Rick wrote: > Jmol-10.00 works fine for about 5k-30k atoms, but crashes when I have > more than > 33,396 atoms. (Thanks to the new renderer, viewing this number of atoms > is > quite nimble). Is the maximum number of atoms hard-coded?
There are no built-in limitations on the number of atoms. I frequently test Jmol with a full rhinovirus of 350,000 atoms > Is this a bug, or is > there a way to work around the restriction? If it isn't working then it must be a bug. > A copy of Jmol's output is below. Thanks for any assistance. [snip] > openFile(Data/relax.xyz) 1483 ms > uncaught exception: java.lang.ArrayIndexOutOfBoundsException: 64 > java.lang.ArrayIndexOutOfBoundsException: 64 > at org.jmol.viewer.Bspt$SphereIterator.hasMoreElements(Bspt.java:321) > at org.jmol.viewer.Frame.rebond(Frame.java:1100) > at org.jmol.viewer.Frame.doAutobond(Frame.java:1058) Very interesting. There seems to be some kind of problem with the 'autobonding' code. The problem seems to be caused by the distribution of the atom coordinates. I suspect that your file may have a large number of atoms with very regular coordinates ... like planes of atoms that all have the same values for the x (or y or z) coordinate. Please send me the file off-list so that I can take a look at it. Miguel ------------------------------------------------------- The SF.Net email is sponsored by: Beat the post-holiday blues Get a FREE limited edition SourceForge.net t-shirt from ThinkGeek. It's fun and FREE -- well, almost....http://www.thinkgeek.com/sfshirt _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
