Set Bond Type

• Select the two atoms forming the bond.
• MolMechanics/Edit Structure/Set Bond Type
• Choose the Bond Type from the drop down arrow.
• Press Apply button

Set Formal Charge

• Select the atom.
• MolMechanics/Edit Structure/Set Formal Chage
• Choose the Charge from the drop down arrow.
• Press Apply button

Set Chirality

• Select the atom.
• MolMechanics/Edit Structure/Set Chirality
• Choose the Chirality from the drop down arrow.
• Press Apply button

Build Hydrogens

• Select the atoms.
• MolMechanics/Edit Structure/Build Hydrogens
• Press Apply button

Set Tether

Theory

A tether is a harmonic restraint pulling an atom in the current object to a static point in space. This point is represented by an atom in another object. Typically, it is used to relate the geometry of an ICM molecular object with that of, say, an X-ray structure whose geometry is considered as a target. Tethers can be imposed between atoms of an ICM-object and atoms belonging to another object, which is static and may be a non-ICM-object. You cannot create tethers in ICM-Browser, however, if the project that you have loaded contains tethers between two objects, then they can be displayed:

• Convert the two structures you wish to tether to an ICM object.
• MolMechanices/Edit Structure/Set Tether
• Right click on the first atom you wish to tether and click on the first option which is the selection language for the atom. This information will automatically be placed in the first atom dialog box. Alternatively you can type in the ICM selection language into the dialog box.
• Right click on the second atom (in a different object) you wish to tether and click on the first option which is the selection language for the atom. This information will automatically be placed in the second atom dialog box. Alternatively you can type in the ICM selection language into the dialog box.
• Press Apply button

Delete Tether

• Select the atoms you wish to delete the tethers from.
• MolMechanices/Edit Structure/Delete Tether