Howdy, This is an NVidia-specific bug. Just type this into PyMOL:
set cylinder_shader_ff_workaround,1 Feel free to add that to your ~/.pymolrc. Cheers, -- Jason On Wed, Apr 11, 2012 at 5:16 PM, <br_...@comcast.net> wrote: > I recently compiled and installed PyMol on Arch Linux > (see https://aur.archlinux.org/packages.php?ID=47323). When I look at > something I pulled from the pdb, it appears somewhat transparent. For > example, in the screenshot linked below, the heme and the molecule behind it > are somewhat transparent. When I rotate it is impossible to tell which one > is on top of the other. I do not have any 3D capabilities on this system. > Glad to provide any additional details. Some output is attached here. > > Thanks! > > Link to screenshot: http://s12.postimage.org/kf9ukr0y3/screenshot.png > > $ pymol > PyMOL(TM) Molecular Graphics System, Version 1.5.0.1. > Copyright (c) Schrodinger, LLC. > All Rights Reserved. > > Created by Warren L. DeLano, Ph.D. > > PyMOL is user-supported open-source software. Although some versions > are freely available, PyMOL is not in the public domain. > > If PyMOL is helpful in your work or study, then please volunteer > support for our ongoing efforts to create open and affordable scientific > software by purchasing a PyMOL Maintenance and/or Support subscription. > > More information can be found at "http://www.pymol.org";. > > Enter "help" for a list of commands. > Enter "help <command-name>" for information on a specific command. > > Hit ESC anytime to toggle between text and graphics. > > Detected OpenGL version 2.0 or greater. Shaders available. > Detected GLSL version 4.20. > OpenGL graphics engine: > GL_VENDOR: NVIDIA Corporation > GL_RENDERER: GeForce GTS 450/PCIe/SSE2 > GL_VERSION: 4.2.0 NVIDIA 295.40 > Detected 4 CPU cores. Enabled multithreaded rendering. > > ------------------------------------------------------------------------------ > Better than sec? Nothing is better than sec when it comes to > monitoring Big Data applications. Try Boundary one-second > resolution app monitoring today. Free. > http://p.sf.net/sfu/Boundary-dev2dev > _______________________________________________ > 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, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev _______________________________________________ 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
