Mol* and files in the molecule's own frame

/molviewer draws the same molecule and the same surfaces with two engines: 3Dmol.js and Mol*. The same surfaces can also be downloaded as standard files. Either way they stay on the atoms, because there is only one coordinate frame.

#One frame

/api/model returns one RDKit conformer twice: as atoms[].position and as a MolBlock with exactly the same coordinates (16.1). Every field the browser computes is evaluated in that frame:

• the π layer (pi_field), on a grid in Å;
• the hybrid and lone-pair orbitals, centred on atoms[].position.

A viewer that keeps the MolBlock's coordinates therefore needs nothing else: the files below land on the atoms. Both engines are checked rather than trusted:

• After loading, the viewer reads the atoms back out of its own scene and compares them with /api/model. The R pill shows the largest deviation; 4·10⁻⁵ Å is the MolBlock's 4-decimal rounding.
• If an engine had moved the molecule (some re-centre their scene), the measured offset would be added to every surface. The pill then says how far the surfaces were moved.

#Mol*

The Mol* tab is the Mol* viewer by Sehnal and colleagues (Nucleic Acids Research 49, W431, 2021; MIT licence). It is built for large biomolecules: sequence view, selections, measurements, assemblies, and any PDB entry ("Load PDB" or Mol*'s own panels). This molecule arrives in it as:

Changes in the side panel are sent again automatically while the tab is open.

PDB entries keep their deposited coordinates, so a protein and this molecule do not overlap. For orbitals on a protein, use /sites (16.4). It cuts a motif or metal site out of the structure, computes that fragment, and draws its surfaces on the whole protein in Mol*, in the protein's own frame.

The Mol* bundle (about 5 MB, 1.3 MB gzipped) loads only when a visitor opens the tab. Install it on the server with ./install_molstar.sh; until then the tab loads the same pinned build (4.5.0) from cdn.jsdelivr.net. Loading a PDB entry fetches it from the RCSB PDB in the visitor's browser.

#Files

The three buttons under "Files" write what the page shows, in the MolBlock's frame. Opened together, they line up in any viewer.

• π field .cube: the selected π field (π density when none is selected). Gaussian cube format, read by Mol*, VMD, PyMOL, Jmol and Avogadro.
  • Lengths in bohr.
  • Values in atomic units: ψ in bohr^−3/2, densities in e/bohr³, the potential in hartree/e (1 hartree/e = 27.211 V).
  • The atoms are written into the file as well.
• surfaces .ply: every surface drawn in the 3Dmol tab, as an ASCII PLY mesh (Turk, 1994) with RGBA per vertex, in Å to 1 mÅ. Read by Mol*, MeshLab, Blender and ParaView. The surfaces are closed, every triangle faces out of its lobe and the vertices carry smooth normals (qo-mesh.js), so viewers that do not draw back faces show them whole.
• molecule .mol: the conformer.

#Tested, and not yet

• tests/test_export.js writes cube files of real π fields and reads them back:
  • every value lands in the right place (the format runs x outer, z inner; the engine x fastest);
  • grid, origin and atoms survive the bohr conversion to 10⁻⁵ Å;
  • a shifted frame moves the field and the atoms together.
• tests/test_molstar_bridge.js checks against a recording Mol* stand-in what the tab sends:
  • the MolBlock as mol, the cube with ± isovalues and colours, the PLY;
  • the R check, and a Mol* that moves the molecule by (3, −1, 2) Å, with every surface following;
  • only the tab's own nodes are replaced (nothing else the visitor loaded is cleared);
  • malformed PDB IDs are refused.
• A headless-browser run of the page with the same stand-in: tabs, keyboard, downloads, no horizontal scroll at 390 px.
• Not yet tested against the real Mol* bundle: the sandbox this was built in could not download it. The tab uses Mol*'s public Viewer API (Viewer.create, loadStructureFromData, loadVolumeFromUrl, loadPdb). For the PLY mesh it uses the plugin's data-format registry, as Mol*'s "Open Files" does. Every call is guarded: if a Mol* version differs, the tab says which part it could not show.