I'll need a sample file
On Mon, Nov 10, 2008 at 3:15 PM, Angel Herráez <[EMAIL PROTECTED]> wrote:
> Hi Jaime
>
> Have you checked
> http://wiki.jmol.org:81/index.php/File_formats#Open_DX
> ?
> There is some info and 3 links there
>
>
> I've done some test, and this looks like a bug.
>
> My DX file loads Ok in 11.2.14, 11.4.6, 11.5.6, but not in 11.6.4
>
>
> After
> load "lisozima.pdb";
> isosurface "lisozima.pqr.potential.dx"
>
> The error is
> # Jmol 11.6.4
>
> FileManager opening
> F:/webs/biomodel/Jmol/surfaces/APBS-Gemstone/lisozima.pdb
>
>
> FileManager.openFile(F:/webs/biomodel/Jmol/surfaces/APBS-Gemstone/lisozima.pdb)
> //F:/webs/biomodel/Jmol/surfaces/APBS-Gemstone/lisozima.pdb
> FileManager opening
> F:\webs\biomodel\Jmol\surfaces\APBS-Gemstone\lisozima.pdb
> The Resolver thinks Pdb
> openFile(F:/webs/biomodel/Jmol/surfaces/APBS-Gemstone/lisozima.pdb): 81 ms
> ModelSet: haveSymmetry:false haveUnitcells:true haveFractionalCoord:false
> 1 model in this collection. Use getProperty "modelInfo" or getProperty
> "auxiliaryInfo" to
> inspect them.
> ModelSet: autobonding; use autobond=false to not generate bonds
> automatically
> isosurface "lisozima.pqr.potential.dx";
> FileManager opening F:\webs\biomodel\Jmol\surfaces\APBS-
> Gemstone\lisozima.pqr.potential.dx
> reading isosurface data from F:/webs/biomodel/Jmol/surfaces/APBS-
> Gemstone/lisozima.pqr.potential.dx
> data file type was determined to be Apbs
> # Data from APBS 0.4.0
> #
> # POTENTIAL (kT/e)
> #
> APBS OpenDx DATA object 1 class gridpositions counts 97 97 97
> see http://apbs.sourceforge.net
>
> voxel grid origin:(-39.225002, -18.002499, -20.6175)
> voxel grid count/vector:97 0.8333333 0.0 0.0
> voxel grid count/vector:97 0.0 0.8333333 0.0
> voxel grid count/vector:-2147483648 0.0 0.0 0.8333333
> Read 97 x 97 x -2147483648 data points
> Exception in thread "QueueThread0" java.lang.NullPointerException
> at org.jmol.jvxl.calc.MarchingCubes.<init>(Unknown Source)
> at org.jmol.jvxl.readers.VoxelReader.generateSurfaceData(Unknown
> Source)
> at org.jmol.jvxl.readers.VoxelReader.createIsosurface(Unknown
> Source)
> at org.jmol.jvxl.readers.SurfaceGenerator.generateSurface(Unknown
> Source)
> at org.jmol.jvxl.readers.SurfaceGenerator.setParameter(Unknown
> Source)
> at org.jmol.shapesurface.Isosurface.setProperty(Unknown Source)
> at org.jmol.modelset.ModelSet.setShapeProperty(Unknown Source)
> at org.jmol.viewer.Viewer.setShapeProperty(Unknown Source)
> at org.jmol.viewer.Eval.setShapeProperty(Unknown Source)
> at org.jmol.viewer.Eval.isosurface(Unknown Source)
> at org.jmol.viewer.Eval.instructionDispatchLoop(Unknown Source)
> at org.jmol.viewer.Eval.runEval(Unknown Source)
> at org.jmol.viewer.Viewer.evalStringWaitStatus(Unknown Source)
> at
> org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runScript(Unknown
> Source)
> at
> org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runNextScript(Unknown
> Source)
> at org.jmol.viewer.ScriptManager$ScriptQueueRunnable.run(Unknown
> Source)
> at java.lang.Thread.run(Unknown Source)
>
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's
> challenge
> Build the coolest Linux based applications with Moblin SDK & win great
> prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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
-------------------------------------------------------------------------
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
