Also if there are specific strands you’re interested in, downloading the file as a .oxview from either oxView or Scadnano will keep coloring. Then you can load the oxView file followed by your simulation configuration, it will keep the coloring on the loaded configuration.
February 7, 2025 at 12:09 PM
Also if there are specific strands you’re interested in, downloading the file as a .oxview from either oxView or Scadnano will keep coloring. Then you can load the oxView file followed by your simulation configuration, it will keep the coloring on the loaded configuration.
If you change something in the candano file, it has to be loaded again from scratch into oxview. The scadnano tool has recently been expanded to also allow for visualization in embedded oxview window. Having an interactive cadnano-like interface inside oxView is currently on our TBD wishlist
February 5, 2025 at 9:15 PM
If you change something in the candano file, it has to be loaded again from scratch into oxview. The scadnano tool has recently been expanded to also allow for visualization in embedded oxview window. Having an interactive cadnano-like interface inside oxView is currently on our TBD wishlist
DNA nanotech is getting so easy we’re replacing grad students with cats. #oxview #academicCatter
November 12, 2024 at 5:58 AM
DNA nanotech is getting so easy we’re replacing grad students with cats. #oxview #academicCatter
The Blender package for molecular visualization, Molecular Nodes, can natively read oxDNA files (thanks @bradyajohnston.bsky.social) Alternatively, oxView can export stl files which can be loaded in Blender. 🧬
January 24, 2025 at 12:49 PM
The Blender package for molecular visualization, Molecular Nodes, can natively read oxDNA files (thanks @bradyajohnston.bsky.social) Alternatively, oxView can export stl files which can be loaded in Blender. 🧬
Karikó and Weissman might have gotten a Nobel Prize, but my PhD project got 5 seconds of screen time in yesterday’s #1 trending video on YouTube. Can I have a parking spot too? 🧪
October 2, 2023 at 4:06 PM
Karikó and Weissman might have gotten a Nobel Prize, but my PhD project got 5 seconds of screen time in yesterday’s #1 trending video on YouTube. Can I have a parking spot too? 🧪
We made the oxView export so we could 3D print structures. The Molecular Nodes visualization is going to be much more flexible as far as blender styling and is also able to load trajectories. Here are some tiny resin prints of Holliday junctions I made for an outreach project.
January 24, 2025 at 1:00 PM
We made the oxView export so we could 3D print structures. The Molecular Nodes visualization is going to be much more flexible as far as blender styling and is also able to load trajectories. Here are some tiny resin prints of Holliday junctions I made for an outreach project.
Tools:
The RNA helix was generated using oxView (oxview.org), a oxDNA viewer and structure editor.
QRNA (github.com/sunandanmukherjee/QRNAS) for relaxation, specifically of the backbones.
All-atom forcefield OL3 (kfc.upol.cz/ff_ol/index.php), currently the best out-of-the-box RNA forcefield.
The RNA helix was generated using oxView (oxview.org), a oxDNA viewer and structure editor.
QRNA (github.com/sunandanmukherjee/QRNAS) for relaxation, specifically of the backbones.
All-atom forcefield OL3 (kfc.upol.cz/ff_ol/index.php), currently the best out-of-the-box RNA forcefield.
oxView
oxview.org
October 28, 2025 at 10:21 AM
Tools:
The RNA helix was generated using oxView (oxview.org), a oxDNA viewer and structure editor.
QRNA (github.com/sunandanmukherjee/QRNAS) for relaxation, specifically of the backbones.
All-atom forcefield OL3 (kfc.upol.cz/ff_ol/index.php), currently the best out-of-the-box RNA forcefield.
The RNA helix was generated using oxView (oxview.org), a oxDNA viewer and structure editor.
QRNA (github.com/sunandanmukherjee/QRNAS) for relaxation, specifically of the backbones.
All-atom forcefield OL3 (kfc.upol.cz/ff_ol/index.php), currently the best out-of-the-box RNA forcefield.
Hope the community finds this tutorial useful! We're extremely proud of this app and continue to develop it as our own research needs evolve.
Try oxView at <a href="http://oxView.org!" class="hover:underline text-blue-600 dark:text-sky-400 no-card-link" target="_blank" rel="noopener" data-link="bsky">http://oxView.org!
Direct comments, questions and frothing rage to our GitHub issues page:...
Try oxView at <a href="http://oxView.org!" class="hover:underline text-blue-600 dark:text-sky-400 no-card-link" target="_blank" rel="noopener" data-link="bsky">http://oxView.org!
Direct comments, questions and frothing rage to our GitHub issues page:...
November 12, 2024 at 7:28 AM
Hope the community finds this tutorial useful! We're extremely proud of this app and continue to develop it as our own research needs evolve.
Try oxView at <a href="http://oxView.org!" class="hover:underline text-blue-600 dark:text-sky-400 no-card-link" target="_blank" rel="noopener" data-link="bsky">http://oxView.org!
Direct comments, questions and frothing rage to our GitHub issues page:...
Try oxView at <a href="http://oxView.org!" class="hover:underline text-blue-600 dark:text-sky-400 no-card-link" target="_blank" rel="noopener" data-link="bsky">http://oxView.org!
Direct comments, questions and frothing rage to our GitHub issues page:...
