1.0 Features

[dsehnal]

This is turning into a very nice application. The goal of this post is to scope and track features for 1.0.

• Polish overall UI/UX (@dsehnal) UX Improvements #31
  • Better scene navigation
  • Better examples section on the landing page (showcasing the Stories) (Improve examples UI #57)
  • Add "story developer notes"
  • Add up and normalized direction vectors + "as clipping plane/sphere" helper buttons to camera info to make it easier to build clipping plane expression
  • Assets: support images and audio (+ m4a in Mol* too), add "download" button next to asset in the asset manager (Improve assets #52)
  • Make top left logo a normal link that can open the app in a new window
  • Markdown editor improvements (UX imprivements #55)
  • Add Embed option in Publish dialog (include allow="autoplay" in the iframe)
  • Better error reporting in scene editor (UX imprivements #55)
• CI/CD improvements
  • Production deploy (@TerkaSlan)
  • Dev deploy (@TerkaSlan) (CI/CD for development environment #47)
• Stories
  • 1st RCDB Molecule of the Month @corredD (initial work on MOM number 1 with audio comments molstar#1624)
    • Base story in Mol* repo examples
    • Port to MolVeiwStories
  • NPC basket (@brindakv @victoria-dos)
  • Example(s) that deals with volumetric/tomogram data (@annsek)
  • AlphaFind explanation story (@TerkaSlan)
  • P450 cytochrome story with channel visualization (@victoria-dos)
  • Cycle Conformations (@victoria-dos)
  • Exosome story (@corredD)
  • Back to the future story / Terms of Entrapment (@corredD)
  • EMDB Story (@neliebi)
  • MolViewSpec feature tour
• Improve story composer (@dsehnal)
  • Pass index of the frame
  • Expose Mol*'s Vec3, Quat, Mat3, Mat4, and Color namespaces to the builder (+ typings) (Vec3, Mat3, Mat4, Quat accessible in the code editor #39)
  • Expose decodeColor
• Use specific version of Mol* in the generated HTML documents to ensure compatibility (check if it's possible to use @^4.5.0 in jsdeliver) @dsehnal
• Save sessions (including code) and Host stories (with a "Share" button that provides a link) (@dsehnal @TerkaSlan) (Save sessions host stories #25)
  • "Remember me" login (@TerkaSlan)
  • Fix uploading larger states (@TerkaSlan)
  • Publish session alongside of story (Extend story publish to include sessions #41)
  • Self-hosted publish option (@dsehnal) (Self-hosting support #56)
  • Create "full-standalone" zip file with story, including viewer JS/CSS (@dsehnal ) (Self-hosting support #56)
• Enable code completion for the builder
  • Ideally @midlik can help with generating the required .d.ts file (done via rollup, thanks @midlik)
  • Implement in the app by @dsehnal / @zachcp / @midlik (fix code completion #29 and Code completion #28 be correctly resolved in the Monaco editor
• MolViewSpec extensions (@dsehnal)
  • Additional custom extensions in the description markdown (palettes, color swatches, on-hover highlight, tables?) Snapshot Markdown Improvements molstar#1555 Markdown Commands and MVS improvements molstar#1597
  • Per-representation clipping objects Clipping support mol-view-spec#82 MVS: clip node support molstar#1553
  • Support clickable primitives that navigate to different states (MVS: grid-slice volume representation, label improvements, state transitions via 3D interactions, instacing molstar#1570)
  • Support primitive label backgrounds and tethers ((MVS: grid-slice volume representation, label improvements, state transitions via 3D interactions, instacing molstar#1570))
  • Add slice representation support for volumes (MVS: grid-slice volume representation, label improvements, state transitions via 3D interactions, instacing molstar#1570)
  • Control the camera spin and rock to start for a given snapshot
  • Animation node and builder support (Animation Support mol-view-spec#89)
  • Trajectory support (MVS: additional formats and trajectory support molstar#1613)
  • backbone and line representations (MVS: Add backbone and line representation types molstar#1617)
  • Consider supporting skydomes (supported via cavnas.custom.molstar_posprocessing.background)
• Mol* extensions (@dsehnal )
  • Support highlight-query=MolQL in markdown commands Markdown Commands and MVS improvements molstar#1597
  • Add createMVSX helper function MVS Stories and related updates molstar#1609
  • Support MVS-based animations (MVS: Animations molstar#1606)
  • Add "open in mol-view-stories" button to the mvs-stories app
  • Fix markdown commands for focusing on transformed structures (Fix Markdown Commands query focus molstar#1626)
• Add stories-viewer top level app (e.g., http://molstar.org/stories-viewer?params) (@dsehnal )
  • Use it as default to view the stories
  • Add "download MVS State" link/button to the app (MVS Stories: Add "Download MVS State" link molstar#1580)
• Experimental WebXR support (@arose) (WebXR molstar#1590)
• CLI support (@zachcp) (see Port Library and CLI Code to this Repo #53 for initial work and comments about how to implement)
  • Setup monorepo (@dsehnal @zachcp) (Setup monorepo #54)
• Documentation
  • Setup mkdocs repo (Setup Docs #43)
  • Initial content
  • Iterate and add more stuff
• Write a publication about the app (everyone)

Ideally, this should be available by Nov 15 2025, which is a deadline for Protein Science David Goodsell special issue. If we miss that, we could go for another journal (e.g., NAR Web Server) or ask for extension.

To enable the session saving and story sharing, we will have support from MUNI ICS and https://www.e-infra.cz (user will be able to login via their academic organization, google, etc., accounts)

[zachcp]

@dsehnal thanks for organizing; this is a great list. The next few weeks are a bit tight for me but I can contribute. Note: one major unlock for me in terms of dev speed will be the next Molstar Major release with TS/Deno compatibility. Basically I'd like to cleanup the MVS API and offer it as a TS-only library that mirrors the python app. Deno compatibility will (should!) also open up a few CLI options for building stories which can mirror the webapp work.