From: John Stone (
Date: Fri Oct 05 2007 - 01:35:41 CDT


On Thu, Oct 04, 2007 at 01:56:56PM -0700, Christoph Weber wrote:
[...differing algorithms used by different programs...]
> 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.

Yes, absolutely. VMD actually implements 3 different transparency
algorithms depending on what graphics hardware you're using.
One uses "stippling" ("normal" rendering mode), and the other two
use alpha blending ("GLSL" mode, and a Sun-specific rendering mode).
It's unfortunate that in your case neither stippling nor GLSL are
working, that really says something about the lack of testing those
drivers have had. Stippling is typically a "CAD" feature rather than
something that games use, so Apple probably didn't exercise their driver
enough there. Anyway, I'll have to work with you to provide the Apple
engineers with test cases. It's kind of a laborious process to report
the bugs and help them reproduce them, as it can often take some months
before they even acknowledge receipt of the bug and begin taking
action on it. (I just got a response for a Mac stereo bug I filed well over
a year ago several weeks back....)

> Normal rendering refuses to "go transparent".

That's OpenGL stippling, a standard required feature since
OpenGL 1.0 in about 1994... Sad.

> 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.

I have filed various shader bugs with Apple on GLSL previously but there
seems to be little progress thus far.

> >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?

What apple actually needs for the bug filing process is a dump of
one of their system snapshot utilities which records all of the
system hardware/software details, and then instructions on how
to run the app to reproduce the problem. The difficulty with
reporting VMD bugs (historically at least) is that Apple always
wants me to write them a simple standalone OpenGL program that
exhibits the bug so that it's easier for them to understand.
Needless to say I typically don't have time for this so there's
usually a bit of give and take on that point but often I have been
able to explain it to them by giving them special VMD builds that
enable/disable certain graphics code to illustrate the issues...

  John Stone

NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email:                 Phone: 217-244-3349
  WWW:      Fax: 217-244-6078