be fixed soon, and we will let you know once it is resolved.

Best regards,

Xiang-Jun

12

RNA structures (DSSR) / Re: overlapping area calculation - stacking interactions

« Last post by Agnieszka on August 25, 2026, 07:02:21 am »

Dear Xiang-Jun,
Recently, we have noticed that when using the 3DNA server and uploading a PDB file directly from a computer, the output does not include the overlapping area calculation. However, when a PDB code is entered instead, the output does contain this calculation.

Could you please check this issue and, if possible, restore this functionality for uploaded files?

Thank you very much,
Agnieszka

13

FAQs / Re: Where to download x3DNA

« Last post by xiangjun on August 16, 2026, 11:38:51 pm »

Hi,

The issue should be fixed now. It was due to my negligence.

Best regards.

Xiang-Jun

14

FAQs / Re: Where to download x3DNA

« Last post by deantuan on August 16, 2026, 07:50:12 pm »

Hello Dr. Lu,

My account has already been manually activated, and I can log in successfully. However, I still cannot see the “Download” link or the member-only “Downloads” section on the forum homepage.

I registered using my University of Washington email address and would like to download 3DNA for non-commercial academic research on DNA molecular dynamics trajectory analysis.

Could you please check whether my account still requires approval for download access?

Thank you very much for your help.

15

General discussions (Q&As) / Re: Could you tell me where l can download 3DNA?

« Last post by xiangjun on July 24, 2026, 09:16:16 am »

Hi Gai,

You should now be able to see the Download link in the top of the Forum.

Because you registered with a personal email address, it is difficult to verify your account and filter out spam. By default, new unverified accounts are assigned to a restricted category where the Download link is hidden and posts are moderated. This policy prevents spam and ensures the Forum remains clean and trustworthy.

Best regards,

Xiang-Jun

16

General discussions (Q&As) / Could you tell me where l can download 3DNA?

« Last post by gai on July 24, 2026, 07:51:15 am »

Dear Dr. xiangjun
I hope to download 3DNA v2.4 to carry out structural analysis of nucleic acids in my project. All usage will be limited to non-commercial academic research.

Thank you very much for your maintenance of this excellent software.

Best regards
Gai

17

RNA structures (DSSR) / Re: Can 3DNA DSSR handle Left-handed DNA?

« Last post by xiangjun on July 10, 2026, 01:34:37 pm »

Hi Jiaolong,

Thank you for providing the technical details and verification of the DSSR implementation for the classification of L-sugars. Detailed responses like this help improve the software and set a standard for community interaction.

I compiled four examples based on the information you provided to illustrate how the signs of the base-pair parameters are defined. See the Practical Guide associated with the 2020 DSSR-PyMOL paper for details. The base blocks and the standard base-reference frame attached to each base clarify the sign convention of base-pair and step parameters. PyMOL session files are attached so users can easily verify the results.

DSSR is under active development, and community interactions improve the software. I address questions and bug reports quickly. Users are encouraged to seek clarification regarding execution errors or unsupported features on the forum for their own benefit and that of the community as a whole.

Best regards,

Xiang-Jun

18

RNA structures (DSSR) / Re: Can 3DNA DSSR handle Left-handed DNA?

« Last post by JiaolongBao on July 06, 2026, 10:31:11 pm »

Hi Community,

The DSSR has been updated to v2.9.1 and it could be requested license at http://innovation.columbia.edu/technologies/CU20391. Regarding the update, the newest version is able to classify L-sugar to correct puckering type while retaining the original phase angle for L-sugar. The sugar class classification for L-sugar is omitted due to some compatibility reason with D-sugar.

Many thanks to Xiang-Jun's continued dedication to DSSR which makes it more and more powerful.

Jiaolong

19

RNA structures (DSSR) / Re: Can 3DNA DSSR handle Left-handed DNA?

« Last post by JiaolongBao on June 17, 2026, 09:08:34 pm »

Hi Xiang-Jun,

Certainly! I will email you for a video meeting.

Many Thanks,
Jiaolong

20

RNA structures (DSSR) / Re: Can 3DNA DSSR handle Left-handed DNA?

« Last post by xiangjun on June 17, 2026, 06:50:45 am »

Hi Jiaolong,

Thanks for the detailed explanation—this kind of feedback is exactly what I have been looking for.

I will certainly investigate the sign convention further. In this post, I would like to address the sugar-class issue. Currently, the L-sugar class is determined based on the pseudorotation phase angle, using the exact same criteria as for D-sugars. I have attached the dssr-torsions.txt output for 1BNA_L.pdb. Honestly, I had not paid close attention to this specific aspect of L-DNA before. Please let me know the correct way to determine the sugar class in these cases.

For this type of discussion, a phone call or a video meeting might be more convenient. Please let me know if you would like to connect online or over the line to discuss this topic further.

Best regards,

Xiang-Jun