Unfortunatley, it seems that some genius at the 'folding at home' project decided to create a new file format and give it the '.xyz' extension.
The CVS HEAD version of Jmol support this becaue Nico did the work to implement it. Miguel > what format is p2003.xyz? Not XYZ? It has numbers down the left and bonds > on the right? > > 2564 p2003_ab1-42_4mer_opls-dummy > 1 N 59.758348 96.822567 129.784012 2 509 > 511 512 > 2 H1 58.801394 96.799278 130.106173 1 > 3 CG2 65.115614 93.481274 125.277843 4 5 > 6 7 > > My version of jmolApplet doesn't read this at all, and Chime chokes as > well. > > Bob Hanson > > > SourceForge.net wrote: >> Bugs item #1192487, was opened at 2005-04-29 17:32 >> Message generated for change (Tracker Item Submitted) made by Item >> Submitter >> You can respond by visiting: >> https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1192487&group_id=23629 >> >> Category: None >> Group: None >> Status: Open >> Resolution: None >> Priority: 5 >> Submitted By: Nicolas (nicove) >> Assigned to: Nobody/Anonymous (nobody) >> Summary: NullPointerException in Monomer.scanForOffsets >> >> Initial Comment: >> I already posted the problem in the Jmol developers list. >> I don't know what to do for this problem. >> >> The file causing problem is in Jmol-web: >> fah/projects/p2003.xyz.gz >> >> FileManager.openFile(../fah/projects/p2003.xyz.gz) >> SmarterJmolAdapter:The Resolver thinks:FoldingXyz >> openFile(../fah/projects/p2003.xyz.gz) 2804 ms >> Exception in thread "Thread-14" >> java.lang.NullPointerException >> at org.jmol.viewer.Monomer.scanForOffsets >> (Monomer.java:81) >> at >> org.jmol.viewer.AminoMonomer.validateAndAllocate >> (AminoMonomer.java:46) >> at >> org.jmol.viewer.Frame.distinguishAndPropogateGroup >> (Frame.java:434) >> at org.jmol.viewer.Frame.finalizeGroupBuild >> (Frame.java:374) >> at org.jmol.viewer.Frame.<init> >> (Frame.java:192) >> at org.jmol.viewer.ModelManager.setClientFile >> (ModelManager.java:73) >> at org.jmol.viewer.Viewer.openClientFile >> (Viewer.java:1026) >> at org.jmol.viewer.Viewer.getOpenFileError1 >> (Viewer.java:999) >> at org.jmol.viewer.Viewer.getOpenFileError >> (Viewer.java:984) >> at org.jmol.viewer.Eval.load(Eval.java:1651) >> at >> org.jmol.viewer.Eval.instructionDispatchLoop >> (Eval.java:351) >> at org.jmol.viewer.Eval.run(Eval.java:291) >> at java.lang.Thread.run(Unknown Source) >> >> >> ---------------------------------------------------------------------- >> >> You can respond by visiting: >> https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1192487&group_id=23629 >> >> >> ------------------------------------------------------- >> SF.Net email is sponsored by: Tell us your software development plans! >> Take this survey and enter to win a one-year sub to SourceForge.net >> Plus IDC's 2005 look-ahead and a copy of this survey >> Click here to start! http://www.idcswdc.com/cgi-bin/survey?id=105hix >> _______________________________________________ >> Jmol-developers mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/jmol-developers > > -- > > 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 > > > > > ------------------------------------------------------- > SF.Net email is sponsored by: Tell us your software development plans! > Take this survey and enter to win a one-year sub to SourceForge.net > Plus IDC's 2005 look-ahead and a copy of this survey > Click here to start! http://www.idcswdc.com/cgi-bin/survey?id=105hix > _______________________________________________ > Jmol-developers mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-developers > > -------------------------------------------------- Michael T. Howard [EMAIL PROTECTED] 23 Algonquin Avenue tele 978-474-4559 Andover, MA 01810-5527 cell 978-886-3697 USA fax 978-662-3126 -------------------------------------------------- ------------------------------------------------------- This SF.Net email is sponsored by: NEC IT Guy Games. Get your fingers limbered up and give it your best shot. 4 great events, 4 opportunities to win big! Highest score wins.NEC IT Guy Games. Play to win an NEC 61 plasma display. Visit http://www.necitguy.com/?r _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
