Modernizing the 3DNA/DSSR Ecosystem: Welcome to Our New GitHub Home

Over the past two decades, the 3DNA and DSSR software ecosystem has grown alongside the structural biology community. What began in 2003 with the classic 3DNA suite has evolved into DSSR—our automated engine for dissecting the spatial structure of RNA—and most recently into wDSSR, our registration-free web platform for 3D nucleic acid analysis and modeling.

As part of our ongoing efforts under the X3DNA-DSSR National Resource (supported by NIH/NIGMS grant R24GM153869), we are transitioning our development workflow and community support to modern, open infrastructure on GitHub.

A New GitHub Organization: x3dna-dssr

We have centralized our software repositories, plugins, and web resources under an official GitHub organization:

https://github.com/x3dna-dssr

This organization serves as the primary home for:

• wDSSR (Shuxiang Li): The official repository for our web interface, tracking front-end enhancements, feature roadmaps, and server releases.
• DSSR-PyMOL: (Eric Chen and Bener Dulger) an integrated PyMOL plugin that bridges 3D structural analysis, stylized cartoon block modeling, and an interactive pure-Python RNA 2D layout studio. Powered by DSSR (Dissecting the Spatial Structure of RNA), the plugin allows structural biologists to explore, identify, select, and edit secondary/tertiary nucleic acid features seamlessly in real time.
• Historical Source Code Archives: Preserving foundational codebases—including SCHNAaP/SCHNArP, 3DNA v1.5 (accompanying the 2003 NAR paper), and 3DNA v2.4—for long-term reproducibility.

Retiring the 3DNA Forum & Transitioning to GitHub Discussions

Since December 2011, the self-hosted 3DNA Forum (forum.x3dna.org) has been the primary venue for user support, troubleshooting, and scientific exchanges. Over nearly 15 years, our community has expanded to 5,918 members, generating 958 topics and 3,770 posts.

While the forum has served us well, maintaining a legacy Simple Machines Forum (SMF) board has become increasingly unsustainable due to broken SMTP email relays and relentless automated bot registrations.

To provide a modern, frictionless experience, community discussions and user support have moved to GitHub Discussions:

https://github.com/orgs/x3dna-dssr/discussions

Benefits of the New Discussion Platform

• No Separate Registration: Anyone with a GitHub account can participate immediately—no manual account approvals or verification delays.
• Reliable Email Notifications: Subscribe to threads or categories to receive immediate updates when someone replies.
• Native Markdown & Formatting: Easily paste command outputs, syntax-highlighted scripts, and inline mathematical notation.
• Seamless Screenshots: Drag and drop or paste images directly into posts to illustrate structural questions and bug reports.

The 3DNA Forum Is Now a Permanent Read-Only Archive

All 958 historical topics and 3,770 posts remain permanently online and searchable at forum.x3dna.org. To eliminate spam registrations and administrative overhead, new postings and account creations have been disabled, but no historical knowledge has been removed.

Key Community Resources

Whether you are looking for web-based analysis or downloads, here is where to find our core tools:

• Web Interface (wDSSR): web.x3dna-dssr.org
  Analyze, Rebuild, Model, Circularize, Mutate, Assemble, and Visualize 3D nucleic acids directly in your browser without registration.
• Community Q&A & Support: github.com/orgs/x3dna-dssr/discussions
  Ask questions, report edge cases, and share feature ideas across the entire tool suite.
• Legacy Downloads (DSSR v1.9.10): docs.x3dna-dssr.org/download.php
  Freely accessible binaries accompanying our 2020 NAR DSSR-PyMOL publication.
• Software Releases & Legacy Downloads: github.com/x3dna-dssr
  Access software distributions, including standalone binaries DSSR v1.9.10 (accompanying our 2020 NAR DSSR-PyMOL publication), 3DNA v2.4, 3DNA v1.5, and foundational SCHNAaP/SCHNArP packages.

Acknowledgements

We express our gratitude to every researcher, student, and collaborator who contributed questions, shared datasets, and reported edge cases on the 3DNA Forum over the past 15 years. Your feedback has directly guided the evolution of 3DNA and DSSR.

We invite you to star our repositories, join our discussions on GitHub, and help us shape the next generation of nucleic acid structural bioinformatics tools!