8. Exporting oxView scenes to Blender for pretty rendering with fancy materials:
November 12, 2024 at 7:09 AM
8. Exporting oxView scenes to Blender for pretty rendering with fancy materials:
Currently, UNF is mostly a draft specification. I wrote a reader/writer for it in #oxView and David Kurtak wrote a series of scripts to provide conversion to/from Cadnano and PDB which can be found in this GitHub:
(7/10)
https://github.com/barisicgroup/unf
(7/10)
https://github.com/barisicgroup/unf
GitHub - barisicgroup/unf: Unified Nanotechnology Format
Unified Nanotechnology Format. Contribute to barisicgroup...
github.com
November 12, 2024 at 6:59 AM
Currently, UNF is mostly a draft specification. I wrote a reader/writer for it in #oxView and David Kurtak wrote a series of scripts to provide conversion to/from Cadnano and PDB which can be found in this GitHub:
(7/10)
https://github.com/barisicgroup/unf
(7/10)
https://github.com/barisicgroup/unf
6. Loading PDB files in oxView and preparing proteins for anisotropic network model (ANM) + DNA/RNA simulations.
November 12, 2024 at 6:51 AM
6. Loading PDB files in oxView and preparing proteins for anisotropic network model (ANM) + DNA/RNA simulations.
5. The oxView scripting interface. There are now a bunch of example scripts which can be found on the examples page of the GitHub to help new users learn the API:
https://github.com/sulcgroup/oxdna-viewer/tree/master/examples
https://github.com/sulcgroup/oxdna-viewer/tree/master/examples
November 12, 2024 at 6:43 AM
5. The oxView scripting interface. There are now a bunch of example scripts which can be found on the examples page of the GitHub to help new users learn the API:
https://github.com/sulcgroup/oxdna-viewer/tree/master/examples
https://github.com/sulcgroup/oxdna-viewer/tree/master/examples
4. Preparing oxDNA simulations and analyzing results using oxDNA Analysis Tools and oxView.
November 12, 2024 at 6:34 AM
4. Preparing oxDNA simulations and analyzing results using oxDNA Analysis Tools and oxView.
We pushed out some big updates to the #oxView GitHub this morning! If you’re using the software locally, please remember to pull. If you’re using it on our GitHub Pages, it is already updated.
Some highlights include:
Some highlights include:
November 12, 2024 at 6:24 AM
We pushed out some big updates to the #oxView GitHub this morning! If you’re using the software locally, please remember to pull. If you’re using it on our GitHub Pages, it is already updated.
Some highlights include:
Some highlights include:
Our paper introducing oxView and the Python toolkit we wrote for analyzing #oxdna simulations was formally published in @NAR_Open this morning! Huge shoutout all the coauthors for their dedication to the...
November 12, 2024 at 6:15 AM
Our paper introducing oxView and the Python toolkit we wrote for analyzing #oxdna simulations was formally published in @NAR_Open this morning! Huge shoutout all the coauthors for their dedication to the...
There are a lot of great tools for rational design of structural DNA, RNA and protein nanotechnology. From the old stalwarts like CaDNAno and Tiamat to new tools which automate more of the design pipeline like MagicDNA, sCadnano and #oxView (and many more I can't fit). (2/10)
November 12, 2024 at 6:15 AM
There are a lot of great tools for rational design of structural DNA, RNA and protein nanotechnology. From the old stalwarts like CaDNAno and Tiamat to new tools which automate more of the design pipeline like MagicDNA, sCadnano and #oxView (and many more I can't fit). (2/10)
2. Free-form design of small structures in oxView.
November 12, 2024 at 6:15 AM
2. Free-form design of small structures in oxView.
(this is me celebrating tracking down the bug that caused this to happen in oxView)
November 12, 2024 at 6:06 AM
(this is me celebrating tracking down the bug that caused this to happen in oxView)
In order to get the network to show up in the iFrame there I had to rewite the #oxView file handling system. It now accepts multiple auxiliary files at the same time (loaded with the initial configuration and topology or after as I do in the video)!
November 12, 2024 at 6:06 AM
In order to get the network to show up in the iFrame there I had to rewite the #oxView file handling system. It now accepts multiple auxiliary files at the same time (loaded with the initial configuration and topology or after as I do in the video)!
Now you can visualize a file from your simulation directory with
oxview trajectory topology
Please note that it is not recommended to open very large trajectories this way (use the browser) and video creation is not supported from this app.
oxview trajectory topology
Please note that it is not recommended to open very large trajectories this way (use the browser) and video creation is not supported from this app.
November 12, 2024 at 6:06 AM
Now you can visualize a file from your simulation directory with
oxview trajectory topology
Please note that it is not recommended to open very large trajectories this way (use the browser) and video creation is not supported from this app.
oxview trajectory topology
Please note that it is not recommended to open very large trajectories this way (use the browser) and video creation is not supported from this app.
Updates are just for the standalone executable, <a href="http://oxview.org" class="hover:underline text-blue-600 dark:text-sky-400 no-card-link" target="_blank" rel="noopener" data-link="bsky">http://oxview.org gets features as soon as we develop them.
oxView
oxview.org
November 12, 2024 at 6:06 AM
Updates are just for the standalone executable, <a href="http://oxview.org" class="hover:underline text-blue-600 dark:text-sky-400 no-card-link" target="_blank" rel="noopener" data-link="bsky">http://oxview.org gets features as soon as we develop them.