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Frequently Asked Questions

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General

Clavis supports .gro, .pdb, .cif, and .mmcif text structures. It also opens native GROMACS binary trajectory sessions when users select a paired .gro + .xtc, .gro + .trr, .tpr + .xtc, or .tpr + .trr set together.
Current analysis and visualization workflows are designed around browser-side parsing, WebAssembly analysis, workers, and local rendering. Account, billing, and usage APIs still use hosted services, but structure analysis does not require a Python backend upload path.
Free users have a monthly frame quota. Pro subscribers have unlimited frame analysis and Pro export features.
TRACE focuses on cage detection and face signatures, HTR focuses on hydrogen-bond topology/ring analysis, and GRADE classifies hydrate structure type from cage populations.

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Analysis

The default 3.5 Å (0.35 nm) is a common starting point. Adjust it for pressure, force field, and trajectory-specific behavior.
Incomplete cages are partially formed or imperfect cage-like structures. They are common near interfaces, defects, or hydrate formation fronts.
Yes. After TRACE, GRADE, or complete-cage HTR analysis, Clavis reports θ_S, θ_L, Overall occupancy, filled/empty cage counts, and per-cage-type guest counts when guest residues are present.
Yes. The occupied guest highlight control is independent from cage wireframe visibility, while still using cage assignment data from analysis.

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Files and Sessions

Yes. Large .gro trajectories use a streaming worker so the browser can inspect frames without loading the entire trajectory into memory. Paired GROMACS .gro + .xtc/.trr and .tpr + .xtc/.trr trajectories decode locally in a dedicated browser worker and use selected-frame timeline controls for dense native sessions. Native frames render with the full instanced-sphere molecular style (matching a static .gro of the same system); frame jumps stay responsive because each frame streams its coordinates into the existing geometry, and the full selected frame is used when Clavis runs current-frame analysis. Use .gro + .xtc/.trr when you need exact residue labels from the text topology — it is also the reliable path when a .tpr binary is not supported by the browser decoder.
Normal-size scenes can recover from session-local browser storage, including layers, settings, analysis overlays, and camera view. Large streaming trajectories intentionally skip this recovery path.
Structure workflows are browser-local for analysis and visualization. Session recovery may store normal-size scene text in your own browser session storage; clearing browser storage removes it.

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Account & Billing

Click the account or upgrade entry point in the app. Checkout and subscription management are handled through Lemon Squeezy.
Yes. Use the account or billing portal. Access generally remains available until the end of the paid billing period.
No. Free usage quotas reset on the configured monthly cycle.

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Path Tracer and Export

Path-traced rendering is available to Pro subscribers in the RENDER tab.
Yes. The RENDER tab supports custom width/height, aspect presets, Preview Mode, and centered render-frame composition. Standard PNG export and path-traced still export both use the Preview Mode render frame when it is active. The default 16:9 output is 1280 × 720 for faster first path-traced previews; choose the 1080p preset or custom dimensions for larger exports.
Yes. Pro video export supports frame ranges, step size, FPS, quality, loop count, and standard or path-traced render modes.
Increase sample count or enable denoising. Use lower dimensions and samples for previews, then increase quality for final export.

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Contact

For support, use the channels provided in the Clavis application or documentation.