Wonderful! Thank you very much. Brian
On Thu, Apr 28, 2011 at 10:07:52AM -0500, Robert Hanson wrote: > OK, ignore me. > > That's fixed for 12.0.42 and 12.1.45. See > http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip > > On Thu, Apr 28, 2011 at 9:42 AM, Robert Hanson <[email protected]> wrote: > > > Brian, how did you create sucrose2.spt? It is that white space -- if the > > first is from saving the script, what is the second, with the white space, > > from? You can't expect Jmol to read data statements correctly with random > > white space. That's asking too much. > > > > Bob > > > > > > On Thu, Apr 28, 2011 at 9:36 AM, Robert Hanson <[email protected]> wrote: > > > >> thanks. Blank line in the data statement. I will track that down. > >> > >> On Thu, Apr 28, 2011 at 8:56 AM, Brian McMahon <[email protected]> wrote: > >> > >>> There is an apparent bug, or at least over-sensitivity in the way Jmol > >>> reads in a state script for a small molecule which contains calculated > >>> hydrogen bonds. I attach two scripts derived from Bob's sucrose example > >>> ("load sucrose.cif {1 1 1}; hbonds calculate;"). The first is as written > >>> out > >>> by the signed applet with "Save script with state"; the second is > >>> identical > >>> except for some white-space changes (most notably the inclusion of a > >>> blank > >>> > >>> line within the data "connect_atoms" block). > >>> > >>> The first loads and renders fine; the second causes the applet to crash > >>> and the Java console shows the following error trace: > >>> > >>> Exception in thread "QueueThread0" > >>> java.lang.ArrayIndexOutOfBoundsException: 0 > >>> at org.jmol.modelset.ModelSet.connect(Unknown Source) > >>> at org.jmol.viewer.Viewer.connect(Unknown Source) > >>> at org.jmol.script.ScriptEvaluator.data(Unknown Source) > >>> at org.jmol.script.ScriptEvaluator.instructionDispatchLoop(Unknown > >>> Source) > >>> at org.jmol.script.ScriptEvaluator.runFunction(Unknown Source) > >>> at org.jmol.script.ScriptEvaluator.runFunction(Unknown Source) > >>> at org.jmol.script.ScriptEvaluator.function(Unknown Source) > >>> at org.jmol.script.ScriptEvaluator.instructionDispatchLoop(Unknown > >>> Source) > >>> at org.jmol.script.ScriptEvaluator.runFunction(Unknown Source) > >>> at org.jmol.script.ScriptEvaluator.runFunction(Unknown Source) > >>> at org.jmol.script.ScriptEvaluator.function(Unknown Source) > >>> at org.jmol.script.ScriptEvaluator.instructionDispatchLoop(Unknown > >>> Source) > >>> at org.jmol.script.ScriptEvaluator.evaluateCompiledScript(Unknown > >>> Source) > >>> at org.jmol.viewer.Viewer.evalStringWaitStatus(Unknown Source) > >>> at > >>> org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runScript(Unknown > >>> Source) > >>> at > >>> org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runNextScript(Unknown > >>> Source) > >>> at org.jmol.viewer.ScriptManager$ScriptQueueRunnable.run(Unknown > >>> Source) > >>> at java.lang.Thread.run(Unknown Source > >>> > >>> Can this be easily fixed? (The IUCr enhanced figure toolkit saves scripts > >>> is a manner that is not guaranteed to preserve whitespace.) > >>> > >>> The problem appears to have been present since at least Jmol 12.0.10, but > >>> is > >>> still present in 12.1.44. > >>> > >>> Thanks > >>> Brian > >>> > >>> > >>> ------------------------------------------------------------------------------ > >>> WhatsUp Gold - Download Free Network Management Software > >>> The most intuitive, comprehensive, and cost-effective network > >>> management toolset available today. Delivers lowest initial > >>> acquisition cost and overall TCO of any competing solution. > >>> http://p.sf.net/sfu/whatsupgold-sd > >>> _______________________________________________ > >>> Jmol-users mailing list > >>> [email protected] > >>> https://lists.sourceforge.net/lists/listinfo/jmol-users > >>> > >>> > >> > >> > >> -- > >> Robert M. Hanson > >> Professor of Chemistry > >> St. Olaf College > >> 1520 St. Olaf Ave. > >> Northfield, MN 55057 > >> http://www.stolaf.edu/people/hansonr > >> phone: 507-786-3107 > >> > >> > >> 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 > >> > > > > > > > > -- > > Robert M. Hanson > > Professor of Chemistry > > St. Olaf College > > 1520 St. Olaf Ave. > > Northfield, MN 55057 > > http://www.stolaf.edu/people/hansonr > > phone: 507-786-3107 > > > > > > 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 > > > > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr > phone: 507-786-3107 > > > 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 > ------------------------------------------------------------------------------ > WhatsUp Gold - Download Free Network Management Software > The most intuitive, comprehensive, and cost-effective network > management toolset available today. Delivers lowest initial > acquisition cost and overall TCO of any competing solution. > http://p.sf.net/sfu/whatsupgold-sd > _______________________________________________ > Jmol-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users ------------------------------------------------------------------------------ WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
