Bugs item #1450367, was opened at 2006-03-15 13:21
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Category: File Input/Output
Group: None
Status: Open
Resolution: None
Priority: 5
Submitted By: Rolf Huehne (rhuehne)
Assigned to: Miguel (migueljmol)
Summary: PDB reader - formula error
Initial Comment:
The RCSB supplies 'Biological Unit' PDB files for all
PDB entries at its new FTP site. Jmol
(V.10.00.36,10.00.48) has a problem reading at least
749 of them.
After investigation the problem narrowed down to the
'FORMUL' lines of these files:
If there is no formula present in this line, Jmol
aborts loading with the error message shown below.
Example: entry 1p84
--- Asymmetric Unit File ---
FORMUL 18 3PE 2(C41 H82 N1 O8 P1)
FORMUL 20 3PH 2(C39 H76 O8 P1 1-)
FORMUL 22 PC1 C44 H88 N1 O8 P1
--- Biological Unit File 1 ---
FORMUL 18 3PE
FORMUL 20 3PH
FORMUL 22 PC1
Substituting those lines is sufficient to enable Jmol
to load the file.
--- Java Console Error Message ---
FileManager.openFile(http://www.fli-leibniz.de/cgi-bin/idb_send.pl?CODE=1P84&MODE=biological1)
SmarterJmolAdapter:The Resolver thinks:Pdb
java.lang.NullPointerException
at
org.jmol.adapter.smarter.PdbReader.formul(PdbReader.java:423)
at
org.jmol.adapter.smarter.PdbReader.readAtomSetCollection(PdbReader.java:94)
at
org.jmol.adapter.smarter.Resolver.resolve(Resolver.java:59)
at
org.jmol.adapter.smarter.SmarterJmolAdapter.openBufferedReader(SmarterJmolAdapter.java:55)
at
org.jmol.viewer.FileManager$FileOpenThread.openReader(FileManager.java:405)
at
org.jmol.viewer.FileManager$FileOpenThread.openInputStream(FileManager.java:398)
at
org.jmol.viewer.FileManager$FileOpenThread.run(FileManager.java:375)
at
org.jmol.viewer.FileManager.openFile(FileManager.java:90)
at org.jmol.viewer.Viewer.openFile(Viewer.java:986)
at org.jmol.viewer.Eval.load(Eval.java:1690)
at
org.jmol.viewer.Eval.instructionDispatchLoop(Eval.java:354)
at org.jmol.viewer.Eval.run(Eval.java:294)
at java.lang.Thread.run(Thread.java:534)
error opening
http://www.fli-leibniz.de/cgi-bin/idb_send.pl?CODE=1P84&MODE=biological1
java.lang.NullPointerException
openFile(http://www.fli-leibniz.de/cgi-bin/idb_send.pl?CODE=1P84&MODE=biological1)
1057 ms
--- Java Version ---
Java(TM) Plug-in: Version 1.4.2_10
Using JRE version 1.4.2_10 Java HotSpot(TM) Client VM
----------------------------------------------------------------------
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