I get around this by rendering both items separately and then combining the two images in photoshop.
Is there a way to do what Nasir is asking directly in PyMOL? > On Feb 16, 2016, at 8:15 AM, Nasir Bashiruddin <nasir...@gmail.com> wrote: > > Hello! > > So, I've had this problem for a while now. > > I have a ligand that goes deep into a protein. > > I have the ligand with stick representation. > > I have the protein in cartoon representation. > > I have both ligand and protein surfaced with 0.5 transparencies. > > The ligand surface is yellow and the protein surface is gray80. > > The protein cartoon is set to transparency, 0.5 as well. > > I want to show how the ligand goes deep into the binding site of the protein. > > I can see the ligand surface going into the protein surface but when I Ray, > the yellow ligand surfaces that go into the protein disappear. > > How do I get the Ray quality and keep the ligand surface that is within the > protein from disappearing? > > Hope I explained this well. > BTW, surface mode is set to 1 to include all atoms > > Nasir > ------------------------------------------------------------------------------ > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140_______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net ------------------------------------------------------------------------------ Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
