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Connect and Fuse Panel |
The Connect and Fuse Panel can be used to perform rigid-body connection or fusion of atom pairs.
To open the Connect and Fuse panel, you can:
Choose Edit → Connect and Fuse in the main window.
This panel is dockable, so it opens by default in the Workspace. You can change this behavior in the Preferences panel, under General – Panels.
To connect or fuse two molecules, you must first define the pairs of atoms that will be connected or fused. When you pick atom pairs, the first atom of each pair must always come from the same molecule. Likewise, the second atom of the pair must also come from the same molecule, but this molecule must be different from the molecule that the first atom of a pair comes from.
If Show markers is selected, then the selected atom pairs are connected with green dashed lines. As each pair is selected it is added to the list at the top of the panel.
Once you have selected all the atom pairs to be connected or fused, click Connect or Fuse. After the operation, the markers are deleted and the list is cleared. Hydrogen atoms are deleted to maintain correct valence, but other atoms are not. If a valence violation would result from the operation, a warning is given and the operation is canceled.
If you connect or fuse molecules that belong to different entries, a Choose Entries dialog box is displayed when you click Connect or Fuse. You must choose one of the two entries. The chosen entry now contains the new molecule, and the other entry is deleted. This operation, including the entry deletion, can be undone.
This list contains the pairs of atoms that have been picked for connection or fusion. The first atom in every pair must belong to one of the two molecules and the second to the other molecule.
These buttons can be used to delete individual atom pairs from the list or to delete all atoms from the list. To delete an atom pair, select the pair in the list and click Delete. If markers are displayed, the marker is deleted as well.
When selected, this option allows you to pick atom pairs to be connected or fused. The option is selected when you first open the panel.
When selected, the atom pairs are connected with green dashed lines. The currently selected atom pair is marked wit two solid lines on either side of the dashed line.
When you click this button, the atom pairs are connected with a single bond, and hydrogen atoms are deleted if necessary to maintain the correct valence.
When you click this button, the second atom in each pair is replaced by the first atom in each pair, and attached hydrogen atoms are deleted to maintain the correct valence.
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