Adjusting Bond Lengths, Angles, and Dihedrals

To change the geometry of a structure manually, you can adjust the bond lengths, angles, or dihedral angles. These operations can be particularly useful when building a structure.

To define the adjustment, pick the atoms in the Workspace:

• Two atoms or one bond for a bond length or distance adjustment.
• Three atoms that are connected or two adjacent bonds. The apex of the angle is the center atom.
• Four atoms that are connected or three adjacent bonds for a dihedral adjustment.
• Two atoms or one bond for a dihedral rotation.

The atoms should be chosen so that the two ends of the adjustment can move freely, i.e. they are not part of a ring system. Adjusting distances or angles in a ring changes distances or angles other than the one selected. Adjusting ring dihedrals can be done indirectly by changing the ring conformation (see Adjusting Peptide and Ring Conformations); adjusting ring angles and distances can be done by moving atoms (see Moving Atoms).

The atom selection defines two "fragments", one at each end of the selection. By default, the atoms in the smaller fragment are the ones that are moved. There is a large arrow pointing to the fragment to be moved, and a small one pointing to the stationary fragment. The current value of the quantity is displayed near this arrow. You can change the moving fragment by clicking on the smaller arrow. The moving fragment cannot be connected to the stationary fragment other than through the selected bonds.

After selecting the atoms, you can do one of the following:

• Right-click on the selection and choose the Adjust item.
• Edit → Adjust and select a type of adjustment.

A banner for the adjustment is displayed, like the one below.

You can open the banner before picking the atoms: Edit → Adjust and select a type of adjustment. A banner opens for the adjustment type. You can then pick the atoms, and the banner for the specific adjustment type opens.

If the Move Atoms banner is already displayed, you can click the ... button to choose the type of adjustment, then pick the atoms. This banner also offers some features not available from the other locations. If you don't want to move the entire smaller fragment, you can click the ... button and select Attached Terminal Atoms or Single Atom Only from the Atoms to Move submenu, to move the atom at the moving end of the selection with its terminally attached atoms (H or halogen) or just the atom itself.

Measurements can be used to select the atoms for an adjustment, by right-clicking on a measurement and choosing Adjust Distance, Adjust Angle, or Adjust Dihedral (depending on the measurement type). The appropriate banner opens, and you can make the adjustment.

Once you have the atoms selected, you can adjust the geometry by dragging with the left mouse button. The value of the adjusted quantity changes as you drag.

You can also set the value for a distance, angle, or dihedral by right-clicking on a measurement or an appropriate atom selection and choosing Set Distance, Set Angle, or Set Dihedral. A small pane opens, in which the current value is reported, there is a text box for changing the value, a check mark to click when you have made the change. After you click the check mark, the structure is updated, the measurement is updated (or created if it doesn't exist) and the pane closes. Press Esc to close the pane without making any changes.