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Frequently Asked Questions

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General

Clavis supports .gro, .pdb, .cif, and .mmcif text structures. UPLOAD STRUCTURE opens an import guide so you can choose GROMACS, LAMMPS, or Static Structure before the system file picker appears. The GROMACS path covers .gro plus paired .gro + .xtc, .gro + .trr, .tpr + .xtc, or .tpr + .trr sets. The LAMMPS path covers paired .data + .lammpstrj/.dump/.lammpsdump inputs and standalone dumps with ITEM: ATOMS type rows for mapped dump-frame playback, selected-frame WASM analysis, and sampled TRACE/HTR/GRADE/F3F4 ranges.
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 finds general face-signature cages with SEC/nSEC/IC quality. HTR uses a fixed 0.35 nm oxygen-only graph for primitive rings and generalized n4-n5-n6 cages. Native GRADE finds only 5^12, 5^12·6^2, and 5^12·6^4 cages and their filled counts; it does not produce a crystal-structure verdict or confidence score.
CHILL+ classifies each cage-forming water into liquid/other, hexagonal ice, cubic ice, interfacial ice, gas hydrate, or interfacial hydrate environments. It is useful for spatial maps and time-series fractions. Use TRACE when you need explicit closed-cage topology and cage types. See CHILL+ Classification.

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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.
In current versions, it should not. CHILL+ class visibility applies only to classified cage-forming waters. Non-water residue channels such as SDS and NA keep independent visibility and atom/bond styling, and toggling them does not clear CHILL+. Changing the water channel can require a classification refresh because it changes the analyzed water set.
Yes. CHILL+ class colors, its O–O network, and the H-bond overlay are independent and can be shown together. The H-bond network refreshes when its cutoff or supported trajectory frame changes.

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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. Choose the GROMACS card in the upload guide for paired .gro + .xtc/.trr and .tpr + .xtc/.trr trajectories; they index frame byte ranges locally in a dedicated browser worker and decode selected XTC/TRR frame slices for dense native sessions. Large scenes temporarily use a capped instanced-sphere preview without bonds during loading, playback, or dense visualization commits, then return to full atoms and bonds when settled. Current-frame analysis can request the full selected frame independently. 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/large GRO, mapped LAMMPS, and native XTC/TRR sessions support selected TRACE/HTR/GRADE/F3F4 ranges.
Partially. Choose the LAMMPS card in the upload guide, then select either a paired .data + .lammpstrj/.dump/.lammpsdump upload or a standalone dump with atom type rows. Clavis asks for unit style and atom-type roles, then can play or jump between mapped dump frames and run current-frame or sampled TRACE/HTR/GRADE/F3F4 analysis when the mapping yields water molecules. Dump-only water analysis fails closed unless mapped water atoms include mol grouping and form exactly 1 O + 2 H per molecule. Restricted triclinic dump cells use cell-aware WASM paths when the frame carries that metadata.
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.
They are omitted for a single-frame scene because there is no frame range to export. On a multi-frame scene, open the RENDER tab and check the Export Center; an unavailable action displays the trajectory, account, or render requirement that applies.
The Pro Export Center can download the current displayed scene as a schema-v2 .claviscage.zip. The ClavisCage Blender extension imports its structure, available current-frame CHILL+/H-bond data, selected TRACE/HTR/GRADE cage analysis with provenance, and supported editable styles. This is an offline, single-frame handoff—not direct .blend generation, a trajectory container, or live synchronization.
Keep the downloaded .claviscage.zip intact and import the archive itself through ClavisCage → Input → ClavisCage Bundle → Import Web Bundle. manifest.json describes the bundle format, schema, originating app version, and warnings. scene.json carries the current structure, matching analysis, algorithm/frame/parameter cage provenance, and supported styles. They are extension payloads rather than separate Blender inputs; direct JSON editing is not a supported workflow because the extension validates the complete archive strictly. The extension accepts legacy v1 HTR bundles and current v2 algorithm-owned bundles. If the Input panel shows only Topology, Trajectory, and Guests, that installed extension does not yet include web-bundle import and must be updated first.
Clavis stops the export rather than silently producing incomplete output or reusing stale TRACE/H-bond geometry. It reports the failed frame or stage, then restores the original frame and the overlay visibility state from before export. Hide HTR ring or occupied-guest overlays if the app reports that they cannot be refreshed safely for a multi-frame capture.
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.