Editing Atoms

This tutorial covers how to edit atomic structures in ACoord.

Adding Atoms

Method 1: 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 2: 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 3: 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

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