Bugs item #1290941, was opened at 2005-09-14 08:18 Message generated for change (Comment added) made by migueljmol You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1290941&group_id=23629
Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: File Input/Output Group: v10 >Status: Closed >Resolution: Fixed Priority: 5 Submitted By: Rolf Huehne (rhuehne) Assigned to: Miguel (migueljmol) Summary: Unable to load file of PDB entry "1SOM" Initial Comment: Version 10.00.36 and 10.00.00 are unable to load the PDB file of PDB entry "1SOM". The error occurs independently of the method to provide the file (opened directly using the application or by specifying an URL that sends the original PDB file to the applet). The java console shows the following messages: FileManager.openFile(http://www.fli-leibniz.de/cgi-bin/idb_send.pl?CODE=1SOM) SmarterJmolAdapter:The Resolver thinks:Pdb java.lang.NullPointerException at org.jmol.adapter.smarter.AtomSetCollectionReader.parseToken(AtomSetCollectionReader.java:224) at org.jmol.adapter.smarter.PdbReader.formul(PdbReader.java:437) at org.jmol.adapter.smarter.PdbReader.readAtomSetCollection(PdbReader.java:95) at org.jmol.adapter.smarter.Resolver.resolve(Resolver.java:60) at org.jmol.adapter.smarter.SmarterJmolAdapter.openBufferedReader(SmarterJmolAdapter.java:56) at org.jmol.viewer.FileManager$FileOpenThread.openReader(FileManager.java:350) at org.jmol.viewer.FileManager$FileOpenThread.openInputStream(FileManager.java:343) at org.jmol.viewer.FileManager$FileOpenThread.run(FileManager.java:320) at org.jmol.viewer.FileManager.openFile(FileManager.java:89) at org.jmol.viewer.Viewer.openFile(Viewer.java:982) at org.jmol.viewer.Eval.load(Eval.java:1682) at org.jmol.viewer.Eval.instructionDispatchLoop(Eval.java:351) at org.jmol.viewer.Eval.script(Eval.java:1813) at org.jmol.viewer.Eval.instructionDispatchLoop(Eval.java:366) at org.jmol.viewer.Eval.run(Eval.java:291) at java.lang.Thread.run(Thread.java:534) error opening http://www.fli-leibniz.de/cgi-bin/idb_send.pl?CODE=1SOM java.lang.NullPointerException ---------------------------------------------------------------------- >Comment By: Miguel (migueljmol) Date: 2005-11-28 11:18 Message: Logged In: YES user_id=1050060 Good bug report. Problem was caused by an unusual formula entry in 1SOM.pdb FORMUL 4 DUM 10() Note that there are no elements in the formula. Jmol will now handle this without crashing. Checked in to cvs with 10.00.44 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1290941&group_id=23629 ------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
