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1. Create Molecular Surface by going to Compute--> MSMS
2. Click on the DejaVu button.
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3. In DejaVu, turn on the clipping plane.
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4. In DejaVu, toggle between Clip and Object under "Mouse Transforms" to manipulate the clipping plane and the object alternately. Your 3 button mouse translates, scales, and rotates the clipping plane the same as it does your object.
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5. For additional clarity, modify the object's 'Back Material' in DejaVu under Object->'Back'
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6. Additionally, you can select the individual object to be clipped, like the molecualar surface and leave in tact features such as a stick and ball representation of a heme group.
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