3DXView

3DXView is the ChemistryAtlas 3Dmol.js viewer for fast small-molecule and lightweight structure inspection. It is the best first viewer when a chemist wants to upload a MOL, SDF, XYZ, PDB, or simple CIF file, rotate it immediately, change style, and export a PNG without launching a backend job.

Best For

• Small molecules, ligands, conformers, salts, and simple molecular structures.
• Quick PDB inspection when a full macromolecular Mol* interface is not needed.
• Fast style switching between stick, ball-and-stick, sphere, cartoon, and surface views.
• PNG snapshots for notebooks, reports, teaching material, or quick discussion.
• Multi-file review with the ChemistryAtlas structure navigator.

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 in the same formats.
• PDB ID input for quick remote PDB loading when the browser can reach the PDB service.

Multi-File Navigation

Use the upload control to select several structure files at once. The navigation/search toolbar above the viewer shows the active file number and filename.

• Use the left and right arrows to move through uploaded structures.
• Use the search box to filter by filename, for example aspirin, *.sdf, O4, or *MoS*.cif.
• When the filter changes, the first matching structure becomes active.
• Render and Reset act on the active structure only.

Main Controls

• Render reloads the active structure with the current format and style.
• Reset restores the default camera orientation and zoom for the active structure.
• PNG exports the current canvas image after the scene has rendered.
• Export downloads or copies the active source payload for reproducibility.
• Style controls switch the representation without changing the source file.

CIF Notes

3Dmol.js handles many molecular and crystallographic files, but ordinary crystallographic CIF files can vary widely. ChemistryAtlas includes a coordinate fallback for common _atom_site CIF loops. If a CIF lacks explicit atom coordinates or uses unusual loop labels, use WESTA for crystal inspection or MacroVis/WeNGL for macromolecular mmCIF files.

Choosing Another Viewer

• Use WESTA for VESTA-style crystal/polyhedra/unit-cell inspection.
• Use WeNGL for high-performance protein, nucleic-acid, complex, PDB, mmCIF, and trajectory preview.
• Use MacroVis when you want Mol* sequence, hierarchy, and biological assembly controls.
• Use JSMolView when you need Jmol-style commands or teaching scripts.
• Use WyMOL when you need PyMOL-quality publication figure generation.

Troubleshooting

• If the view is blank, confirm that the selected format matches the file contents.
• For SDF files with multiple records, start with a single-molecule file when debugging.
• If PNG export produces an empty image, click Render first and wait for the scene to finish.
• If Reset seems to clear the view, reload the active file with Render; this usually means the source file could not be parsed after a format change.

Acknowledgements And Validation

• 3DXView uses 3Dmol.js for browser molecular visualization.
• ChemistryAtlas adds multi-file upload, navigation, search, snapshots, and CIF fallback behavior around the viewer.
• Verify structural interpretation against the original file, crystallographic metadata, or experimental structure source before publication.