Spin 3D

Spin 3D

This page explains how to rotate a generated conformer into a two-dimensional perspective drawing, choose refinement settings, and understand the separate interactive 3D sidecar.

Rotate a drawing into perspective

A conformer is a three-dimensional arrangement of a molecule with the same connectivity. Spin 3D uses a conformer to help draw perspective views of rings, bulky groups, and crowded structures. Its output remains an editable two-dimensional molecule, not proof of a unique experimental conformation.

1. Select an editable molecule and choose Spin 3D from the toolbar.
2. Wait for its conformer. An embedded geometry can appear before force-field cleanup finishes.
3. Drag the molecule to rotate the live overlay.
4. Click outside to flatten the chosen view into the document.
5. Use Undo to restore the previous drawing, or press Esc before committing to cancel.

Releasing a rotation drag lets you inspect the current angle; the current app's status message directs you to click outside to flatten. Do not assume that every mouse release commits the drawing.

The command is structure.spin3d. The same drawing workflow is implemented for macOS and Windows. Use Cmd+Z for Undo on macOS and Ctrl+Z on Windows. See Keyboard Shortcuts for the full shortcut reference.

Flattening must preserve chemistry

Flattening projects three-dimensional coordinates into the page and re-encodes supported stereochemistry in the two-dimensional depiction. It must preserve atom and bond identity, charge, isotopes, radicals, and encoded configuration. Wedges and hashes are chemical annotations; over/under gaps at line crossings are display information.

The live overlay, flattening, reopening, and rotation use a shared placement contract. That keeps the committed result aligned with the view you selected. Depth can author front/back crossing overrides for the final drawing rather than relying on arbitrary line order.

An edge-on view can make a specified stereocentre impossible to encode clearly. If the safety checks refuse a flatten, the overlay can remain open while the status bar explains why. Rotate to a clearer view and try again, or cancel. Do not remove stereo to force a perspective through.

The conformer and committed orientation are stored separately from ordinary two-dimensional atom coordinates, allowing Spin 3D to reopen a valid stored model at its committed orientation. Flattening is one undoable document action. Later chemistry edits can invalidate a stored model; the saved perspective is not an independent authority on molecular identity.

Choose an engine and refinement

Open View → Preferences…. These are implemented controls, shared across macOS and Windows; on Windows use the document window's menu.

Setting	Choices and effect
3D refinement	Fast uses the embedded conformer without refinement; Balanced requests shorter cleanup; Quality requests longer cleanup and is the default
Embedding engine	Automatic, RDKit ETKDG, or OpenChemLib (legacy)
Force field	MMFF94s, MMFF94, or UFF

Embedding generates starting coordinates. A force field is an approximate energy model used to refine them. RDKit uses ETKDGv3, an embedding method informed by distance geometry and torsion knowledge. Automatic prefers the shipped RDKit WebAssembly engine and falls back to OpenChemLib if it cannot load. The explicit RDKit preference also allows that loading fallback.

The defaults are Automatic, Quality, and MMFF94s. A requested spin can also try OpenChemLib after an unsuccessful RDKit embedding; speculative background prefetch does not trigger that slower fallback. UFF requires RDKit. OpenChemLib refinement uses MMFF94 regardless of the selected RDKit force-field choice. Read the actual engine/force-field report if you are comparing geometries.

Quality means a larger cleanup budget, not a global-minimum guarantee. A capped minimization need not converge, and one geometry does not establish conformer populations, solvent effects, a metal coordination geometry, or experimental stability. Unsupported metal-containing cases can be refused instead of drawn with unjustified geometry.

The separate interactive 3D sidecar

Interactive 3D Workspace (structure.openInteractive3d) is a related experimental desktop action. It attaches a native mechanics session to the Spin 3D overlay:

• Drag an atom to tug the geometry.
• Drag empty space to rotate.
• Click outside to flatten, or press Esc to cancel.

A sidecar is a separate helper process. Here the native sidecar performs constrained force-field optimization, while ChemDraft renders the visible result. Its implemented mechanics use Avogadro Core/Calc and UFF. The binary is platform-specific; an unavailable native bridge or missing sidecar produces an unavailable message rather than fabricated mechanics.

Ordinary Spin 3D conformer generation and this native tug session are distinct paths. Choosing UFF in Preferences refers to RDKit refinement; it does not select the interactive sidecar. The sidecar is a local component rather than a remote simulation service.

Current limits

The older force-field plan records a blocked OpenBabel integration requiring a local binary and licensing review. That proposal is separate from today's implemented RDKit force-field controls and Avogadro-backed sidecar; the plan's older “nothing native exists” wording does not describe the current repository.

The shipped abbreviation work also records a limitation: Spin 3D, flattening, cleanup, and its sidecar can still see one placeholder atom per condensed group label rather than the expanded graph used for analysis. Do not interpret a conformer around such a label as a fully modelled substituent.

For native-session, cancellation, and geometry checks, consult Testing and CI. A successful conformer generation alone does not verify the separate native tug, cancellation, and flattening paths.

See also

• Bonds and Stereochemistry
• Chemistry Guarantees
• Toolbars and Palettes
• Rendering and Layout Engine