Bugs item #2573313, was opened at 2009-02-06 16:59
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Category: File Input/Output
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Rolf Huehne (rhuehne)
Assigned to: Miguel (migueljmol)
Summary: ANISOU records block load filter
Initial Comment:
In the latest SVN build (revision 10621) and also in version 11.6.8 there seems
to be a problem with the load filter option if ANISOU records are present in
the PDB file. I got the following error messages after trying to load a number
of PDB files with ANISOU records like 2ODK:
load pdb2odk.ent.gz FILTER "*.CA";
filtering with ;*.CA;
biomolecule 1: number of transforms: 1
biomolecule 2: number of transforms: 1
java.lang.NullPointerException
at org.jmol.adapter.readers.cifpdb.PdbReader.anisou(Unknown Source)
at
org.jmol.adapter.readers.cifpdb.PdbReader.readAtomSetCollection(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.Eval.load(Unknown Source)
at org.jmol.viewer.Eval.instructionDispatchLoop(Unknown Source)
at org.jmol.viewer.Eval.runEval(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(Thread.java:534)
file ERROR: pdb2odk.ent.gz
Error reading file at line 595:
ANISOU 1 N MSE A 1 4166 4306 4342 -188 -102 -122 N
null
for file pdb2odk.ent.gz
type pdb
openFile(pdb2odk.ent.gz): 671 ms
eval ERROR: Error reading file at line 595:
ANISOU 1 N MSE A 1 4166 4306 4342 -188 -102 -122 N
null
for file pdb2odk.ent.gz
type pdb
----
load "pdb2odk.ent.gz" filter >> "*.CA" <<
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