JSMolView

JSMolView is the ChemistryAtlas JSmol/Jmol-compatible viewer for molecules, crystals, teaching examples, and command-driven visualization. It exists for users who already know Jmol habits or need a reproducible command-script style view in the browser.

Best For

• Jmol/JSmol-style scripting and teaching workflows.
• Quick CPK, wireframe, ball-and-stick, and spacefill rendering.
• Molecule and crystal files that users historically inspected with Jmol.
• Reproducible command snippets that can be shared with a class, notebook, or collaborator.
• Offline production use when the vendored JSmol assets are present.

Inputs

• Built-in samples: caffeine XYZ, aspirin MOL, and a mini peptide PDB.
• Uploaded files: .xyz, .mol, .sdf, .pdb, .ent, .cif, .mcif, and .mmcif.
• Pasted structure text.
• Jmol-style command text, such as:

load $caffeine; wireframe 0.15; spacefill 23%; color cpk;

Multi-File Navigation

Select multiple files in the upload control to build a temporary review set. The navigation/search toolbar sits directly above the JSmol view area.

• The title shows the current file index and filename.
• The arrow buttons move through the uploaded files.
• The search box supports filename fragments and wildcard-style searches such as *.cif or ligand*.
• Changing files reloads the active structure into the JSmol applet.

Main Controls

• Render loads the active file or pasted text into JSmol.
• Reset returns to the default script, white background, CPK colors, and standard camera.
• Export saves the active structure/script payload so the view can be reproduced.
• JSmol commands can be used to refine style after loading.

Local Runtime Requirement

ChemistryAtlas expects the JSmol runtime at:

frontend_v2/public/vendor/jsmol/

The important files are JSmol.min.js and the j2s/ runtime directory. If this folder is missing in production, the app reports the missing asset path rather than silently failing.

Choosing Another Viewer

• Use 3DXView for faster small-molecule snapshots and PNG export.
• Use WESTA for crystal structures, unit cells, polyhedra, and materials-style CIF inspection.
• Use MacroVis for proteins, complexes, AlphaFold models, and Mol* sequence-aware controls.
• Use WeNGL for large structures or NGL-based preview of molecular-dynamics inputs.

Troubleshooting

• If the applet flashes and disappears, hard-refresh the browser and confirm the local JSmol assets are being served.
• If a CIF does not load, try WESTA for crystal-oriented CIF files or MacroVis for mmCIF/PDBx files.
• If commands do not appear to run, click Render first so JSmol has an active model.
• If the canvas is blank after file switching, confirm the active file has parseable atom coordinates.

Acknowledgements And Validation

• JSMolView uses the open JSmol/Jmol viewer runtime.
• ChemistryAtlas adds multi-file upload, search, local asset management, and export wiring.
• Verify any structural conclusion against the original file, database record, or crystallographic source.