User Guide

How to install Orbitron, load data, and operate the desktop viewer, automation CLI, terminal UI, and Python bindings. Each topic is its own page — use the sidebar, or start here:

• Install — prebuilt apps, Python wheels, web viewer
• Quick Start - open a file in the desktop viewer, CLI, TUI, or Python
• Data Support — every format Orbitron parses, and per-format charge coverage
• Several Files, One Calculation — a resubmitted HPC job, or unrelated runs read together, as one study
• GROMACS and MD Trajectories: GRO/XTC pairing, periodic views, analysis, and export provenance
• Analysis Results: dipoles, task provenance, SCF histories, bond orders, excited states, and periodic electronic structure across every frontend
• Graphical Viewer — launching, controls, analysis, and the molecular builder: SMILES, conformers, charge/multiplicity, metal complexes, and residue mutation
• Automation CLI — orbitron headless commands and the selection grammar
• Metal sites: oxidation states, electron counts, trust grades, non-innocent ligands, boron clusters and the ligand-field picture, and how to read a report
• Metal sites: accuracy and limits: how often the state is right, what each trust grade means, and where the tool declines
• Multi-panel Figures — orbitron plot panels drawn to line up in a paper figure
• Terminal UI — orbitron view --tui for ssh-into-HPC inspection
• Bundles (.orbpack) — exporting on an HPC system and opening locally
• Python Bridge — Jupyter, scripting, and headless rendering
• Web Viewer Embedding — HTML for slides, the <orbitron-viewer> web component
• Live Examples: interactive molecules, crystals, proteins, MD snapshots, and density maps
• Notebook Quick Start — the Python API as a runnable notebook
• Troubleshooting
• Quick Reference — one-line recipes
• Scope and known limits — what Orbitron is and isn’t for