Re: [Jmol-developers] Either I misunderstand or JmolData.jar has a problem...

[Gutow, J. H <gu...@uw...>]

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 <ha...@st...> 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
> 
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                        Dr. Jonathan H. Gutow
Chemistry Department                                 gu...@uw...
UW-Oshkosh                                           Office:920-424-1326
800 Algoma Boulevard                                 FAX:920-424-2042
Oshkosh, WI 54901
                http://www.uwosh.edu/facstaff/gutow/