From: Warren G. <wg...@ua...> - 2012-09-27 16:02:24
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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 |
From: Jason V. <jas...@sc...> - 2012-09-27 16:52:54
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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 <wg...@ua...> 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, Inc. (e) Jas...@sc... (o) +1 (603) 374-7120 |