Tips for 3D editing

Tips for 3D Editing

How to Successfully Perform Conformation Changes

When using the 3D Edit Mode, you may notice that after dragging an atom to significantly change the molecule's conformation (e.g., flipping a cyclohexane from chair to boat) and then clicking "Optimize 3D," the structure snaps back to its original shape.

This happens because the force field optimization algorithm seeks the nearest low-energy minimum from its starting point, which is often the original, stable conformation.

To avoid this and successfully lock in your intended conformation, the key is to drag an atom that has fewer bonds and is located at a terminal position of the molecule.

Why This Works

Atoms that form the core skeleton of a molecule are highly constrained by numerous bonds. If you move one of these atoms slightly, the optimization process will exert strong forces to pull it back to its original, stable position.

In contrast, terminal atoms, such as hydrogens or carbons in a methyl group, are less constrained. By moving one of these atoms a significant distance, you can more effectively guide the entire molecule into a different energy well (a new conformation). This provides a better starting point for the optimizer, encouraging it to find a new stable structure instead of reverting to the old one.

Practical Example

• Good Practice: To flip a cyclohexane from a chair to a boat conformation:

  • Instead of dragging a carbon atom in the ring, grab an axial hydrogen atom and pull it significantly across to the other side of the ring.

• Bad Practice:

  • Slightly nudging a carbon atom within the ring.
  • → In this case, the optimization will almost certainly force the structure back into its original, more stable chair conformation.

As a general rule, remember to "move the leaves of the tree, not the trunk." This principle will help you succeed with conformation changes in a wide variety of molecules.

A More Reliable Alternative: Constrained Optimization

If dragging a terminal atom still doesn't produce a stable result (e.g. the ring keeps relaxing back, or the conformation you want is a higher-energy state that the optimizer actively avoids), use 3D Edit > Constrained Optimization... instead of the plain Optimize 3D button.

1. Open the dialog and select the atoms defining the geometry you want to hold (2 atoms for a distance, 3 for an angle, 4 for a dihedral).
2. Click Add Constraint to lock in that value.
3. Run Optimize — the force field will relax every other degree of freedom while keeping your chosen distances/angles/dihedrals fixed.

This lets you force a specific dihedral angle (e.g. to hold a ring in boat form, or set a torsion for a rotamer scan) instead of relying on the optimizer landing there by chance. See 5.8. Constrained Optimization in the User Manual for the full dialog reference.

Other Relevant 3D Editing Tools

• 3D Edit > Move Selected Atoms... / Move Group...: useful for moving/rotating a whole fragment (e.g. a substituent) into place before optimizing, rather than dragging individual atoms one at a time. Move Group in particular lets you left-drag a connected fragment (translate) or right-drag it (rotate about its own center of mass), which is often a gentler way to seed a new conformation than single-atom dragging.
• Real-time 3D Drag setting (Settings > Settings... > Scene tab): with this on (the default for molecules ≤ 300 atoms), the structure redraws continuously as you drag, which makes it easier to see when you've pulled an atom far enough into a new energy well. For very large structures this is automatically disabled (updates apply only on mouse release) since per-frame redraws would be slower than the drag itself.
• Alt key: hold Alt in the 3D view to temporarily enter 3D Drag mode without toggling the toolbar button — handy for a quick one-off nudge.