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Supported File Formats (Nanome v2)
This page lists the file formats supported in Nanome v2, current through 2.6.0. Per-release changes are in the version history below.
All parsing is server-side, and the format is detected by file extension.
Capability key: 👁 view static · ▶️ animates (substrate noted) · ✏️ editable · 💾 exportable · 🆕 new or changed in 2.6.0.
Structures
Small molecule and macromolecule formats.
| Format | Extensions | Import | Animates? | Export |
|---|---|---|---|---|
| PDB | .pdb .ent | 👁 ✏️ | ▶️ model-index (multi-MODEL) | 💾 PDB |
| mmCIF / PDBx | .cif .mmcif .mcif .bcif | 👁 ✏️ | ▶️ model-index | — |
| SDF | .sdf .sd .mol | 👁 ✏️ | ▶️ model-index (multi-record) | 💾 SDF |
| MOL / MOL2 | .mol .mol2 | 👁 ✏️ | — | — |
| SMILES | .smi .smiles / typed | 👁 ✏️ | — | 🆕 💾 SMILES |
| XYZ | .xyz | 👁 ✏️ | 🆕 ▶️ model-index (playback fixed in 2.6.0) | — |
| PQR | .pqr | 👁 ✏️ | — | — |
| PDBQT | .pdbqt | 🆕 👁 (imported as PDB; charges dropped) | — | — |
Session and proprietary
| Format | Extensions | Import | Notes |
|---|---|---|---|
| MAE (Maestro) | .mae | 👁 | Schrödinger. Also the LiveDesign ingestion format. |
| MAEGZ | .mae.gz .maegz | 👁 | Via the LiveDesign gadget. |
| MOE | .moe | 👁 | CCG's Molecular Operating Environment. |
| PSE (PyMOL session) | .pse | 👁 | QM/MM link atoms can break loading. |
Trajectory / Molecular Dynamics
Frame-trajectory formats. See How animation works for the difference between a frame trajectory and a multi-model file.
| Format | Extensions | Import | Animates? | Limits |
|---|---|---|---|---|
| GRO | .gro | standalone | ▶️ frame-trajectory | ≤ 2000 frames |
| XTC | .xtc | attach to a loaded model | ▶️ frame-trajectory | atom count must match the host |
| TRR | .trr | attach to a loaded model | ▶️ frame-trajectory | atom count must match the host |
| DCD | .dcd | attach to a loaded model | ▶️ frame-trajectory | 64-bit CHARMM DCD and fixed-atom DCD are not supported |
Maps / volumetric
| Format | Extensions | Import | Notes |
|---|---|---|---|
| DX (electrostatic map) | .dx | overlay | Attaches to a loaded model; not standalone. |
Export
Molecule export is single-frame, to PDB, SDF, or SMILES. PDB and SDF are offered on every export surface. SMILES (new in 2.6.0) is produced through the WorkspaceAPI/MCP export_entry route, and is not yet a download option in the client or MARA.
Import and export surfaces
Every surface funnels into the same server-side parser.
| Surface | Imports | Exports |
|---|---|---|
| XR / WebGL client | RCSB fetch (PDB/CIF by code); local entry files (SDF/SMILES/XYZ); session files (MAE/MOE/PSE) | view-only |
| MARA (web app) | all structures, trajectory attach (GRO/XTC/TRR/DCD), and DX | PDB, SDF (molecules); CSV (data tables); FASTA/GenBank (tools) |
| WorkspaceAPI (GraphQL / REST / MCP) | every format above | PDB, SDF, SMILES |
| LiveDesign gadget | MAE / MAEGZ (one-way: LiveReport → Nanome) | — |
Not supported
- Electron density maps — CCP4, MRC, and DSN6 are not supported.
- LAMMPS native trajectories (
.lammpstrj/ dump) — not supported; XYZ is the only bridge. - No workspace-file export — workspaces live in the database; there is no portable workspace file.
- No trajectory export — export is single-frame only.
- No export for mmCIF, MAE, MOE, or PSE (import-only).
- Surfaces are disabled during trajectory playback — recompute-per-frame is too slow today.
How animation works
Both animation types are driven by the same play, pause, and scrub controls, but they step over different things.
| Substrate | A "step" is… | Source formats |
|---|---|---|
| Model-indexing | a whole model (full topology) | multi-MODEL PDB / mmCIF, multi-record SDF, multi-block XYZ |
| Frame-trajectory | a coordinate set on one shared model | GRO (standalone), XTC / TRR / DCD (attached to a loaded model) |
Frame trajectories are limited to 2000 frames, and an attached frame's atom count must equal the host model's.
A helpful way to keep the terms straight:
- Multi-entry — several separate structures in the workspace (they don't animate together).
- Multi-model — one entry holding many models, each a full topology; animates by stepping through models.
- Multi-frame — one model with many coordinate frames; animates by stepping through frames.
Version history
Each row names the format or IO capability that changed in that release.
| Version | Format / IO change |
|---|---|
| 2.0.x | SDF (charges, aromatic, multi-model) and SDF export; MAE parser; PDB / mmCIF parsing; PSE loading |
| 2.1.x | SDF metadata; SMILES load; PSE multi-state |
| 2.2.0 | PSE metadata parsing |
| 2.3.0 | PDB export (.pdb); mmCIF parser refactor; multi-model annotations |
| 2.4.x | XYZ import (.xyz); component export as PDB / SDF; model-index playback for multi-model files |
| 2.5.0 | MAE / PSE / MOE as entries; PQR import (.pqr); frame-trajectory playback (GRO / XTC / TRR / DCD); DX map overlay |
| 2.5.1 | WebGL instanced rendering — real-time playback of 20k+ atom MD trajectories |
| 2.6.0 | PDBQT import (.pdbqt → PDB, charges dropped); SMILES export (.smi, via MCP export_entry); multi-block XYZ playback fixed |