got it -- but it loads just fine for me. You sure you are using 13.0.12 or
13.0.13?
On Sun, Jan 27, 2013 at 2:45 AM, Gutow, Jonathan H <gu...@uwosh.edu> wrote:
> I may have found the issue. The application is happy to load a file that
> is only built from surfaces and does not contain any atoms. However, if I
> launch JmolData.jar it appears to be looking for a file containing atoms in
> the directory I launched it in. I got the following error by launching
> JmolData.jar with only the -J SCRIPT option.
>
> chemistrymac08:sage0-size500-359165447.jmol gutow$ java -Xmx512m -jar
> $JMOLPATH -J $LAUNCHSCRIPT
> JmolData using command options ["-J", "load",
> "file:/Users/gutow/Desktop/BBtickplacement.jmol.png"]
> Add -n (NOGRAPHICS) for faster performance if you are not creating images.
> (C) 2012 Jmol Development
> Jmol Version: 13.1.12 2013-01-23 21:58
> java.vendor: Oracle Corporation
> java.version: 1.7.0_11
> os.name: Mac OS X
> Access: ALL
> memory: 13.6/88.2
> processors available: 2
> useCommandThread: false
> Executing script: load
> "file:/Users/gutow/Desktop/BBtickplacement.jmol.png";load
> FileManager opening file:/Users/gutow/Desktop/BBtickplacement.jmol.png
> FileManager opening
> file:/Users/gutow/Desktop/BBtickplacement.jmol.png|JmolManifest.txt
> FileManager opening file:/Users/gutow/Desktop/BBtickplacement.jmol.png
> FileManager opening
> file:/Users/gutow/Desktop/BBtickplacement.jmol.png|state.spt
> FileManager opening file:/Users/gutow/Desktop/BBtickplacement.jmol.png
> ColorManager: color "roygb" range 0.0 0.0
> isosurface ID "testpmesh" select ({}) pmesh
> /*file*/"file:/Users/gutow/Desktop/BBtickplacement.jmol.png|obj_102506.pmesh";
> reading isosurface data from
> file:/Users/gutow/Desktop/BBtickplacement.jmol.png|obj_102506.pmesh
> FileManager opening
> file:/Users/gutow/Desktop/BBtickplacement.jmol.png|obj_102506.pmesh
> FileManager opening file:/Users/gutow/Desktop/BBtickplacement.jmol.png
> data file type was determined to be Pmesh
> pmesh file contains 1600 vertices and 1521 polygons for 3042 triangles
> boundbox corners {-6.0 -6.0 -3.0} {6.0 6.0 3.0}
> isosurface ID "testpmesh" fill noMesh noDots notFrontOnly frontlit;
>
> FileManager.getAtomSetCollectionFromFile(zapped)
> FileManager opening
> /Users/gutow/Desktop/sage0-size500-359165447.jmol/zapped
> file ERROR: /Users/gutow/Desktop/sage0-size500-359165447.jmol/zapped
> java.io.FileNotFoundException:
> /Users/gutow/Desktop/sage0-size500-359165447.jmol/zapped (No such file or
> directory)
> Time for openFile(zapped): 70 ms
> eval ERROR: java.io.FileNotFoundException:
> /Users/gutow/Desktop/sage0-size500-359165447.jmol/zapped (No such file or
> directory)
> ----
> >> load <<
>
> Previously I was using -ionx options as well, which seems to have hidden
> much of the information.
>
> I have also sent the offending example file to you off-list.
>
> Jonathan
> On Jan 26, 2013, at 1:40 AM, Robert Hanson wrote:
>
> > or maybe even 13.0.12 --- you are several versions back using 13.0.9
> (Nov, 2012)
> >
> >
> > On Sat, Jan 26, 2013 at 9:35 AM, Robert Hanson <hans...@stolaf.edu>
> wrote:
> > Can you try that with Jmol 13.1.12 and tell me if that is still a
> problem? I'm not seeing it:
> >
> > >jmoldata -s plwilliamson.png
> >
> > JmolData using command options ["-s", "plwilliamson.png"]
> > Add -n (NOGRAPHICS) for faster performance if you are not creating
> images.
> > (C) 2012 Jmol Development
> > Jmol Version: 13.1.12 2013-01-23 14:58
> > java.vendor: Oracle Corporation
> > java.version: 1.7.0_10
> > os.name: Windows 8
> > Access: ALL
> > memory: 12.1/95.0
> > processors available: 4
> > useCommandThread: false
> > Executing script from file: plwilliamson.png
> > FileManager opening C:\jmol-dev\bobtest\plwilliamson.png
> > FileManager opening C:\jmol-dev\bobtest\plwilliamson.png|JmolManifest.txt
> > FileManager opening C:\jmol-dev\bobtest\plwilliamson.png
> > FileManager opening C:\jmol-dev\bobtest\plwilliamson.png|state.spt
> > FileManager opening C:\jmol-dev\bobtest\plwilliamson.png
> >
> >
> FileManager.getAtomSetCollectionFromFile(C:/jmol-dev/bobtest/plwilliamson.png|2a
> > gv.pdb.gz)
> > FileManager opening C:\jmol-dev\bobtest\plwilliamson.png|2agv.pdb.gz
> > FileManager opening C:\jmol-dev\bobtest\plwilliamson.png
> > The Resolver thinks Pdb
> > ....
> >
> > Bob
> >
> >
> > --
> > Robert M. Hanson
> > Larson-Anderson Professor of Chemistry
> > Chair, Chemistry Department
> > St. Olaf College
> > Northfield, MN
> > http://www.stolaf.edu/people/hansonr
> >
> >
> > If nature does not answer first what we want,
> > it is better to take what answer we get.
> >
> > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
> >
> >
> >
> >
> > --
> > Robert M. Hanson
> > Larson-Anderson Professor of Chemistry
> > Chair, Chemistry Department
> > St. Olaf College
> > Northfield, MN
> > http://www.stolaf.edu/people/hansonr
> >
> >
> > If nature does not answer first what we want,
> > it is better to take what answer we get.
> >
> > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
> >
> >
> ------------------------------------------------------------------------------
> > Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
> > MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
> > with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft
> > MVPs and experts. ON SALE this month only -- learn more at:
> >
> http://p.sf.net/sfu/learnnow-d2d_______________________________________________
> > Jmol-developers mailing list
> > Jmol-developers@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/jmol-developers
>
> Dr. Jonathan H. Gutow
> Chemistry Department gu...@uwosh.edu
> UW-Oshkosh Office:920-424-1326
> 800 Algoma Boulevard FAX:920-424-2042
> Oshkosh, WI 54901
> http://www.uwosh.edu/facstaff/gutow/
>
>
>
> ------------------------------------------------------------------------------
> Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
> MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
> with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft
> MVPs and experts. ON SALE this month only -- learn more at:
> http://p.sf.net/sfu/learnnow-d2d
> _______________________________________________
> Jmol-developers mailing list
> Jmol-developers@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
------------------------------------------------------------------------------
Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft
MVPs and experts. ON SALE this month only -- learn more at:
http://p.sf.net/sfu/learnnow-d2d
_______________________________________________
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