MacroVis

MacroVis is the ChemistryAtlas Mol* viewer for macromolecular visualization. It is designed for proteins, nucleic acids, complexes, biological assemblies, PDB IDs, AlphaFold structures, and mmCIF-heavy workflows that benefit from Mol* sequence and hierarchy controls.

Best For

• Proteins, nucleic acids, complexes, and biomolecular assemblies.
• PDB IDs and AlphaFold/UniProt IDs.
• PDBx/mmCIF files from structural biology databases.
• Sequence-aware navigation, chain selection, hierarchy panels, and biological display presets.
• Comparing multiple uploaded structures with the ChemistryAtlas file navigator.

Inputs

• PDB ID, such as 1CRN.
• AlphaFold/UniProt ID, such as P69905.
• Uploaded files: .pdb, .ent, .cif, .mcif, and .mmcif.
• Pasted PDB, CIF, or mmCIF text.

Multi-File Navigation

Upload multiple structures to review them one by one in the same Mol* panel. The navigator/search toolbar sits directly above the viewer window.

• The title shows the current file index and filename.
• Arrow buttons move through the uploaded structures.
• The search box filters by filename and supports simple wildcard patterns such as *.cif, 1crn*, or *ligand*.
• The active file is reloaded into Mol* when the selection changes.

CIF And mmCIF Behavior

Mol* is strongest for macromolecular mmCIF/PDBx files. Ordinary crystallographic CIF files can be different from structural-biology mmCIF files. ChemistryAtlas now handles this in two steps:

1. MacroVis first tries Mol* native loading. 2. If native loading fails, ChemistryAtlas tries a coordinate fallback for common CIF _atom_site loops and renders the coordinates as a PDB-style scene.

This fallback is useful for many simple CIFs, but it is not a replacement for a full crystal viewer. Use WESTA for unit-cell, symmetry, supercell, polyhedra, and materials-style CIF inspection.

Main Controls

• Render reloads the active source into Mol*.
• Reset restores the default Mol* scene/camera for the active structure.
• Export saves the active source payload.
• Mol* built-in panels provide sequence, hierarchy, component, representation, and selection controls.

Choosing Another Viewer

• Use 3DXView for small molecules and quick PNG snapshots.
• Use WeNGL for high-performance NGL rendering and molecular-dynamics preview.
• Use WESTA for VESTA-style crystal and materials CIF visualization.
• Use ChimeraXWeb for backend ChimeraX analysis, contacts, clashes, surfaces, density fitting, and publication rendering.

Troubleshooting

• If a remote PDB or AlphaFold ID fails, try a known PDB ID such as 1CRN or upload a local file.
• If an ordinary CIF still fails, it may lack explicit _atom_site coordinates or use nonstandard labels.
• If the Mol* UI appears too large or overlaps the toolbar, reload the page after the current frontend bundle is deployed.
• For very large assemblies, allow the viewer several seconds before changing style or resetting.

Acknowledgements And Validation

• MacroVis uses Mol* for browser macromolecular visualization.
• ChemistryAtlas adds PDB/AlphaFold entry points, multi-file navigation, search, export, and CIF fallback handling.
• Validate biological interpretation against the original PDB/mmCIF record, structure factors or validation reports when available, and the primary structure publication.