[Chimera-users] Hbond in CLI + cacheDA

[Eric Pettersen]

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?

Hi Maciek,
	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.

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu


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