> RE: Jmol Tutorial-Authoring Template (JTAT), nearing release (I hope). > Near final demo at http://bioinformatics.org/jmol-tutorials > > There is a major unresolved problem which calls into question the > usability of tutorials using Jmol, and JTAT in particular: running > out of java memory.
Eric, I think you will have to consider the strategy taken by others -- perhaps pop-up windows that can be closed. One way to do this is to put a static picture in a div and then click on that to activate a pop-up window. Or, alternatively, use code to deactivate applet divs that are not in use. It will take some thinking and experimentation to get this right. I think there is no direct Chime-->Jmol solution, specifically because of the known memory issues. You can save loads of memory just by using ZAP when a model's use is over. Another idea would be to make sure that on page loading the applets are NOT loading full models. This is very inefficient of resources. > > Suggestions are welcome: How does one force java to flush its memory? Java does this automatically, as needed. Don't go there. Basically, get rid of unnecessary memory-consuming objects, especially large molecular systems, cartoons, isosurfaces, etc. > Since Jmol can report memory used, I suppose it can message that > somehow. Would it be possible to force the java memory flush FROM > JAVASCRIPT when it becomes critical? Or better yet, from within Jmol > itself, when it detects that memory is running out? > There is nothing to do but take care in how many objects you have live at one time. Java will take care of the rest. I have taken great pains to make sure that Jmol does not persist with objects that you think are gone. If they are gone, they are gone. > JTAT's design may make unnecessary demands on java memory: currently > it restarts Jmol between chapters, even when the same molecule is > used in both chapters. (This design, making each chapter independent > of the others, greatly simplified the internal structure.) Keeping > the same Jmol loaded between chapters would require major redesign of > JTAT, and a more complicated internal structure. And it would only > solve part of the problem. Using different PDB files in the same > tutorial, and making comparisons side by side, will still be > demanding on the memory limits. It isn't much of a load to add applets, only models. More later... Bob > > The fact that IE7 works gives some hope that the java memory bug will > eventually be solved without any changes in JTAT or Jmol. Apple java > lags behind java development at Sun. It is currently at 1.5.0_13 vs. > 1.6.0_3 on Windows. That may be part of the Safari problem. But I am > mystified that in Windows, Firefox, using the same java as IE7, runs > out of memory, while IE7 doesn't. > > In one test, IE6 did run out of memory, but lasted through the > present 5 chapters before doing so. So it did better than Firefox, > but not as well as IE7. > > I bring this up because you may want to give it consideration when > you assign priorities to developing complex tutorials. The future is > uncertain! > > -Eric > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Jmol-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users > ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
