[Chimera-users] computer advice

Greg Couch gregc at cgl.ucsf.edu
Tue Jun 21 17:02:10 PDT 2011

On 06/21/2011 11:44 AM, Ryan Woltz wrote:
> Dear Chimera,
>            We are looking at getting a new computer for our lab to 
> used for only modeling.  We are planning using chimera, pymol, and 
> dock 6.4 as primary programs for this.  What specifications i.e. 
> graphic cards, ram, do you recommend us getting?
> Thank you,
> Ryan Woltz
> UC Davis Cardiology

It depends on how big your data is, how you want to visualize it, and 
your budget.  All of the programs would benefit from faster CPUs and 
more RAM, and the visualization programs benefit from faster graphics.  
Dock can run in parallel, so the more CPUs the better.  Chimera gets 
more benefit from faster individual CPUs, but is starting to use some 
parallelized code.  Don't know about pymol.  So, if you can do your 
docking on a computational cluster, then I'd suggest just getting a 
quad-core computer.

Take a look at the chimera benchmark results, 
http://plato.cgl.ucsf.edu/trac/chimera/wiki/benchmarks, for an idea of 
the relative performance of graphics cards.  The benchmark results are 
submitted by chimera users (using Tools / Utilities / Benchmark, please 
submit your results too), so the coverage of graphics cards is spotty.  
Another good source of relative graphics card performance is Tom's 
Hardware's, http://www.tomshardware.com/, "Best Graphics Cards For the 
Money" articles.  The last page has a "Graphics Card Hierarchy Chart" -- 
note that the best performing cards are the most power hungry and the 

If you want to display 3D stereo graphics with chimera, you'll need a 
workstation graphics card, a NVidia Quadro or AMD/ATI FirePro, instead 
of a consumer card (AMD/ATI Radeon, NVIDIA GeForce) and a suitable 
display.  Stay away from Intel integrated graphics.  Graphics on Linux 
is typically slightly faster with identical hardware than Apple Mac OS X 
or Microsoft Windows, but that should not be a major consideration.



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