Wayne Decatur wrote: >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? > > I don't think so. The ZAP command would be it, but it is automatically given between structure loads anyway. You can monitor the memory usage with the popup menu ABOUT Jmol submenu. The problem is generally that some installations of Java, particularly on Macs, I think, come with a default memory allocation allowance that is too small for the sort of molecule size you are working with. It's the main problem I've seen with Java across the board. Jmol pushes the limit, and crossed it in the case of this user, I think.
>Any help or insight would be appreciated as I cannot replicate these problems >on the computers I built the site on. >Thanks, >Wayne > > > > I wonder if putting the data in segments and loading only pieces at a time, with LOAD APPEND would be a smart option in this case. Some parts might not load, but at least there would be a baseline set of atoms that would be there. Just a thought. Bob Hanson > > > ____________________________________________________________________________________ >Don't let your dream ride pass you by. Make it a reality with Yahoo! Autos. >http://autos.yahoo.com/index.html > > > > >------------------------------------------------------------------------- >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 > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 ------------------------------------------------------------------------- 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
