[Chimera-users] Hbond in CLI + cacheDA
pett at cgl.ucsf.edu
Thu Jul 28 11:06:07 PDT 2011
On Jul 28, 2011, at 3:35 AM, Maciek Wójcikowski wrote:
> Hello everyone,
> I'm trying to compute hbonds for quite large molecular database, so
> i do it in CLI. I've added cacheDA parameter which speeds up whole
> process at first by 10 times, although after time cache is getting
> bigger and bigger operations slows down as one can expect, because
> Chimera is caching every compound. Is there a way to limit the size
> of a cache, or even better to tell chimera to cache only protein
> donors and acceptors?
Are you closing the compound models after you do the H-bond
computation? I ask because the caching uses a "weak key dictionary"
where the key is the model. What this means is that if the model is
closed it should simply disappear from the cache, no fuss no muss. If
you are closing the models then either the slowdown is due to
something else, or the models aren't being properly removed from the
cache. Let me know if your script is closing the models but still
having this problem and I will investigate.
UCSF Computer Graphics Lab
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