Quoting Wayne Decatur <[EMAIL PROTECTED]>: > Hi, > I was wondering if anyone else has experienced problems with using > multiple large structures at a site in implementations of Jmol where > you might view multiple structures in a single browsing session? We > have set up a database > (http://people.biochem.umass.edu/fournierlab/3dmodmap/main.php) that > uses several rather large structure files because it deals with the > ribosome. All files are gzipped to minimize load time but a > reviewer of the manuscript describing the database complained about > load time when he switched from using a lower resolution 5.5 > angstrom model > (http://people.biochem.umass.edu/fournierlab/3dmodmap/ec3dmodsribo55/index.htm) > to a higher resolution 2.8 angstrom structure > (http://people.biochem.umass.edu/fournierlab/3dmodmap/ec3dmodsribo28/index.htm). > Actually he said only the 2.8 angstrom one never loaded even after multiple > attempts. There are some other higher resolution ribosome structures at the > site as > well > > (http://people.biochem.umass.edu/fournierlab/3dmodmap/ec3dmodsriboem/index.htm > or > http://people.biochem.umass.edu/fournierlab/3dmodmap/ec3dmodsriboem/index.htm) > if looking for other structures to > test > Perhaps there is some Jmol or Java 'reset' command I should be using > when switching between multiple large structures in a single > browsing session? > Any help or insight would be appreciated as I cannot replicate these > problems on the computers I built the site on. > Thanks, > Wayne >
I observed the same problem as the reviewer on my laptop with WinXP and Java 1.6.0: I could load the 5.5 Angstrom structure but when I tried the 2.8 Angstrom structure afterwards I got an out of memory error. And it didn't help to close the low resolution viewer. The other way around it worked (after restarting the browser): I could load the high resolution structure first and then open the low resolution structure additionally. I think one problem is that the default memory available was 128 MB a while ago (as far as I remember) and now was reduced to only 95 MB. The other problem is that Jmol seems to need initially more memory than after loading is finished. This makes it difficult to estimate the real memory requirements for loading a structure. This is illustrated by the free memory size that Jmol reported on my laptop after both structures were loaded succesfully in different windows: 45 MB. Therefore I think that Bob's suggestion of splitting up the structure and loading it in several portions might help. Regards, Rolf ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
