WeNGL

WeNGL is the ChemistryAtlas NGL Viewer app for high-performance browser visualization of proteins, nucleic acids, complexes, molecular structures, and molecular-dynamics preview files. It is the general-purpose web viewer for users who want fast loading and broad file-format support without starting a backend job.

Best For

• PDB, mmCIF, CIF, MOL, SDF, XYZ, and common structural biology files.
• Proteins, nucleic acids, complexes, ligands, and mixed biomolecular systems.
• Fast browser preview before running VMDWeb, ChimeraXWeb, or WyMOL.
• Multi-file review with navigation and filename search.
• Switching between cartoon, ball-and-stick, spacefill, stick, wire, surface, and line styles.

Inputs

• Built-in sample structures.
• PDB ID input such as 1CRN.
• Uploaded files: .xyz, .mol, .sdf, .pdb, .ent, .cif, .mcif, .mmcif, and other NGL-readable structures.
• Pasted structure text.

Multi-File Navigation

Select several files at once in the upload control. The toolbar above the viewer lets you move through them without reopening the upload dialog.

• The title shows the active file number and filename.
• The left and right arrows move through uploaded structures.
• The search box filters by filename and supports simple wildcard patterns such as *.cif, ligand, or *protein*.
• The active file is rendered with the selected style.

Main Controls

• Render reloads the active file or pasted text into NGL.
• Reset restores the default camera, zoom, and orientation.
• Export saves the active source payload.
• Style controls change the active representation.

CIF And mmCIF Notes

NGL can load many CIF/mmCIF files, but the format is broad. Macromolecular mmCIF is usually the safest path. Ordinary crystallographic CIF files with unusual atom loops can still fail in a molecular viewer. If a CIF does not render in WeNGL:

• Try WESTA for crystal/unit-cell/polyhedra inspection.
• Try MacroVis when the file is really a PDBx/mmCIF biological structure.
• Confirm the file includes parseable atom-site coordinates.

Choosing Another Viewer

• Use WESTA for crystal structures and VESTA-style materials visualization.
• Use MacroVis for Mol* sequence and biological hierarchy controls.
• Use VMDWeb for trajectory analysis and VMD atom selections.
• Use ChimeraXWeb for structural biology analysis and publication rendering.

Troubleshooting

• If Reset does not restore the expected view, click Render to reload the active file, then Reset again.
• If a PDB ID does not load, upload a local PDB file to rule out network restrictions.
• If a CIF file fails, test whether it opens in WESTA; the issue may be CIF dialect rather than a blank viewer.
• Very large biological assemblies can take time; wait for loading to finish before changing style.

Acknowledgements And Validation

• WeNGL uses NGL Viewer for browser structure rendering.
• ChemistryAtlas adds multi-file upload, navigation, search, style controls, export, and integration with downstream visualization tools.
• Verify structural conclusions against the original PDB/mmCIF/CIF source and any experimental validation reports.