From: John Stone (
Date: Wed Oct 03 2007 - 19:12:40 CDT

Hi Christoph,
  It is almost certainly some sort of display driver bug. Whether you see
a symptom in another program like PyMol depends greatly on whether the
other program is using the same rendering path that VMD uses. In this
case they are probably quite different. I suspect it is indeed
some sort of OpenGL driver bug.

Which transparency mode of VMD isn't working, the "Normal" rendering
mode, or the "GLSL" rendering mode? They use totally different rendering
code, so knowing which one is causing you trouble would be very helpful.

Once we narrow it down to either a problem with polygon stippling or
a problem with blending in GLSL, I can report the bug to Apple, or
have you do it.

  John stone

On Wed, Oct 03, 2007 at 05:05:21PM -0700, Christoph Weber wrote:
> I'm wondering if anyone else has seen this, and what to do about it?
> On our brandnew iMacs VMD seems to be incapable to display transparent
> materials. Everything is displayed solid until the transparency slider
> is down to 0.07, at which point the object disappears altogether.
> At first I thought it might be a bug in the ATI drivers, but PMV
> (Python Molecular Viewer) can smoothly and effortlessly display
> transparent objects from solid down to nothing.
> Ours are the new aluminum clad iMacs with ATI Radeon HD 2400 XT
> graphics cards, running OSX 10.4.10 with all the latest software updates.
> training201:~ rcadmin$ /Applications/VMD\
>; exit
> Info) VMD for MACOSXX86, version 1.8.6 (April 6, 2007)
> Info)
> Info) Email questions and bug reports to
> Info) Please include this reference in published work using VMD:
> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) Multithreading available, 2 CPUs detected.
> Info) OpenGL renderer: ATI Radeon HD 2400 XT OpenGL Engine
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (4096x4096), 3-D (256x256x256), Multitexture (8)
> Oh, and while we're at it, GLSL rendering does not work under MacOSX
> either. It just yields a blank OpenGL display and a spinning
> beachball. The same iMac booted into WindowsXP works really well with
> VMD, with transparency, GLSL and excellent frame rates (30% higher
> than under MacOSX). Hmm...
> Thanks for any insight,
> Christoph
> --
> | Dr. Christoph Weber Sen. Applications Specialist
> | Research Computing, TPC21 858-784-9869 (phone)
> | The Scripps Research Institute 858-784-9301 (FAX)
> | La Jolla CA 92037-1027
> |
> Children are likely to live up to what you believe of them.
> -- Lady Bird Johnson

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