somehow that build did not get done properly on the JavaScript side. Looks to me that it is specific to the JSmol in that the Java application itself has no problem.
So I will re-release that. On Mon, Nov 2, 2015 at 4:36 AM, <si...@publcif.co.uk> wrote: > I'm afraid I'm still seeing problems with the mmcif reader: > > Jmol Version: 14.4.0_2015.10.22b 2015-10-22 13:25 > > FileManager.getAtomSetCollectionFromFile( > http://www.rcsb.org/pdb/files/4jdg.cif) > FileManager opening url http://www.rcsb.org/pdb/files/4jdg.cif > The Resolver thinks MMCif > loadClass J.adapter.readers.cif.MMCifReader > TITLE: Plant nuclease TBN1 involved in apoptotic processes blocks its > active site by a surface loop > > Setting space group name to HM:H 3 > Reader error: TypeError: this.getField(...) is undefined > Time for openFile(http://www.rcsb.org/pdb/files/4jdg.cif): 817 ms > File Error:Error reading file at line 521: > loop_ > this.getField(...) is undefined > 0 function () > 1 J.adapter.smarter.AtomSetCollectionReader.setError(a) > 2 J.adapter.smarter.AtomSetCollectionReader.readData() > 3 J.adapter.smarter.SmarterJmolAdapter.staticGetAtomSetCollection(a) > 4 J.adapter.smarter.SmarterJmolAdapter.getAtomSetCollection(a) > 5 J.io.FileReader.run() > 6 JV.FileManager.createAtomSetCollectionFromFile(a,c,b) > 7 JV.Viewer.openFileFull(a,c,b,e) > 8 JV.Viewer.loadModelFromFile(a,c,b,e,f,g,h,k,m,l) > 9 JS.ScriptEval.cmdLoad() > 10 JS.ScriptEval.processCommand(a) > 11 JS.ScriptEval.commandLoop(a) > 12 JS.ScriptEval.dispatchCommands(a,b,c) > 13 JS.ScriptEval.executeCommands(a,b) > 14 JS.ScriptEval.evaluateCompiledScript(a,b,c,e,f,p) > 15 JS.ScriptManager.evalStringWaitStatusQueued(a,b,c,e,f) > 16 JV.Viewer.evalStringWaitStatusQueued(a,c,b,e,f) > 17 JS.ScriptQueueThread.runNextScript() > 18 JS.ScriptQueueThread.run1(a) > 19 J.thread.JmolThread.run() > 20 start() > 21 function () > 22 JS.ScriptManager.startScriptQueue(a) > 23 JS.ScriptManager.addScr(a,b,c,e) > 24 JS.ScriptManager.addScript(a,b) > > for file http://www.rcsb.org/pdb/files/4jdg.cif > type MMCif > > Example at: http://www.publcif.co.uk/jmol-14.4.0/jsmol/mmcif_test.htm?4jdg > > Cheers > > Simon > > Quoting Robert Hanson <hans...@stolaf.edu>: > > > Sorry -- yes, definitely. That link should now be to "2015.10.22b" > > > > On Thu, Oct 29, 2015 at 9:53 AM, <si...@publcif.co.uk> wrote: > > > >> Hi Bob > >> > >> Has this been fixed yet? > >> > >> Cheers > >> > >> Simon > >> > >> > >> Quoting Robert Hanson <hans...@stolaf.edu>: > >> > >> > that bug did not get fixed for JavaScript, unfortunately. Will update > >> later > >> > tonight. > >> > > >> > On Thu, Oct 22, 2015 at 7:41 AM, Robert Hanson <hans...@stolaf.edu> > >> wrote: > >> > > >> >> Jmol.___JmolVersion="14.5.0_2015.10.22" > >> >> > >> >> bug fix: CIF parser fails to read CIF files containing only a single > >> >> (non-loop) _struct_ref_seq_dif.align_id > >> >> > >> >> https://sourceforge.net/projects/jmol/files/latest/download > >> >> > >> >> This update is probably only important if you use Jmol in a database > >> that > >> >> reads MMCIF files. Certain files (2mvv, for example) will not load, > and > >> >> others with only one _struct_conn entry will not make that bond. > >> >> > >> >> 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 > >> >> > >> >> > >> > > >> > > >> > -- > >> > 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 > >> > > > > > > > > -- > > 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 > -- 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
