To smooth your surface representation try: set surface_quality, 1
or higher if you wish, though it will take longer and might look odd. The easiest way to do the other things would be to create separate objects for each type of display. Example: Show solid surface over most of a protein, with a transparent window into the interior showing an underlying stick representation. 1) Load your protein - load P1.pdb 2) Select residues for window - use some method to select the residues you'd like to set transparent - rename the selection: A > rename selection; type: window 3) Make Sticks representation - duplicate the protein object using the Actions menu (button labeled 'A') A > duplicate object - rename this to p1_sticks A > rename object type: p1_sticks - show as sticks and color as you wish 4) Create Solid Surface representation - on command prompt type: create p1_surface, (P1 and not window) - show as surface; S > as > surface 5) Create Window representation - on command prompt type: create p1_window, (P1 and window) - show as surface; S > as > surface - on command prompt type: set transparency, 0.5, p1_window 6) Cleanup - hide original P1 object - hide window selection - color objects for nice contrast Its not a perfect solution as the surface you get isn't continuous, but it demonstrates how to combine transparent/nontransparent elements of the same protein to make a figure. Hope this helps, -Tzintzuni Garcia -----Original Message----- From: pymol-users-ad...@lists.sourceforge.net on behalf of Paula Salgado Sent: Wed 3/16/2005 9:35 AM To: pymol-users@lists.sourceforge.net Cc: Subject: [PyMOL] surfaces and transparency Hi, I'm a new pymol user and have been trying to generate an image of a solvent-accessible surface in pymol. How can I smooth the surface representation? Another questions relates to transparency: is it possible to have bits of a protein transparent and others coloured? If so, how can you do it? and for 2 different proteins, can you get one transparent and not the other? Thanks for your help! Paula Paula Salgado Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Roosevelt Drive Headington Oxford OX3 7BN UK ------------------------------------------------------- SF email is sponsored by - The IT Product Guide Read honest & candid reviews on hundreds of IT Products from real users. Discover which products truly live up to the hype. Start reading now. http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click _______________________________________________ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
