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9.8 Refine Side Chains

Available in the following product(s): ICM-Pro

Once a molecular model has been constructed it is generally a good idea to analyze it using the Protein Health macro. The results from protein health will indicate which part of the molecule is strained or has unusual geometry. A way of solving these problems is to refine or optimize the side-chains. Other ways to minimize or optimize the structure are available in the MolMechanics/Minimize menu.

To refine or optimize a selection of side chains the structure needs to be an ICM object.

  • Make a selection of the side chains you wish to optimize. See how to make selections section.
  • Right click on the selection in the graphical display. A selection will be displayed as green crosses.
  • Select from the right click menu Advanced/Optimize Side Chains and a data entry box as shown below will be displayed.
  • Enter the number of calls per variable you wish to use for the simulation. For more details on this please see the ICM language manual.

A stack of energy conformations will be displayed in a table. Each conformation can be viewed simply by clicking in the table.

Make Disulfide Bond

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