[Jmol-developers] [ jmol-Bugs-1882603 ] 11.4.RC2 - PDB file load problems

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Bugs item #1882603, was opened at 2008-01-30 07:01
Message generated for change (Comment added) made by hansonr
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Category: None
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Rolf Huehne (rhuehne)
>Assigned to: Bob Hanson (hansonr)
Summary: 11.4.RC2 - PDB file load problems

Initial Comment:
While batch-processing all PDB entries (remediated PDB format) with Jmol for automatic image generation all parallel processes where halted by exceptions similar to this one:

Jmol Version 11.4.RC2  2007-12-20 06:37
java.vendor:Sun Microsystems Inc.
java.version:1.4.2_13
os.name:Linux
memory:6.4/6.7
appletId:
User macros dir: 
       exists: false
  isDirectory: false
FileManager opening /scratch/pdb/gz/au/pdb2cv1.ent.gz

FileManager.openFile(/scratch/pdb/gz/au/pdb2cv1.ent.gz) ///scratch/pdb/gz/au/pdb2cv1.ent.gz
FileManager opening /scratch/pdb/gz/au/pdb2cv1.ent.gz
The Resolver thinks Pdb
openFile(/scratch/pdb/gz/au/pdb2cv1.ent.gz)177 ms
ModelSet: haveSymmetry:false haveUnitcells:true haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
java.lang.ArrayIndexOutOfBoundsException: 11143
        at org.jmol.modelsetbio.AminoMonomer.isBondedCorrectly(Unknown Source)
        at org.jmol.modelsetbio.AminoMonomer.isBondedCorrectly(Unknown Source)
        at org.jmol.modelsetbio.AminoMonomer.validateAndAllocate(Unknown Source)
        at org.jmol.modelsetbio.Resolver.distinguishAndPropagateGroup(Unknown Source)
        at org.jmol.modelset.ModelLoader.distinguishAndPropagateGroup(Unknown Source)
        at org.jmol.modelset.ModelLoader.finalizeGroupBuild(Unknown Source)
        at org.jmol.modelset.ModelLoader.initializeModelSet(Unknown Source)
        at org.jmol.modelset.ModelLoader.<init>(Unknown Source)
        at org.jmol.viewer.ModelManager.setClientFile(Unknown Source)
        at org.jmol.viewer.Viewer.openClientFile(Unknown Source)
        at org.jmol.viewer.Viewer.getOpenFileError(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.runScript(Unknown Source)
        at org.jmol.viewer.ScriptManager.runNextScript(Unknown Source)
        at org.jmol.viewer.ScriptManager$ScriptQueueRunnable.run(Unknown Source)
        at java.lang.Thread.run(Thread.java:534)


I don't know how many additional entries are affected because Jmol unfortunately doesn't exit on such kinds of exceptions in batch mode but just runs indefinitely. At least the 24 following entries are affected:
2cv1, 1bei, 1jaa, 1syw, 1ebk, 1jcp, 1p1w, 1b0r, 1d5x, 1lb8, 1ee7, 1fff, 1d5m, 1fej, 1jc8, 1dw6, 1k2b, 1ida, 1fgx, 1zj7, 1k1u, 1v6d, 2fmn (biol.unit. 1), 2ci5 (biol. unit 2)

The exception is thrown directly after the load command. No additional script is involved.
The same problems also occur with Jmol 11.4.RC1 but not with Jmol 11.3.47.


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>Comment By: Bob Hanson (hansonr)
Date: 2008-01-31 09:08

Message:
Logged In: YES 
user_id=1082841
Originator: NO

The exception is due to the fact that Jmol is interpreting the N-CA-C
linkage in GAU as indicating that it is an amino acid, which it is not, and
along with that, there is a bug in the code that I have just fixed for 11.4
and 11.5.4 in the case where an (apparent) amino acid has N, CA, and C but
not O. 

GAU is still being read as an amino acid, though.
 

----------------------------------------------------------------------

Comment By: Nobody/Anonymous (nobody)
Date: 2008-01-31 08:10

Message:
Logged In: NO 

please send file scratch/pdb/gz/au/pdb2cv1.ent.gz to ha...@st...

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