| Launch GUI viewer |
orbitron-viewer file.xyz |
See §3.1 for extra flags. orbitron view file.xyz (no --tui) only prints a text summary. |
| Launch TUI |
orbitron view fixtures/benzene.xyz --tui |
Keyboard shortcuts listed in §5. |
| Headless render |
orbitron render input.xyz -o output.png --camera cameras/front.json |
Camera presets documented in §3.10 and §4.3. |
| Publication figure |
orbitron plot spectrum freq.log -o ir.svg |
Also excited, levels, ligand-field, bands, dos, pdos, opt, scf, md and more; SVG or PNG by extension. orbitron plot list <file> says which figures a file supports. See CLI §4.3.4. |
| Write an orbital as a cube |
orbitron cube run.fchk -o homo.cube --mo homo |
Needs a basis set and MO coefficients; --density writes the total density instead, --spin-density the alpha minus beta density of an open-shell run, and --degenerate sums the orbital’s whole degenerate set. See CLI §4.3.5. |
| Self-contained web page |
orbitron web run.orbpack -o run.html |
The viewer and the bundle in one HTML file, like File → Export → Web View; any readable file is exported to a bundle first. See CLI §4.3.5. |
| Animate a mode or trajectory |
orbitron animate freq.log -o mode7.gif --mode 7 |
--trajectory plays a trajectory, --orbit vertical turns the camera; an output path without an extension gets PNG frames. See CLI §4.3.5. |
| Python quickstart |
extensions/python-bridge/examples/api_quickstart.ipynb |
Build instructions in §7. |
| Python wheel install |
pip install orbitron-*.whl |
Platform-specific wheels available from releases. See §1.3. |
| Web viewer embedding |
Download orbitron-viewer-web-v*.zip or standalone HTML |
Full integration guide in §10. |
| Reset viewer to defaults |
Delete ~/Library/Application Support/dev.Orbitron.Orbitron/config.toml on macOS, ~/.config/orbitron/config.toml on Linux, %APPDATA%\Orbitron\Orbitron\config\config.toml on Windows |
orbitron config show prints the resolved path. If ORBITRON_CONFIG is set to a non-empty path, that file is the configuration instead. Configuration schema covered in the Developer Guide, §8.2 UI State & Panels. |
| Keyboard cheat sheet |
Press H in the viewer or use Help → Keyboard Controls |
Full table in §3.3. |
| Turn off the idle cats |
Uncheck View → Idle Companions → Show cats when idle |
The same submenu sets the delay (1–60 min, default 5) and how many cats come. See Idle companions. |
| Inspect run summary |
orbitron inspect io/pipelines/tests/fixtures/gaussian/water_two_stage.log |
Lists the stages or tasks with their kind, method, basis, energy, and SCF cycles. |
| Open several files as one calculation |
orbitron inspect part_1.out part_2.out part_3.out |
Name them in the order they ran. The task list spans all of them; nothing merges the structures. See Studies. |
| Identify a structure |
orbitron identify fixtures/benzene.xyz |
InChI, InChIKey, SMILES, and molecular formula from the loaded scene. For a metal complex, --json adds metal_states and an identifier_state_differs warning where the identifier’s state and the reported one disagree. |
| Preflight a large source |
orbitron resources run.out --mode scene --json |
Reads metadata and at most 64 KiB, without parsing the source. Use trajectory only when the operation retains every frame. |
| Prepare a portable bundle |
orbitron canonical export run.out -o run.orbpack --skip-cache --json |
Run beside the source on an HPC system, then transfer the bundle. Add --mo N to keep one volumetric dataset. |
| Open a portable bundle |
orbitron view run.orbpack --tui |
Replays retained grids, trajectories, modes, and presentation state without the original source file. Drop --tui for a text summary instead. |
| Inspect a GROMACS trajectory |
orbitron view production.xtc --topology system.gro --tui |
XTC is read-only and requires a topology-bearing structure with matching atom order. Drop --tui for a text summary instead. See GROMACS and MD. |
| Superpose two structures |
orbitron align mutant.pdb wild_type.pdb --pairing sequence --output fitted.pdb |
--pairing site (the default) needs matching residue numbers and atom names; sequence aligns globally first, sequence-local only the shared region. |
| Triage metal coordination spheres |
orbitron analyze metal-sites complex.xyz |
Coordination number, geometry, donor distances, oxidation state, d-electron and electron count, a trust grade, and a sigma-only ligand-field picture. --oxidation-state N overrides the inferred state. See CLI §4.9 and Metal sites: accuracy and limits. |
| Draw a ligand-field diagram |
orbitron plot ligand-field complex.xyz -o lf.svg |
The d-orbital levels a sigma-only model gives a metal’s four to seven donors, with high-spin and low-spin fillings. Needs an oxidation state, given or resolved as analyze metal-sites does. |
| Read a QMC run |
orbitron analyze qmc run.xml --figure blocking.png |
Point it at the input deck, not the stat.h5. Every scalar comes back with its blocked error; --trace picks which one the figure draws. |
| Analyze an MD trajectory |
orbitron --topology system.gro analyze md production.xtc --rmsd --rmsf residue --output analysis.csv |
