Hello Muhammad, The comments thus far are spot on, but the choice depends on your objective. If you are looking for the probable substrate trajectory, CAVER (though I'd suggest MOLE http://mole.chemi.muni.cz/web/), but these lack detail of the solvent accessible surface. If you want fast rendering for analysis, the PyMol Setting..Surface..Cavities & Pockets Only (play around with the radius, culling, and cutoff), but the surface is hard to edit and each parameter effects the surface displayed (make sure to use maximum quality display to get a accurate surface). For illustration and editing with detail try our program HOLLOW (http://hollow.sourceforge.net), but it is not as simple and is more computationally intensive. The website gives step by step instructions under the examples. For HOLLOW, I'd still suggest maximum quality display in PyMOl (only use when you are nearly finished because it is really slow) and open the channel by using the cylindrical search and hide surface for the generated object with q=0 to open the channel.
Good luck. Franz Gruswitz Department of Biochemistry and Biophysics UCSF Mission Bay 600 16th St. S414 San Francisco, CA 94158
