This is incorporated into the latest version of Jmol, uploading now. On Fri, Oct 16, 2015 at 12:01 PM, <si...@publcif.co.uk> wrote:
> I think I have found a possible bug in the polyhedra command. > > By way of example, if I load this CIF at chemapps: > > > http://chemapps.stolaf.edu/jmol/jmol.php?source=http://scripts.iucr.org/cgi-bin/sendcif?hb0009 > > and try > > polyhedra BONDS {aluminium} > > I get > > script ERROR: TypeError: a.equals is not a function > J.shapespecial.Polyhedra set generate > > Whereas doing the same with previous versions of Jmol worked. > > Cheers > > Simon > > Quoting si...@publcif.co.uk: > > > Otis: > > > > In my case its the "alert where Jmol formerly died without alert" > > problem you describe. > > > > I can live with alerts for failing scripts (i.e. they shouldn't fail > > in the first place if I do my job properly), > > but it is now clear that its not just one of my scripts that is > > failing with Jmol 14.4 (though they worked with previous versions). > > > > Looks like it may take some time to identify exactly where the > > problems are... > > > > Thanks for the info anyway. > > > > Cheers > > > > Simon > > > > > > Quoting Otis Rothenberger <osrot...@chemagic.com>: > > > >> Simon, > >> > >> I was seeing this where the script WAS completing after the alert > >> box was dismissed. Bob correctly pointed out that I was running some > >> Bootstrap related scripts that imposed JavaScript ?use strict.? When > >> I removed this from the Bootstrap related scripts, the problem > >> disappeared. > >> > >> However, like you, I continue to see these alert boxes where the > >> script has an error where previous versions of Jmol would have died > >> without the alert. One example of this is the following: > >> > >> Jmol.evaluateVar(jmolApplet0, "'hexane'.find('SMILES','CCC') > 0?) > >> > >> I know the script is ridiculous, but it happened because of an > >> answer key error. Earlier versions of Jmol did not throw an error > >> alert with this script. > >> > >> To summarize, I was seeing two problems - one seems to be corrected > >> by editing ?use strict? out of my Bootstrap .js files. The other > >> problem, alert where Jmol formerly died without alert, seems to > >> remain. > >> > >> Otis > >> > >> -- > >> Otis Rothenberger > >> o...@chemagic.com > >> http://chemagic.com > >> > >>> On Oct 16, 2015, at 7:12 AM, si...@publcif.co.uk wrote: > >>> > >>> Just installed this. > >>> > >>> For some of my pages I now get alerts boxes popping up saying: > >>> > >>> TypeError: a.equals is not a function try/catch path: > >>> 0 function (b,d) > >>> args[0]=TypeError: a.equals is not a function > >>> args[1]=function (){a.instantialize(this,arguments)} > >>> 1 JS.ScriptEval.executeCommands(a,b) > >>> args[0]=false > >>> args[1]=true > >>> 2 JS.ScriptEval.resumeEval(a) > >>> args[0]=[JS.ScriptContext object] > >>> 3 function () > >>> > >>> This occurs when running a script that renders polyhedra. > >>> > >>> Apart from the fact that a script that has worked for years now > >>> seems to fail, > >>> why does an alert box popup rather than just the messages being > >>> written to the console? > >>> > >>> Do I need to set something to turn off alerts in this version of Jmol? > >>> > >>> I'll try to figure out exactly what causes the script to fail, but in > >>> the meantime any help with preventing the alert boxes would be > >>> appreciated. > >>> > >>> Thanks > >>> > >>> Simon Westrip > >>> > >>> > >>> > >>> > >>> > >>> Quoting Robert Hanson <hans...@stolaf.edu>: > >>> > >>>> I have recompiled Jmol 14.4.0 with a newly signed certificate. > >>>> > >>>> This is important only if your site uses the Jmol Java applet. > >>>> > >>>> This applet will not work again until this update is installed. Your > >>>> current applet will fail indicating that its certificate has been > revoked. > >>>> This fixes that issue. If you want, you may be able to just extract > the > >>>> jsmol/java directory from Jmol.zip and copy the JAR files to your > site to > >>>> the same directory. But I recommend you upload the entire package. > >>>> > >>>> You can see proper operation of the Java applet at > >>>> > >>>> http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=SIGNED > >>>> > >>>> I am very sorry for this inconvenience. > >>>> > >>>> Bob > >>>> > >>>> -- > >>>> Robert M. Hanson > >>>> Larson-Anderson Professor of Chemistry > >>>> Chair, Department 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 > >>>> > >>> > >>> > >>> > >>> > ------------------------------------------------------------------------------ > >>> _______________________________________________ > >>> Jmol-users mailing list > >>> Jmol-users@lists.sourceforge.net > >>> https://lists.sourceforge.net/lists/listinfo/jmol-users > >>> > >>> > >> > >> > >> > >> > >> > ------------------------------------------------------------------------------ > >> _______________________________________________ > >> Jmol-users mailing list > >> Jmol-users@lists.sourceforge.net > >> https://lists.sourceforge.net/lists/listinfo/jmol-users > >> > > > > > > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > > Jmol-users mailing list > > Jmol-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > > > ------------------------------------------------------------------------------ > _______________________________________________ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Department 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
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