Editing Atoms

This tutorial covers how to edit atomic structures in ACoord.

Adding Atoms

Method 1: Top Toolbar Atom Brush

1. Choose an element from Add Atom... in the top toolbar.
2. Enable Brush. The active button and crosshair cursor indicate brush mode.
3. Press the left mouse button on an existing atom, drag in the desired direction, and release to create one new atom at the preview endpoint.
4. Set Max length to cap how far the new atom can be pulled. The default is 1.54 Å, approximately a typical C–C single-bond length. Dragging farther keeps the endpoint at this limit instead of creating atoms indefinitely.
5. Press Esc, press A, or click Brush again to leave brush mode.

The blue preview line shows direction and the endpoint ring shows the final position. Tiny movements below the activation threshold are ignored, and a drag must start on an existing atom. The gesture runs in the camera-facing plane through the source atom. Atom color and radius come from the current display brush settings.

Copying Cartesian Coordinates

Select one atom and click Copy x, y, z in the right-side Properties panel. The clipboard receives plain comma-separated values such as 1.25,-2,3.123456789, without spaces, parentheses, or an element label.

Copying Selected Atom Indices

The right-side Atom Selection panel simultaneously lists 1-based and 0-based atom indices, each with its own copy button. Runs of three or more consecutive atoms are compressed, for example 1,2,5-8,10, with no spaces.

Method 2: Keyboard Shortcut

1. Press A to enter add atom mode
2. Type the element symbol (e.g., "C", "H", "O")
3. Click in the 3D canvas to place the atom
4. Press Esc to exit add mode

Method 3: Right-Click Menu

1. Right-click in the 3D canvas
2. Navigate to Add atom submenu
3. Select the element
4. Atom is added at the click position

Method 4: Quick Add Panel

1. Locate the Quick Add section in the Properties panel
2. Enter element symbol and coordinates (x, y, z)
3. Click Add

Inserting Ghost Atoms

The right-side Ghost Atom panel inserts a basis-only center. ACoord uses an H basis by default: Gaussian writes Bq, while ORCA writes H:.

1. Select one or more atoms.
2. Choose Geometric center or Center of mass.
3. Enter a signed Plane-normal offset (Å). Use 0 to insert directly at the center; positive and negative values place the ghost on opposite sides.
4. Click Insert H Ghost Atom.

A non-zero normal offset requires at least three non-collinear selected atoms. Three atoms define an exact plane. Four or more atoms use a PCA least-squares best-fit plane, so every selected atom contributes to the normal. If the fitted plane RMS deviation exceeds 0.1 Å, ACoord warns that the selection is noticeably non-planar but still inserts the ghost. Collinear selections are rejected. The normal direction is normalized deterministically, so changing selection order does not randomly swap the positive and negative sides. Ghost and dummy atoms do not participate in automatic bonding or mass calculations.

Ghost versus dummy

A ghost atom has no nucleus or electrons but carries basis functions. A dummy atom is only a geometric reference point and has no basis. They are stored and exported as different atom roles.

Deleting Atoms

1. Select the atom(s) to delete
2. Press Delete or Backspace
3. Or right-click → Delete atom

Moving Atoms

Drag to Move

• Left-click and drag on an atom to move it in the viewing plane

Precise Position

1. Select the atom
2. In the Properties panel, enter exact X, Y, Z coordinates
3. Click Apply

Move Multiple Atoms

• Select atoms, then right-click + Shift + Alt + drag

Rotate Selection

• Select atoms, then right-click + Shift + drag to rotate around center

Copying Atoms

1. Select atom(s)
2. Press Ctrl+C (or right-click → Copy)
3. Press Ctrl+V to paste
4. New atoms appear at offset position

Changing Atom Properties

Change Element

1. Select the atom
2. Right-click → Change element → select new element
3. Color and radius update automatically

Change Color

1. Select the atom(s)
2. Right-click → Set color...
3. Choose a new color

Note: Custom colors are saved only in .acoord format

Fix/Unfix Atoms

Fixed atoms are constrained during geometry optimization (e.g., in VASP calculations).

1. Select the atom(s)
2. Right-click → Fix atom or Unfix atom
3. A white 3D cross marker appears on fixed atoms

Visual Indicator

The 3D cross marker is visible from any viewing angle and respects depth occlusion (hidden when behind other atoms).

Constraint Export

Fixed atoms are synced with format-native movement constraints where supported:

• POSCAR: selective dynamics flags
• QE: ATOMIC_POSITIONS if_pos flags
• ABACUS STRU: atom movement flags
• OpenMX: MD.Fixed.XYZ
• CASTEP cell: IONIC_CONSTRAINTS

If every atom is free, ACoord omits redundant fixed/free flags when the target format allows the constraint fields to be left blank.

Undo and Redo

• Undo: Ctrl+Z (or Cmd+Z on macOS)
• Redo: Ctrl+Y (or Cmd+Y on macOS)

Saving Edits

• Save: Ctrl+S (or click Save button in toolbar)
• Save As: Click Save As button, choose format

For full fidelity (preserving colors, labels, etc.), save as .acoord format.

Keyboard Shortcuts

Key	Action
A	Enter add atom mode
D	Delete mode
V	Select mode
Ctrl+Z	Undo
Ctrl+Y	Redo
Ctrl+S	Save
Ctrl+C	Copy selected atoms
Ctrl+V	Paste atoms
Delete/Backspace	Delete selected
Esc	Cancel current operation