yes, Jmol 11.8.21 bug doesn't allow SPACEGROUP designation in LOAD command.
Fixed for 11.8.22; not a problem for 11.9 -- consider using that for now
until 11.8.22 is released next week (probably).
Bob
On Thu, Mar 18, 2010 at 11:27 AM, Ian Thomas <[email protected]> wrote:
> 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
>
>
>
>
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