WyMOL

WyMOL is the ChemistryAtlas hybrid PyMOL workflow. It gives users an interactive browser preview for immediate inspection, then generates PyMOL scripts and optional backend-rendered publication-style figures when PyMOL is installed.

Best For

• Publication-quality molecular figures.
• PyMOL-style cartoon, surface, stick, sphere, and ray-traced rendering.
• Preparing reproducible PyMOL scripts from uploaded or pasted structures.
• Previewing structures in the browser before sending them to backend PyMOL.
• Creating high-resolution PNG figures for papers, talks, and reports.

Inputs

• Structure files: .pdb, .ent, .cif, .mcif, .mmcif, .mol, .sdf, and .xyz.
• PDB ID or pasted structure text.
• Style options such as cartoon, surface, sticks, spheres, or ligand-focused views.
• Resolution settings such as 1200x900, 1600x1200, or 2400x1800.
• Optional PyMOL command text for advanced users.

Multi-File Navigation

Upload several structures at once to review them before choosing which one to render. The toolbar above the preview window shows the current filename and supports navigation/search.

• Use arrows to move through uploaded files.
• Search filenames using fragments or wildcard-style filters.
• Render acts on the active preview file and current WyMOL settings.
• Reset restores the active preview orientation before backend figure generation.

Main Controls

• Preview/Render reloads the active structure in the browser preview.
• Reset returns the preview to the default camera.
• Backend render generates a PyMOL script and, when PyMOL is available, a high-resolution image.
• Export saves the generated script and manifest.

Backend Requirement

WyMOL can still generate scripts when PyMOL is not installed, but backend image rendering requires PyMOL or pymol-open-source. Configure one of:

CHEMISTRYATLAS_PYMOL_BIN=/path/to/pymol
PYMOL_BIN=/path/to/pymol

or make pymol available on PATH.

PyMOL Versus Browser Viewers

WyMOL is not meant to replace real-time browser rotation. Browser preview is handled by NGL. PyMOL is used for scripted, high-quality, reproducible figure generation. This hybrid design gives users responsive interaction first and publication rendering second.

Troubleshooting

• If Reset does not restore the view, click Render to reload the active preview and then Reset.
• If backend rendering fails, inspect the generated PyMOL script and confirm the PyMOL executable path.
• If a CIF does not preview, try WESTA for crystal-style CIF files or MacroVis for macromolecular mmCIF.
• If the output image is too small or pixelated, increase the resolution setting and enable ray tracing when available.

Acknowledgements And Validation

• WyMOL uses browser preview technology plus backend PyMOL-compatible scripting.
• ChemistryAtlas generates reproducible render manifests, scripts, and optional high-resolution figure outputs.
• Verify final figures against the source structure, intended biological assembly, representation choices, and publication standards.