From: Christoph Weber (
Date: Thu Oct 04 2007 - 15:56:56 CDT

John Stone wrote:
> 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.

I was afraid that'd be the case. MacPyMol does transparency fine, BTW,
as does Chimera and PMV.
Thanks for clarifying how this can be different, depending on code
base and approach taken.

> 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.

Normal rendering refuses to "go transparent".
GLSL doesn't work altogether, see my original message. However, the
GLSL issue does not worry me much just yet, as it is to be expected on
current consumer level graphics cards.

> 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.

Either works. Maybe report twice to make them fix it faster?
Is there a way in VMD to collect more info for the bug report?

> Cheers,
> 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
Shadows in the flame.- The flame is not so bright to itself
as to those whom it illuminates, so also the wise man. -- Nietzsche