MOptima
Chapter 06

Editing and Selection

Selection-driven editing

Editing in MOptima is selection-driven. Pick atoms in the viewer and then apply the change from the Edit panel. Clicking a selected atom again removes it from the selection. The Editor toolbar above the viewer offers All, Invert, Non-H, and Clear. These controls use one selection across every Editor sidebar panel, and the selection remains visible when you switch panels. All selects every atom, Invert selects every currently unselected atom, and Non-H selects every atom except hydrogen.

Clicking an atom always toggles only that atom, regardless of the active panel. The order in which atoms were selected is preserved. Bond, Angle, Torsion, constrained Optimization, and PES Scan may require a specific count and order. If the selection has too many atoms, that action stays disabled. Use Clear before starting a new ordered selection.

Common edit modes

Move and Rotate

Drag selected atoms; Ctrl-drag to move or rotate a complete molecule.

Reset View

Fit the complete assembly without changing any molecular coordinates.

Atom

Change or delete selected atoms; Add H and Sanitize repair routine valence issues.

Bond

Edit distance and choose Bond Type None, Single, Double, or Triple.

Angle

Select atoms 1-2-3; preview the angle and Apply the final value.

Torsion

Select atoms 1-2-3-4; rotate around bond 2-3 and Apply.

Move and Rotate

This is the direct-manipulation mode. The gesture and the atom under the pointer determine the target:

  • Left-drag an atom to move that atom. If it is part of the current multi-atom selection, all selected atoms move together.
  • Ctrl+left-drag an atom to move its complete connected molecule rigidly.
  • Ctrl+right-drag an atom to rotate its complete connected molecule around its centroid.

Starting on the background keeps the camera controls: left-drag pans, middle-drag zooms, and right-drag rotates the view. A completed molecular move or rotation is stored as one Undo step and does not recenter the camera.

Reset View

Fits and centers the complete assembly in the viewer. It changes only the camera framing: molecular coordinates, selection, and Undo/Redo history are not modified.

Atom Edit - select one or more atoms

Changes or deletes the selected atoms. Enter an element symbol such as O, N, or Fe and choose Change, or choose Delete. Add H and Sanitize are global cleanup tools available in this mode.

Bond Edit - select 2 atoms

Bond Edit combines distance and connectivity editing. Enter the desired atom distance and select one Bond Type radio button:

  • None removes a bond if one exists.
  • Single, Double, or Triple adds or changes the selected bond.

There is no separate Add/Delete selector. Automatic endpoint hydrogen adjustment is enabled by default and can be disabled for radicals, unusual valences, or specialized structures.

Adding a bond between disconnected molecules merges their components. Setting a bridge bond to None can split a molecule; both components remain visible in the non-batch Editor. If the selected atoms initially belong to different molecules, changing their distance translates the complete second molecule rigidly instead of distorting it.

For an acyclic existing bond, the fragment beyond the second selected atom moves along the bond axis. For a ring bond, both selected atoms move symmetrically so the bond center stays fixed. The interactive distance slider uses 0.02 Å steps over 0.50-2.50 Å.

For Bond, Angle, and Torsion Edit, MOptima prepares the slider's structure frames in advance from the current geometry. These are geometry previews, without MMFF94 or xTB minimization. Applying an edit commits the chosen geometry; run Optimization separately if you want relaxation.

Angle Edit - select 3 atoms

Sets the angle defined by atoms 1-2-3, with atom 2 as the vertex. Attached fragments move with the edited atom. Ring-aware behavior avoids simply breaking the ring geometry.

Torsion Edit - select 4 atoms

Sets the dihedral defined by atoms 1-2-3-4. The central bond is 2-3. Acyclic fragments rotate as a unit; ring torsions use the ring-aware numerical solver.

Large angle or torsion changes can create strained structures. Run an optimization after substantial manual edits.

  1. Choose the required edit mode.
  2. Select atoms in the viewer in the order requested by the panel.
  3. Confirm the displayed atom indices.
  4. Enter the new value and, for Bond Edit, choose Bond Type.
  5. Choose Apply.

Reasonableness checks

After coordinate or bond changes, MOptima reports clearly suspicious geometry or RDKit valence/sanitization problems. The change is retained so unusual but intentional chemistry is not silently rewritten. Use Add H, Sanitize, or an optimization when cleanup is appropriate.