Hi Dan,

The PDB 3ZLJ only has 13,233 atoms in the PDB. Recent versions of PyMOL _should_ be able to handle that in 3D with transparent surfaces and sticks just fine. I don't have an FX 4800, but have tested on similar hardware with larger systems successfully.

Can anyone out there with a Quadro FX 4800 or similar comment on 3D performance with 3ZLJ? 

For what it's worth, in anaglyph 3D mode (which does double-rendering) for 3ZLJ, shown as described above, on a MacBook Pro with an NVidia GeForce 650M, I'm getting about 48 FPS.


-- Jason

On Mon, Aug 26, 2013 at 10:59 PM, Dan Piraner <danny.goalie.91@gmail.com> wrote:
Hello all,

If anyone is using PyMOL with NVidia's 3D Vision, I am wondering if
you could help me estimate performance with a prospective build. On
the PyMOL web site, the graphics card recommendations for 3D Vision
are as follows:

120Hz) NVidia 3D NVision with:
   (entry) NVidia Quadro 580; entry level cards begin at approximately $99
   (better) NVidia Quadro FX 3800/4800
   (best) NVidia Quadro Q5000/Q6000

As someone used to quantitative benchmarks, I'm not exactly sure what
"entry", "better", and "best" actually mean. I'm thinking of pairing a
Quadro FX 4800 with an i7 4770k. I've never used a 3D Vision setup
before and am wondering what kind of performance to expect. Would it
be able to render a reasonably complex structure (picking at random,
3ZLJ) with a transparent surface and stick representation without

Any quantitative information or suggestions would be greatly appreciated.



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Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.

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