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
