[Chimera-users] Suggestion re Docking Results

Greg Couch gregc at cgl.ucsf.edu
Tue Sep 6 10:13:04 PDT 2005

On Fri, 2 Sep 2005, Philip Crawford wrote:

> Hi. I like Chimera and hit a limit yesterday. (Windows version.)
> We are running DOCK using the ZINC databases, which produces very large
> output_scored.mol2 files. I tried using Chimera to open and sort one of
> these. After an hour, I killed Chimera. John Irwin suggested (via the
> Dock-fans list) that I recommend you set a limit on the size of output file
> to be opened. An alternative may be to set a limit on the number of records
> which will be read, regardless of file size.
> Thanks for a useful product.

Rather than set a limit on how big a file chimera will open (hard to know 
what that limit should be because it depends on the physical configuration 
of the computer and what you're trying to open), the next version of 
chimera will use less memory!  In our internal builds, chimera is using 
approximately 50% less memory per molecule (and is faster too!).  A 
"release candidate" should on our web site next week.

FYI, if chimera takes an hour to open a file, then it has probably 
overflowed the physical memory and is paging memory to/from the disk. 
That should be a really good reason to buy more memory for your computer 
or to buy a new one. :-)

 	Greg Couch
 	UCSF Computer Graphics Lab
 	gregc at cgl.ucsf.edu

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