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. In designing JTAT, my assumption was that a tutorial could show several different PDB files, many views each, and even compare 2, 3, or 4 molecules/views. This is what we could do in Chime. But it contrasts with most Jmol sites I've seen (including FirstGlance in Jmol) where one typically views mostly a single PDB file. JTAT tends to run out of java memory. The symptom is failure of the molecule to appear. You can predict when it is about to happen: on the Jmol menu, under About Jmol, it happens around the time "total" memory usage equals "maximum" memory usage. The JTAT Demo now has content in 6 of the 7 planned chapters. In Internet Explorer 7, using current java (1.6.0_03), I can view all molecular views in all 6 chapters, and then start over again and keep going. It appears that the combination of IE7 and current java have solved the problem, which is basically a bug that fails to free up memory when it is no longer needed. Firefox on Windows and Safari on OSX usually run out of memory about half way through the JTAT Demo. The only workaround I know about is to quit the browser (which quits java), restart the browser, and continue from where you left off. Clearly this is unsatisfactory. So I'll be conducting further tests, reporting the results, and discussing this more on jmol-users. Issues to be tested include using JmolApplet.jar (single file, as I am now doing) vs. the multiple applet .jar files, and whether I get the same memory issues with the simplest possible Jmol page vs. JTAT (rather complicated); and whether reloading an empty Jmol uses up memory, or only a "full" one containing a molecule. It is possible to increase the memory allocated to java from the default 100 megabytes, but doing it is rather fussy, and depending on users to do this will certainly eliminate the majority of potential users (just as the need to install the Chime plugin did for Chime tutorials). Suggestions are welcome: How does one force java to flush its memory? 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? 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. 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
