[ ICM Workspace | Graphical Display ]

The protein data bank has not been storing any information about covalent bond types and formal charges of the chemical compounds interacting with proteins! This oversight makes it impossible to automatically convert those molecules to anything sensible and requires your manual interactive assignment of bond types and formal charges for each compound in a pdb-entry. Therefore, if you apply the convert command to a pdb-entry with ligands, the ligands will just become some crippled incomplete molecules that can not be further conformationally optimized.

Therefore, follow these steps to convert a chemical properly from a pdb form to a correct icm object. There are two ways to do this either via the ICM Workspace (recommended) or via the Graphical Display.

4.3.1 Converting a Chemical from the PDB using the ICM Workspace

• File/Open PDB
• View the ligand in the ICM Workspace by expanding the molecule tree (see below).

Change bond orders:

• Change the bond orders by selecting the bond (highlighted in red).
• Right click and select the desired bond as shown below.

NOTE: Keyboard shortcuts are provided to make editing faster.

Change atom and charge:

• Change the atom or charge by selecting the atom (highlighted in red).
• Right ckick and select the desired atom or charge as shown below.

NOTE: Keyboard shortcuts are provided to make editing faster.

Convert to 3D in MMFF force field:

• Once you have made the changes to the ligand - right click on the name of the ligand in the ICM Workspace and select Move from Object.

• Select the ligand by double clicking on it in the ICM Workspace.
• Select MolMechanics/ICM-Convert/Chemical

NOTE: If you need to add an extra bond you will need to use the full molecular editor. Right click on the name of the ligand in the ICM Workspace and select Edit/Edit Compound.

4.3.2 How to Convert a Chemical from the PDB using the Graphical Display

• Display the molecule in wire chemistry style mode by right clicking on the Wire Representation button (see Wire Representation section).

To change the bond types in your ligand:

• Click on MolMechanics/Edit Structure/Set Bond Type and the Set chemical bond type data entry box will be displayed.

You can either select (see selection menu section)the atoms you wish to change graphically using the rectangular or lasoo selection button OR

You can select the By two atoms tabs and right click on the atoms you wish to change and then selecting the atom descriptor with the left mouse button as shown below.

• Select the desired bond type either single, double, triple or aromatic.

To set the formal charge of a compound:

Click on MolMechanics/Edit Structure/Set Formal Charge and then select the appropriate charge.

The final step is to convert the compound into an ICM object:

• Select the chemical (green crosses in graphical display).
• MolMechanics/ICM-Convert/Chemical