Drawing the Van der Waals shape of the enzyme binding site

Protein crystallography Programs for crystallography X-ray detectors
Basic tutorials:
Protein Peptide

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Step 5a: Stereo picture of the default molecular surface which can be obtained by Tools -> Surface -> Add sequence of commands in WebLab Viewer.

Selection of the default molecular surface

Selection of the default molecular surface

Step 5b: Stereo picture of selected default molecular surface. This is necessary for further changes of view property of the surface.

Step 5c: Changing the surface properties. Call the Display Style window by : View -> display style command sequence. And in this window select next parameters: Surface: Display Style -> VDW - this will generate the exact Van der Waals surface. Surface: Coloring -> Color by: Atom Color - this will color the surface by atom colors with showing potentially charged and neutral parts of the binding pocket. Tick the Transparent box - this will allow to display some objects inside the surface. Then click Ok to apply all changes and exit to the main window. Then click somewhere in the window to deselect the surface.

Display Style: Surface

Step 5d: Actually, previous step can be done from this screen, but in order to show how to manipulate with selected objects we've done the previous step. Now in the Display Style window go to the Atom tab.

Display Style: Atom

Step 5e: In this window select in Atom: Display Style select option Off - to remove atom grid from the picture. Then click Ok to apply all changes and exit to the main window.

Van der Waals surface of the enzyme pocket

Step 5f: Stereo picture of the Van der Waals surface of the enzyme binding pocket. After all described manipulations, picture should be similar to this. It is easy to spot, that the surface now more carefully resemble the atomic structure of the enzyme binding pocket.

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