Out now in @NatureProtocols, a tutorial series using #oxView to design D(R)NA/protein nanostructures and relax them for @ox_DNA simulation! Awesome work by @progolab, @aatmilk, @petr_sulc et al
A quick overview of contents:
(OA link at end of...
Huge thanks to the #FNANO2022 organizers for another awesome conference! It was an honor to get a best contributed talk award, but the real honor is every time I see an #oxView scene during a talk or poster. Huge thanks to @progolab and the team for keeping this going.
This is the #oxView video for all of you who wish you could design and simulate RNA structures from the dancefloor. (audio starts when the simulation does).
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
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)
Update on this #oxView situation, looks like if your graphics drivers are Mesa 630 or Nvidia 495, the renderer works. The way to check if it's dead is to go to about:support and check the graphics section for errors.
Update on this #oxView situation, looks like if your graphics drivers are Mesa 630 or Nvidia 495, the renderer works. The way to check if it's dead is to go to about:support and check the graphics section for errors.
For those using #oxView (or any graphics heavy app) with @firefox on Linux with an Nvidia graphics card, do not update to Firefox 94. The update to EGL breaks hardware acceleration making oxView unusable. Possible that updating Nvidia drivers to 495 fixes but haven’t tried yet.
For our command-line #oxView users, we are updating the Electron packages today. Download the new version for improved sequence setting/searching, direct Nanobase/PDB import, and support for SNUPI files.
github.com/sulcgroup/oxdna-viewer/r...
#oxView just passed its 1000th commit! To celebrate, I re-loaded commit #1, from when it was a @threejs example stapled to a file reader. My computer was wheezing trying to load this structure. Now, I can load over 150 of these at the same time...and the lighting is better!
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)!
Check out Jonah Procyk's poster from #FNANO21! He will be introducing our new protein-DNA ANM model for #oxDNA as well as the new PDB loader and ANM solving in #oxView.
Check out Joakim Bohlin's poster at #FNANO21! He will be giving a live demo on how to design freeform #DNAnanotechnology using #oxView as well as showing off some of the new features the team has added since my talk last year!
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:
