Welcome to Clavis
Clavis is a browser-based workspace for analyzing and visualizing gas hydrate cage structures. It combines WebAssembly-powered analysis, interactive 3D rendering, trajectory tools, guest occupancy workflows, and publication-quality export in a single web app.What is Clavis?
Clavis (Latin for “key”) helps hydrate researchers inspect structure and occupancy without installing a desktop pipeline:- Detect cage structures with TRACE and HTR-derived topology workflows
- Classify hydrate structure with GRADE-style structure typing
- Calculate F3/F4 order parameters for crystallinity and hydrate ordering
- Analyze guest occupancy with θ_S, θ_L, overall occupancy, and per-cage-type summaries across TRACE, GRADE, and complete HTR cage results
- Visualize occupied guests with cage-type and structure-type filters, neon guest highlights, and atom-level multi-atom guest rendering
- Work with trajectories using frame navigation, large-file streaming, and batch frame analysis
- Create publication outputs with configurable render frames, PNG export, MP4 video export, Render Resource visibility, GPU path tracing, and a runtime-supported CPU still-image fallback PRO
Supported File Format
Clavis supports GROMACS.gro, PDB .pdb, and CIF/mmCIF .cif/.mmcif text structures, including water networks, guest-containing systems, and mixed material systems. Large .gro trajectories are streamed in the browser to avoid loading every frame into memory at once. Native GROMACS binary trajectory sessions are available when users upload a paired .gro + .xtc, .gro + .trr, .tpr + .xtc, or .tpr + .trr set; use a matching .gro topology when exact residue labels are more important than TPR-only metadata.
Browser-Local Workflow
Analysis and visualization are designed around browser-side interaction. Normal-size text-structure scenes can be recovered from session-local browser storage after an accidental refresh or quick Changelog visit. Large streaming trajectories intentionally skip scene recovery because browser storage is not appropriate for very large coordinate payloads. Clavis uses live progress overlays for long-running browser-local work, including parsing, frame streaming, analysis, and render preparation, so the scene reports what Clavis is doing instead of appearing frozen.Quick Start
- Upload a supported structure file
- Choose a workflow: visualize, run TRACE/HTR/GRADE, inspect F3/F4, or analyze guest occupancy
- Filter and style atoms, cages, rings, H-bonds, guests, and layers
- Export images, analysis tables, render frames, or trajectory videos
Upload Files
Prepare single-frame files, multi-frame trajectories, and guest-containing structures
Visualization
Learn camera, layer, cage, H-bond, guest, and mobile controls
Guest Occupancy
Calculate θ_S, θ_L, overall occupancy, and occupied guest highlights
Path Tracer
Create photorealistic GPU WebGL renders with Render Resource status and a runtime-supported CPU still-image fallback (PRO)
Pricing
| Plan | Price | Features |
|---|---|---|
| Free | $0/month | Monthly frame quota, standard visualization, core analysis workflows |
| Pro | $19/month | Unlimited frames, path-traced rendering, video export, and priority support |