Objective

To remove clashes from a PDB structure.

Background

Here we will use a macro that calculates the energy strain (Protein Health) within a protein structure. The macro is based on a paper by Maiorov and Abagyan (1998). The regularization macro will remove any clashes and improve the energy of the structure.

Instructions

1. Edit/Delete All . let us begin with a clear ICM session!
2. Search FOR and display the PDB structure 1iva (use PDB search tab).
3. Convert 1iva into an ICM object (see previous lesson or search for "convert")
4. Tools/3D Predict/Protein Health Note red coloring indicates clashes or high strain. Lets remove these clashes using the ICM regularization tool.
5. MolMechanics/Regularization
6. Color and display in wire - all clashes should have been removed.

Notes and Things To Try:

• Always use the Protein Health tool and ICM Regularization after you have constructed a protein model.
• It is always wise to check a protein structure from the PDB with the Protein Health tool and then use ICM Regularization to remove any potential problems you may identify.