| name | molecular-orbital-visualization |
| description | Automatic molecular orbital visualization for computational chemistry. Use when the user includes --MO or asks for HOMO, LUMO, orbital number, molecular orbital, MO cube, frontier orbital, or publication-style front/side orbital views from local wavefunction files such as .fchk, .fch, .wfn, .wfx, .molden, .mwfn, .cube, .cub, .xyz, .mol, .sdf, .pdb, or .mol2. |
Molecular Orbital Visualization
Use this skill to discover local wavefunction/orbital cube files, run Multiwfn when needed, and render requested molecular orbitals as front and side views.
Quick Start
For a user request containing --MO, run:
python3 scripts/mo_pipeline.py --MO HOMO,LUMO --homo <HOMO-index> --workdir <user-project-dir> --execute
Use --input <file> when the user names a wavefunction file. Use --cube <label=path> or repeated --cube <path> when orbital cube files already exist. Use --search-root <dir> repeatedly when the user wants files found outside the current project.
Workflow
- Read
references/mo-workflow.md before running an analysis.
- Run
scripts/mo_pipeline.py --MO ... --workdir ... without --execute when you need to inspect selected files, orbital indices, and tools first.
- Run again with
--execute once the selected inputs and orbital mapping are plausible.
- If Multiwfn fails to generate cube files, read
references/multiwfn-orbital-recipes.md, inspect multiwfn_orbitals.inp and logs, then patch or rerun with --recipe <file>.
- If rendering fails, read
references/orbital-visualization.md, inspect the generated .tcl or .cxc scripts, and rerun with --renderer vmd or --renderer chimerax.
- Return the front/side image paths, manifest path, exact commands used, and caveats about orbital numbering or unvalidated recipes.
Required User Information
Users may provide absolute orbital numbers directly:
python3 scripts/mo_pipeline.py --MO 45,46 --input molecule.fchk --execute
Users may provide frontier labels only when --homo <N> is also known:
python3 scripts/mo_pipeline.py --MO HOMO,LUMO,HOMO-1 --homo 45 --input molecule.fchk --execute
Do not infer the HOMO index silently from filenames or logs in v1.
Output Contract
The pipeline writes an output folder containing:
manifest.json with selected files, discovered tools, orbital mappings, commands, warnings, and outputs.summary.md with the requested orbitals and generated image paths.multiwfn_orbitals.inp and multiwfn_orbitals.log when Multiwfn is used.render_<orbital>_front.tcl and render_<orbital>_side.tcl for VMD, or .cxc scripts for ChimeraX.<orbital>_front.png and <orbital>_side.png when rendering succeeds; VMD may also leave intermediate .tga files.
If a dependency or input is missing, report exactly what was discovered and which file, tool, or orbital index is needed next.
