Dear Jason,

I strongly support Adam's suggestion that the PyMOL website and the Wiki display a clear warning to people planning on using PyMOL with ATI/AMD graphics card. I have had numerous issues with ATI graphics cards + PyMOL over the years and nVidia is unquestionably the better choice when it comes to running professional OpenGL intensive software (like PyMOL and Blender) on Linux or Mac OS.

Best regards,

On Wed, Sep 29, 2010 at 11:07 AM, H. Adam Steinberg <> wrote:
Hi All,

I bought a new MacPro and now get this message when I open PyMOL:

    Note: Radeon HD cards tend not to run PyMOL well.
    Use nVidia or Intel instead, if OpenGL glitches occur.
    Attempting to compensate for known issues... 

So the new Macs only come with Radeon video cards... there are no other choices with a Mac. This means the MacPros no are no longer a good platform for running PyMOL? I just tossed $3K down the drain?

I tried to render the surface of 3L5Q and PyMOL just crashes (6GB RAM). I tried to render just the top half and it still crashes.

What are the OpenGL glitches that occur, are they documented somewhere?
What does PyMOL do to compensate?

I checked the PyMOL web site and under the supported operating systems and hardware there is no mention of the lack of Radeon support/poor Radeon performance. Maybe that should be added because I wouldn't have bought this new Mac if I would have known this. Is there anything I can do to make this new machine work?

I see a 64-bit version is on the horizon, will this address Radeon performance or should I go back to my old MacPro with it's nVidia 7300 video cards? 

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555

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