Eran, you may be interested to see http://firstglance.jmol.org/bigpdb.htm
There I concluded that 99.9% of published PDB files will fit in the default java memory and display in Jmol. There may be problems with deallocating memory when you load multiple PDB files in the same browser session, especially on Apple -- I'm not sure. But you can try quitting the browser (so Java is also quit), then restarting it. I think this frees all java memory so you get a fresh start. Jaime Prilusky's PDB file size analysis server is online. From it, you can find out how many PDB files exceed a specified size, and their PDB codes. Let me know if you are interested. -Eric At 12/12/07, you wrote: >Hi All, > >I'm trying to load a multimodel PDB file into Jmol that has 30 models >with about 5000 atoms each. > >It's not an issue of file format because another similar multimodel >PDB file with 30 models but only 250 atoms each works file. > >Is this a memory problem and if so, what is the method for allocating >more memory to a Jmol applet? -- I remember reading about this once >on the mailing list but couldn't find it when searching. > >Thanks for the help. > >Best, >Eran > >------------------------------------------------------------------------- >SF.Net email is sponsored by: >Check out the new SourceForge.net Marketplace. >It's the best place to buy or sell services for >just about anything Open Source. >http://sourceforge.net/services/buy/index.php >_______________________________________________ >Jmol-users mailing list >[email protected] >https://lists.sourceforge.net/lists/listinfo/jmol-users /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Top Five 3D MolVis Technologies http://Top5.MolviZ.Org Biochem 3D Education Resources http://MolviZ.org See 3D Molecules, Install Nothing! - http://firstglance.jmol.org Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://workshops.proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://atlas.proteinexplorer.org PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List (molvis-list): http://bioinformatics.org/mailman/listinfo/molvis-list - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ------------------------------------------------------------------------- SF.Net email is sponsored by: Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