One bounded-memory pass; frame indices are zero-based. |
| Open an experimental density map |
orbitron-viewer density.map |
orbitron view density.map (CLI, no --tui) only summarizes the file; the volume overlay is desktop-only. For a fitted model, open PDB/mmCIF first and choose Analysis → Surfaces → Add volume…. |
| Clip density around atoms |
Select atoms, expand the volume row, then choose Clip to selection |
Starts with 4 Å padding. Clipping reduces meshing work, not map parsing or retained-grid memory. |
| Build from SMILES |
orbitron from-smiles 'CCO' -o ethanol.sdf |
Deterministic 3D by default; see Viewer §3.7.12 for the accepted subset. |
| Search conformers |
Edit → Generate Conformers… |
Bounded UFF-ranked search with single and combined torsion starts for one connected, non-periodic, non-metal molecule. |
| Set charge and multiplicity |
Edit rail → Molecular state |
Separate from atomic formal charges and parsed calculation evidence. |
| Mutate a residue |
Select one annotated residue, then Edit → Mutate Residue… |
Top8000-derived backbone-dependent rotamers with probability, clash-ranked detached previews, and explicit HID/HIE/HIP histidine states. |
| Repair a missing side chain |
Find and select one incomplete residue, then Edit → Repair Missing Side Chain… |
Replaces the complete side chain with a clash-checked CCD/Top8000 candidate and reports missing atoms, retained-atom displacement, and formal charge before Apply. |
| Retain or delete an alternate location |
Select one residue with named conformers, then Edit → Edit Alternate Locations… |
Residue-local detached preview. Shared blank-location atoms stay; keep-only clears the retained label but preserves source occupancy. |
| Select or remove water and ions |
Enter edit mode, optionally select anchor atoms, then Edit → Clean Up Water/Ions… |
Whole-residue All/Within/Beyond matching with periodic minimum-image distance. Water is the default; ion removal is explicit and warns about structural or catalytic metals. |
| Add a protein terminal cap |
Select one observed fragment end, then Edit → Add Terminal Cap… |
Detached heavy-atom ACE/NME preview with assigned residue identity, removed atoms, formal-charge change, Apply, and Undo. |
| Set a side-chain protonation state |
Select one ASP/ASH, GLU/GLH, CYS/CYM, or LYS/LYN residue, then Edit → Set Protonation State… |
Explicit state and acidic-oxygen tautomer choice with charge and hydrogen preview. Orbitron does not infer pH. |
| Create or break a disulfide |
Select atoms spanning two CYS/CYX residues, then Edit → Edit Disulfide… |
Detached SG-SG, hydrogen, SSBOND, distance, and formal-charge preview. Creation accepts CYS pairs 1.7–2.5 Å apart; cleavage also accepts CYX. |
| Inspect steric clashes |
Scene → Sequence / Residues → Steric clashes |
Worst-first per-pair distance, limit, and overlap; heavy atoms by default, with exact pair selection. |
| Inspect protein backbone |
Scene → Sequence / Residues → Backbone validation |
Top8000 favored/allowed/outlier evaluation with phi, psi, residue type, and whole-residue selection. |
| Find missing heavy atoms |
Scene → Sequence / Residues → Missing heavy atoms |
Lists absent side-chain and backbone heavy atoms for supported coordinate-bearing amino acids and selects each incomplete conformer. |
| Inspect protein side chains |
Scene → Sequence / Residues → Side-chain validation |
Top8000 favored/allowed/outlier evaluation with chi angles, score, and visible-conformer selection. |
| Inspect metal sites |
Scene → Sequence / Residues → Metal sites |
Bonded metal sites with a sphere of their own, with distances and geometry under the active alternate-location view. |
| Find uncapped protein ends |
Scene → Sequence / Residues → Protein termini |
Observed peptide-fragment ends and whether each carries an ACE/NME cap. |
| Export structural validation |
Any validation panel → Export → CSV… or JSON… |
Exports all findings with scene digest, version, model/frame, assembly, alternate-location view, selection, and analysis parameters. |
| Draw a molecular surface |
orbitron render 1ubq.pdb -o s.png --show surface --hide atoms --surface-for 'not resname HOH' |
Solvent-excluded by default; --surface-kind accessible or vdw for the other two. The render prints the grid it used and whether the result is one closed shell. See §4.3.2. |
| Measure solvent-accessible area |
orbitron sasa 1ubq.pdb --by residue --select 'not resname HOH' |
Shrake-Rupley point sampling, not the rendered mesh. The radius table is reported with the result because every number scales with it. See §4.3.3. |
| Run compact surface examples |
examples/molecular-surfaces/run.sh all |
Four cases against a committed ubiquitin fixture: the published picture, all three surfaces, a pale surface over sticks, and the area table. |
| Run compact biology/MD examples |
examples/biology-and-md/run.sh all |
Produces inspectable JSON/CSV, PNG, GRO, and .orbpack outputs from committed fixtures. |
| Browse interactive examples |
Open the Live Examples page |
WASM examples cover molecules, crystals, normal modes, proteins, MD snapshots, and density. |