It's a separate thread, so you can do odd things, like rotate the model while it is minimizing. --- or even set it spinning, I think! I'm thinking what we need is some sort of a minimization callback so that the user can get messages as the model updates. Then we also need to be setting variables like
_minimizationEnergy _minimizationEnergyDifference _minimizationCurrentStep _minimizationStatus something like that, so we can use those programmatically. The callback, as all callbacks, could be to JavaScript or to a Jmol script, which might for instance just update an echo text. I'm also thinking about setting it up so you can get the output normally going to the Logger -- detailed position, angle, torsion vdw information, etc. -- if those are desired. Might as well make it full featured! One other thing I would like to implement is the option to use one's own parameter file. The UFF method is so simple, and some customization might be appropriate. I did try this with the 2D model that Kriangsak sent us, but that one needed some preliminary crude setting of stereochemistry before it would minimize correctly -- which it almost did, except for one inversion of a stereocenter. But, hey, there were no hydrogens! Bob Angel Herráez wrote: > Wonderful, Bob! > > The newest applet is working very well. > > Something funny but very sound: > go to > http://biomodel/Jmol/minimize/minimize.htm > Load the 2D caffeine, then click minimize several times until it > stabilizes; note the sp3 nitrogens > Now click on "recalculate aromaticity" and repeat several > minimizations; the N come now sp2. Great! Jmol really knows how! > > For thyroxine it works pretty well on the first go, better after more > minimization cycles. > > Tripalmitine takes time, but is working much better too (some of the > hydrogen pairs in each methylene group tend to stay together for a > while). > > A message in the console when minimization has ended would be useful. > And how about a clock cursor while it is running (as happens for > isosurface calculation) - I can see it running in the CPU monitor, as > with isosurfaces. > > > This is very exciting! > > >------------------------------------------------------------------------ > >------------------------------------------------------------------------- >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-developers mailing list >Jmol-developers@lists.sourceforge.net >https://lists.sourceforge.net/lists/listinfo/jmol-developers > > -- 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 ------------------------------------------------------------------------- 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-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
