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Hiya In PYMOL, you could use the selection feature to select which residues you want to draw surface over (there are some pretty powerful selection syntaxes in this package so could could select your actve site residues in a number of ways - see http://pymol.sourceforge.net/) - then create surface on the selection, then issue set transparency=0.5 to make it transparent. I often find with this sort of thing that its easiest to work with two separate copies of the same pdb (with different names of course) - so in your example on one copy you do all the cartoony stuff, and the other the surface work. This helps avoid the anguished moment when a single click destroys a lot of unsaved fiddly selection.... Cheers J "Green, Todd" <[log in to unmask]> wrote:> > Hello All, > > I would like to make an illustration which has a semi-transparent surface > rendering for a large cavity. I just want the suface to cover the cavity > not the entire protein (which will most likely exist as a ribbon > drawing). Is there a way to set a boundary for a surface drawing? By > that, I mean pick a point within the cavity and set a radius to draw a > solvent accessible surface and thusly only those points falling within > the radius are shown. Seems simple enough, but I haven't quite figured it > out as of yet. > > Thanks in advance for any advise. > Todd -- Professor James Whisstock NHMRC Principal Research Fellow / Monash University Senior Logan fellow Department of Biochemistry and Molecular Biology Monash University, Clayton Campus, PO Box 13d, VIC, 3800, Australia +613 9905 3747 (Phone) +613 9905 4699 (Fax) +61 418 170 585 (Mobile)