If you are going to make any type of energy calculation in ICM (eg docking, display H-bonds, display electrostatic and binding property surfaces etc..) it is necesary to convert a protein or chemical into an ICM object. Be aware that upon conversion ICM adds missing side-chain atoms (but won‟t try to build missing loops) due to the nature of the internal-coordinate system. The list of residues/ atoms added is presented in the command line shell and can be reviewed. For reference, the original PDB entry is kept in the system. See the command line manual for a more complete description of what the conversion process does.

NOTE: Before converting a protein structure to an ICM object make sure that the chemicals contained within the structure (e.g. ligands) are correct. If an error is found you can edit the ligand as described here.

To convert a PDB structure into an ICM object follow the steps shown below:

• Right click on the name of the protein you wish to convert in the ICM Workspace.
• A dialog box will be displayed.Check the boxes as desired. If you are performing important calculations then it is necessary to optimize all hydrogens and ASN, GLU, PRO, and CYS.

If your object is an ICM object it will tell you in the ICM Workspace: