Recent Posts

11

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

« Last post by Agnieszka on June 03, 2026, 08:29:21 am »

Hi,

I used new online xdna-dssr server and got calculated parmeters. However I can't see anymore the calculation of overlapping area as used to be in older version which I liked it very much. Is this option still available?

Agnieszka

12

Feature requests / Re: where are the torsion angles?

« Last post by xiangjun on June 01, 2026, 10:54:40 pm »

As a follow up, the wDSSR web server has been updated to include a link to torsion angles in the "Analyze" module. See an example output for PDB entry 1msy.

13

Feature requests / Re: where are the torsion angles?

« Last post by xiangjun on May 28, 2026, 10:25:56 pm »

Hi,

Thank you for your question. DSSR calculates a wide range of structural features, including backbone torsion angles. To keep the initial release of the wDSSR web server streamlined and accessible, some of these detailed parameters were intentionally omitted from the default display. In the meantime, you can obtain complete torsion angle profiles using the DSSR command-line tool, as detailed in the DSSR User Manual.

We can update wDSSR to make this data available on the web interface. Would you prefer to have the torsion angles included in a downloadable JSON output file, or displayed explicitly in a new section on the results page?

Best regards,

Xiang-Jun

14

Feature requests / where are the torsion angles?

« Last post by annawacker on May 28, 2026, 10:10:02 am »

I am missing the torsion angle analysis on the new web3DNA server. why is it gone?

15

FAQs / Re: Where to download x3DNA

« Last post by xiangjun on May 11, 2026, 05:09:54 pm »

Hi,

Thank you for joining the 3DNA/DSSR community. For security, initial posts from non-EDU addresses require a one-time approval. This has been completed, and your download link is now active.

Best regards,

Xiang-Jun

16

FAQs / Re: Where to download x3DNA

« Last post by layne on May 11, 2026, 04:51:28 pm »

Hi,

I also got the confirmation email and successfully logged in this forum, but I cannt find the download page. Could you help me check it?

Thank you!

17

FAQs / Re: Where to download x3DNA

« Last post by amtblcd on May 05, 2026, 02:42:48 am »

Hi Xiang-Jun,

 Got it, thanks.

Best regards,
Changdong

18

FAQs / Re: Where to download x3DNA

« Last post by xiangjun on April 27, 2026, 10:24:39 am »

Hi Changdong,

Thank you for the follow-up.

I would like to clarify that the licensing for DSSR is managed by Columbia Technology Ventures (CTVs). While DSSR has a large global community with hundreds of academic users, licenses are generally not issued to institutions in certain countries due to institutional compliance and administrative policies. Unfortunately, this means that even if an academic request is submitted, it may be restricted based on the location of the host institution.

However, you can still access DSSR through the following options:

• DSSR v1.9.10-2020apr23: This version is available for download directly from the 3DNA Forum. It corresponds to the paper "DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL" (2020) published in Nucleic Acids Research.
• wDSSR: You can use the recently released web interface for DSSR at https://web.x3dna-dssr.org/.
  

I appreciate your interest in the software and your understanding of these constraints.

Best regards,

Xiang-Jun

19

FAQs / Re: Where to download x3DNA

« Last post by amtblcd on April 27, 2026, 12:48:41 am »

Hi Xiang-Jun,

Thanks for your reply. Understood — I’ll follow up there and avoid duplicate posts.

I also wanted to note that I’m still unable to download DSSR v2.8.1-2026mar12, even though I submitted an academic account request for a free seat.

Best regards,
Changdong

20

Bug reports / Re: Missing DNA bases with negative residue number

« Last post by shuxiang on April 25, 2026, 10:20:30 pm »

Hi Mihir,

The problem has been fixed. Please have a try and let us know if you have any questions.

Best,
Shuxiang