Hello, I have been using Jmol v11.8.13 since December with no issues. Yesterday I tried updating to v11.8.21 and now I have an issue that prevents me from displaying the unit cell of a structure loaded from a Mol2 file. Nothing else has changed.
Here is the Java console error output I now get: ---- FileManager.getAtomSetCollectionFromFile(http://frog/temp/ABENAX.mol2) //http://frog/temp/ABENAX.mol2 FileManager opening http://frog/temp/ABENAX.mol2 The Resolver thinks Mol2 java.lang.ArrayIndexOutOfBoundsException: 2 at org.jmol.symmetry.SpaceGroup.buildSpaceGroup(Unknown Source) at org.jmol.symmetry.SpaceGroup.<init>(Unknown Source) at org.jmol.symmetry.SpaceGroup.createSpaceGroup(Unknown Source) at org.jmol.symmetry.SpaceGroup.createSpaceGroup(Unknown Source) at org.jmol.symmetry.Symmetry.createSpaceGroup(Unknown Source) at org.jmol.adapter.smarter.AtomSetCollectionReader.applySymmetryAndSetTrajectory(Unknown Source) at org.jmol.adapter.readers.more.Mol2Reader.processMolecule(Unknown Source) at org.jmol.adapter.readers.more.Mol2Reader.readAtomSetCollection(Unknown Source) at org.jmol.adapter.smarter.AtomSetCollectionReader.readData(Unknown Source) at org.jmol.adapter.smarter.Resolver.getAtomCollectionAndCloseReader(Unknown Source) at org.jmol.adapter.smarter.SmarterJmolAdapter.staticGetAtomSetCollectionFromReader(Unknown Source) at org.jmol.adapter.smarter.SmarterJmolAdapter.getAtomSetCollectionFromReader(Unknown Source) at org.jmol.viewer.FileManager$FileReaderThread.createAtomSetCollection(Unknown Source) at org.jmol.viewer.FileManager$FileReaderThread.run(Unknown Source) at org.jmol.viewer.FileManager.createAtomSetCollectionFromFile(Unknown Source) at org.jmol.viewer.Viewer.openFile(Unknown Source) at org.jmol.viewer.ScriptEvaluator.load(Unknown Source) at org.jmol.viewer.ScriptEvaluator.instructionDispatchLoop(Unknown Source) at org.jmol.viewer.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) file ERROR: http://frog/temp/ABENAX.mol2 Unexpected end of file after line 60: 8.4590 16.9420 6.6832 90.0000 96.9290 90.0000 14 1 for file http://frog/temp/ABENAX.mol2 type mol2 openFile(http://frog/temp/ABENAX.mol2): 62 ms eval ERROR: Unexpected end of file after line 60: 8.4590 16.9420 6.6832 90.0000 96.9290 90.0000 14 1 for file http://frog/temp/ABENAX.mol2 type mol2 ---- load "" { 1 1 1 } spaceGroup "x,y,z;x,1/2-y,1/2+z;-x,-y,-z;-x,1/2+y,1/2-z" unitcell { 8.459 16.942 6.6832 90 96.929 90 >> } << ---- I have attached the Mol2 file in question to this email for reference. This error now happens for every single Mol2 file I try, so I don't think there is anything special about this particular structure/file. I should point out that just loading the file into Jmol without displaying the unit cell still works fine as before. In addition, I have just tried exactly the same tests using the latest Jmol v11.9.33 and that works fine in every way including displaying the unit cell. Does anyone know what has changed between v11.8.13 and v11.8.21 that might explain this problem? Is this likely to be resolved on the v11.8.* branch, or do I need to move over to the new v11.9.* branch straight away to avoid this issue? How long will it be until v11.9.* becomes the official release branch? Thanks in advance for your help, Ian Thomas -- Ian Thomas Senior Scientific Software Engineer CCDC LEGAL NOTICE Unless expressly stated otherwise, information contained in t his message is confidential. If this message is not intended for you, please inform [email protected] and delete the message. The Cambridge Crys tallographic Data Centre is a company Limited by Guarantee and a Registered Charity. Registered in England No. 2155347 Registered Charity No. 800579 Reg istered office 12 Union Road, Cambridge CB2 1EZ.
ABENAX.mol2
Description: ABENAX.mol2
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