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@cgl.ucsf.edu