Bugs item #3168380, was opened at 2011-01-30 14:03
Message generated for change (Settings changed) made by hansonr
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Category: File Input/Output
Group: None
>Status: Closed
Resolution: Fixed
Priority: 5
Private: No
Submitted By: Simon Westrip (publcif)
Assigned to: Bob Hanson (hansonr)
Summary: 12.1.xx prereleases not reading multi-model CIFs
Initial Comment:
Current prerelease versions are failing to read CIFs that contain more than one
structure:
java.lang.NullPointerException
at org.jmol.adapter.readers.cifpdb.CifReader.createBonds(Unknown Source)
at
org.jmol.adapter.readers.cifpdb.CifReader.setBondingAndMolecules(Unknown Source)
at
org.jmol.adapter.readers.cifpdb.CifReader.applySymmetryAndSetTrajectory(Unknown
Source)
at org.jmol.adapter.readers.cifpdb.CifReader.initializeReader(Unknown
Source)
at org.jmol.adapter.smarter.AtomSetCollectionReader.readData(Unknown
Source)
at
org.jmol.adapter.smarter.SmarterJmolAdapter.getAtomSetCollection(Unknown Source)
at org.jmol.viewer.FileManager$FileReader.run(Unknown Source)
at org.jmol.viewer.FileManager.createAtomSetCollectionFromFile(Unknown
Source)
at org.jmol.viewer.Viewer.getAtomSetCollection(Unknown Source)
at org.jmol.viewer.Viewer.loadModelFromFile(Unknown Source)
at org.jmol.script.ScriptEvaluator.load(Unknown Source)
at org.jmol.script.ScriptEvaluator.instructionDispatchLoop(Unknown
Source)
at org.jmol.script.ScriptEvaluator.evaluateCompiledScript(Unknown
Source)
at org.jmol.viewer.Viewer.evalStringWaitStatus(Unknown Source)
at org.jmol.viewer.ScriptManager$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)
----------------------------------------------------------------------
Comment By: Simon Westrip (publcif)
Date: 2011-01-31 11:18
Message:
Thank you for such a swift response (especially as it only affected
pre-releases).
----------------------------------------------------------------------
Comment By: Bob Hanson (hansonr)
Date: 2011-01-31 04:33
Message:
OK, I found it. Affects 12.1 only, not 12.0. Fixed for Jmol 12.1.33 --- see
http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
----------------------------------------------------------------------
Comment By: Bob Hanson (hansonr)
Date: 2011-01-30 20:17
Message:
I'll need an example file; the ones I have work fine.
----------------------------------------------------------------------
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3168380&group_id=23629
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