Build Menu#
The Build menu contains commands useful for creating and modifying molecular geometries.
- Atomic Coordinate Editor
Open the Atomic Coordinate Editor.
- Insert
See Insert.
- Hydrogens
See Hydrogens.
- Bond
See Bond.
- Change Elements
Change the selected atoms to a chosen element.
- Add Centroid
Add a dummy atom at the geometric center of the molecule or the selected atoms.
- Add Center of Mass
Add a dummy atom at the center of mass of the molecule or the selected atoms.
- Add Perpendicular
Add a dummy atom perpendicular to the plane of the molecule or the selected atoms.
Note
If the molecule is not planar, the plane that this is perpendicular to is the plane that has the smallest average distance to every atom.
Atomic Coordinate Editor#
The Atomic Coordinate Editor is an extremely useful environment for modifying the existing molecular structure, formatting a set of coordinates, and reordering atomic indices.
The window has several useful features:
- Preset
Select a preset format for the coordinates and update any existing coordinates.
- Format
Specify a custom format for the coordinates (the Help menu on the right includes more information)
- Distance Unit
Select between Angstroms (Å) and Bohrs/Atomic Units (a.u.).
Note
1 Å = 1.88972613 Bohrs
1 Bohr = 0.52917721 Å
- Revert
Reverts any edits.
- Clear
Clears all coordinates.
- Apply
Applies any edits.
Note
The text in the coordinate box will appear green when it has been edited, and black after being applied.
Insert#
- Molecule
Insert a molecule fragment from the Molecules Plugin.
- DNA/RNA
Insert DNA/RNA fragments using the Nucleic Acid Builder.
- InChI
Insert a molecule using an International Chemical Identifier (InChI).
- SMILES
Insert a molecule using a SMILES string.
Hydrogens#
- Adjust Hydrogens Ctrl+Alt+H
Add any missing hydrogen atoms, and remove any extra hydrogen atoms on any atoms that violate the octet rule.
- Add Hydrogens
Add any missing hydrogen atoms on atoms that have incomplete octets.
- Remove Extra Hydrogens
Remove any extra hydrogen atoms on atoms with overfull octets.
- Remove All Hydrogens
Remove all hydrogen atoms in the molecule.
Bond#
- Bond Atoms Ctrl+B
Bond all atoms in the molecule.
Warning
This will change all existing bonds to single bonds!
- Bond Selected Atoms
Bond all selected atoms.
- Perceive Bond Orders
Check all atoms that have unsatisfied octets and add enough double or triple bonds to satisfy the octet.
- Remove Bonds Ctrl+Shift+B
Remove bonds containing selected atom, or remove all bonds in document if there are no selected atoms.
- Configure Bonding
Set a tolerance for automatic bond detection as well as a minimum interatomic distance for bonds.