[Chimera-users] why is Chimera so slow?

Greg Couch gregc at cgl.ucsf.edu
Wed Apr 14 15:51:53 PDT 2010

The short answer is, yes, it is unrealistic to set your surface density 
to 20 for interactive use.

And to quote from the documentation for the "Measure Volume and Area" tool:

"the total analytical solvent-accessible and solvent-excluded areas are 
automatically reported in the *Reply Log* and the values per atom and 
residue are assigned as attributes named *areaSAS* and *areaSES*."

In other words, increasing the surface vertex density does not change 
the computed areas for the solvent excluded surface, the areas are 
computed analytically and are not dependent on the vertex density.

Increasing the vertex density does make a nicer picture though.

     - Greg

On 04/14/2010 03:00 PM, Scott Classen wrote:
> Hi All,
> First off, I'm fairly new to Chimera, and so far I'm very impressed with the functionality. Thanks for the great tool.
> I am embarking on a fairly intensive comparison of a dozen or so structures and I'm running into some serious performance issues.
> I have an older Mac Pro with dual 2.66GHz Intel Xeon processors, 14GB RAM, ATI RadeonX1900 w/512MB VRAM and Chimera (1.4.1 build 30365).
> I've got 3 PDBs loaded up and have calculated surfaces for all three with a vertex density of 20 (perhaps too high? but I need accurate values for the solvent-excluded surface for particular residues).
> With 2 models and 2 surfaces things start to slow down a bit, but are manageable. With 3 models and their associated surfaces I can't even rotate the view at all. Even if I only show one residue and residues with 5A. It's as if Chimera is doing all the behind the scenes calculations to rotate all the surface triangles and atomic coordinates that aren't even being displayed.
> Is there something I'm missing? Is it it unrealistic to set my surface density to 20? Any advice?
> Thanks,
> Scott
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20100414/f64c014d/attachment.html>

More information about the Chimera-users mailing list