> This file loads fine with the current code in the Jmol > application. > > Q: Can you update the applet to the current Jmol-HEAD and > see if it still has this problem? > > > Miguel >
Still a problem with 10pre23:
Jmol Version 10pre23 2004/12/10 17:45 java.vendor:Sun Microsystems Inc. java.version:1.4.2_05 os.name:Windows 2000
appletDocumentBase=http://www.stolaf.edu/people/hansonr/jmol/docs/examples/animation.htm
setting color scheme to:jmol
FileManager.openFile(movie.pdb)
SmarterJmolAdapter:The Resolver thinks:Pdb
java.lang.StringIndexOutOfBoundsException: String index out of range: 16
at java.lang.String.charAt(Unknown Source)
at org.jmol.adapter.smarter.PdbReader.atom(PdbReader.java:119)
at org.jmol.adapter.smarter.PdbReader.readAtomSetCollection(PdbReader.java:57)
at org.jmol.adapter.smarter.Resolver.resolve(Resolver.java:57)
at org.jmol.adapter.smarter.SmarterJmolAdapter.openBufferedReader(SmarterJmolAdapter.java:62)
at org.jmol.viewer.FileManager$FileOpenThread.openReader(FileManager.java:435)
at org.jmol.viewer.FileManager$FileOpenThread.openInputStream(FileManager.java:428)
at org.jmol.viewer.FileManager$FileOpenThread.run(FileManager.java:405)
at org.jmol.viewer.FileManager.openFile(FileManager.java:97)
at org.jmol.viewer.Viewer.openFile(Viewer.java:955)
at org.jmol.viewer.Eval.load(Eval.java:1636)
at org.jmol.viewer.Eval.instructionDispatchLoop(Eval.java:349)
at org.jmol.viewer.Eval.run(Eval.java:289)
at java.lang.Thread.run(Unknown Source)
error opening http://www.stolaf.edu/people/hansonr/jmol/docs/examples/movie.pdb
java.lang.StringIndexOutOfBoundsException: String index out of range: 16
openFile(movie.pdb) 331 ms
SourceForge.net wrote:
Bugs item #1055462, was opened at 2004-10-27 13:25
Message generated for change (Comment added) made by migueljmol
You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1055462&group_id=23629
Category: File Input/Output Group: None
Status: Closed Resolution: Invalid
Priority: 5 Submitted By: Bob Hanson (hansonr) Assigned to: Miguel (migueljmol) Summary: 10pre16 fails to load multimodel movie.pdb
Initial Comment: 10pre16 is refusing to load movie.pdb at http://www.stolaf.edu/people/hansonr/jmol/docs/examples/animation.htm
error:
Java(TM) Plug-in: Version 1.4.1_02 Using JRE version 1.4.1_02 Java HotSpot(TM) Client VM jmol will try to run: -----set echo top left;font echo 14;echo " load movie.pdb;cartoons on;trace on;wireframe off;cpk off";load movie.pdb;cartoons on;trace on;wireframe off;cpk off;set echo bottom left;font echo 16;echo " " -----
setting:echo
notifyFrameChanged(0)
animationReplayMode=0
FileManager.openFile(movie.pdb)
SmarterModelAdapter:The model resolver thinks:Pdb
java.lang.StringIndexOutOfBoundsException: String index out of range: 16
at java.lang.String.charAt(Unknown Source)
at org.jmol.adapter.smarter.PdbReader.atom(PdbReader.java:135)
at org.jmol.adapter.smarter.PdbReader.readModel(PdbReader.java:60)
at org.jmol.adapter.smarter.ModelResolver.resolveModel(ModelResolver.java:57)
at org.jmol.adapter.smarter.SmarterModelAdapter.openBufferedReader(SmarterModelAdapter.java:55)
at org.openscience.jmol.viewer.managers.FileManager$FileOpenThread.openReader(FileManager.java:409)
at org.openscience.jmol.viewer.managers.FileManager$FileOpenThread.openInputStream(FileManager.java:402)
at org.openscience.jmol.viewer.managers.FileManager$FileOpenThread.run(FileManager.java:379)
at org.openscience.jmol.viewer.managers.FileManager.openFile(FileManager.java:100)
at org.openscience.jmol.viewer.JmolViewer.openFile(JmolViewer.java:945)
at org.openscience.jmol.viewer.script.Eval.load(Eval.java:1606)
at org.openscience.jmol.viewer.script.Eval.instructionDispatchLoop(Eval.java:348)
at org.openscience.jmol.viewer.script.Eval.run(Eval.java:290)
at java.lang.Thread.run(Unknown Source)
error opening http://www.stolaf.edu/people/hansonr/jmol/docs/examples/movie.pdb java.lang.StringIndexOutOfBoundsException: String index out of range: 16
openFile(movie.pdb) 1122 ms
-------------------------------
Note that 10pre13 works just fine.
Bob
----------------------------------------------------------------------
Comment By: Miguel (migueljmol)
Date: 2004-12-13 10:59
Message:
Logged In: YES user_id=1050060
Running gunzip on movie.pdb generates an error:
I renamed movie.pdb to movie.pdb.gz in order to unzip it.
[EMAIL PROTECTED] rhanson]$ gunzip movie.pdb.gz
gunzip: movie.pdb.gz: invalid compressed data--crc error
gunzip: movie.pdb.gz: invalid compressed data--length error
[EMAIL PROTECTED] rhanson]$
----------------------------------------------------------------------
Comment By: Miguel (migueljmol) Date: 2004-11-03 10:26
Message:
Logged In: YES user_id=1050060
This file loads fine with the current code in the Jmol
application.
Q: Can you update the applet to the current Jmol-HEAD and
see if it still has this problem?
Miguel
----------------------------------------------------------------------
You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1055462&group_id=23629
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--
Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:[EMAIL PROTECTED] http://www.stolaf.edu/people/hansonr
"Imagination is more important than knowledge." - Albert Einstein
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Read honest & candid reviews on hundreds of IT Products from real users.
Discover which products truly live up to the hype. Start reading now. http://productguide.itmanagersjournal.com/
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