Hi Seán, Enabling multi-layer transparency should do the trick.
From the menu: Setting > Transparency > Multi-Layer From the command line: PyMOL> set transparency_mode, 1 Hope that helps. Cheers, Thomas > On Feb 24, 2020, at 10:32 PM, Seán Downey <downe...@tcd.ie> wrote: > > Hi all, > > I am trying to render an image of a protein structure with a transparent > surface and a slightly less transparent cartoon structure, of the same > colour, in order to show both the cartoon structure and a ligand > (non-transparent) bound within as well as the surface. Using the ray option, > the ligand is visible, but the semi-transparent cartoon is not. Does anyone > have any insight into this. Note I am using version 2.2.3. > > All the best, > > Seán Downey > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
