Re: [Jmol-developers] Either I misunderstand or JmolData.jar has a problem...
I got the same problem with 13.0.12 and I think it may relate specifically to loading files that are not .pdb.gz. I got it to work using a PNGJ scene made with 1lcd.pdb, but not one made with a .pmesh file. I also got some oddities with a .xyz file, but haven't reproduced that. I may have messed up that file.. I will try it with the development version as well. 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 Departmentgu...@uwosh.edu UW-Oshkosh Office: 920-424-1326 800 Algoma BoulevardFAX: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
Re: [Jmol-developers] Either I misunderstand or JmolData.jar has a problem...
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:
