Hi Warren, What commands did you use? I just tested the following on PyMOL v1.5.0.4 and everything worked as advertised:
fetch 1rx1, async=0 fetch 1rx1, type=2fofc, async=0 isosurface mySurf, 1rx1_2fofc, 1.0, (organic) orient organic set transparency, 0.5 ray Can you try the above code and let me know what you get? Cheers, -- Jason On Thu, Sep 27, 2012 at 12:02 PM, Warren Gallin <wgal...@ualberta.ca> wrote: > Hi, > > I have generated isopotential surfaces for a protein that completely > enclose the basic structure using the APBS plugin. > > I can increase the transparency so I can visualize an underlying > cartoon representation of the structure. > > However, when I do a ray tracing to get a publication quality image, > I only get the isopotential surface - the ray tracing seems to view the > surface as 0% transparent, contrary to the settings that were used to > visualize the image in the first place. > > Is this a bug, or am I missing some step that allows the ray tracing > to handle a partially transparent surface? > > Thanks in advance for any advice. > > Warren Gallin > ------------------------------------------------------------------------------ > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://ad.doubleclick.net/clk;258768047;13503038;j? > http://info.appdynamics.com/FreeJavaPerformanceDownload.html > _______________________________________________ > 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 -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://ad.doubleclick.net/clk;258768047;13503038;j? http://info.appdynamics.com/FreeJavaPerformanceDownload.html _______________________________________________ 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
