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Franz, My problem was rightly so as angel said that I didn't have anything in the file and I now see that the _javascript_ and the php down' use a separate space for the file locater ( THX angel). Anyway if your having problems with the file I would suggest try openbabel its very good and I now have the files going in as an xyx format. Which I think Jmol likes better. To all the other uses I have one more question to ask "Can Jmol get the molecule it a 3D manner, so it looks at the bond angles?" and "If a file was loaded with no Hydrogens how can I get Jmol to put them on?". Cheers and THX PB Research Technician Mass Spectrometry o The / o Scripps \ o Research / o Institute franz eder wrote: Hello everybody,is anyone else having problems with the inline opening of files? I seem to run out of heapspace every now and then even if i dont do much in the background. (I am using jmol als an import for my java applet). It crashes especially with big files such as nmr-Files. However if i load them directly with jmol there is no error and they get displayed correctly. Also sometimes i get the error below. Anyone an idea why i am getting it and how i can fix it? Cheers Franz FileManager.openStringInline(,0,0,0,0) SmarterJmolAdapter:The Resolver thinks:Pdb : String index out of range: 70 java.lang.String - 1935 - substring org.jmol.adapter.smarter.PdbReader - 482 - het org.jmol.adapter.smarter.PdbReader - 102 - readAtomSetCollection org.jmol.adapter.smarter.Resolver - 69 - resolve org.jmol.adapter.smarter.SmarterJmolAdapter - 66 - openBufferedReader org.jmol.viewer.FileManager$FileOpenThread - 527 - openBufferedReader org.jmol.viewer.FileManager$FileOpenThread - 511 - run org.jmol.viewer.FileManager - 179 - openStringInline org.jmol.viewer.Viewer - 1153 - openStringInline org.jmol.viewer.Viewer - 1212 - loadInline org.jmol.viewer.Viewer - 1176 - loadInline my.praktikum.PocketViewerPicker - 183 - Load_from_file my.praktikum.CPocketViewerPicker - 211 - actionPerformed javax.swing.AbstractButton - 1995 - fireActionPerformed javax.swing.AbstractButton$Handler - 2318 - actionPerformed javax.swing.DefaultButtonModel - 387 - fireActionPerformed javax.swing.DefaultButtonModel - 242 - setPressed javax.swing.plaf.basic.BasicButtonListener - 236 - mouseReleased java.awt.Component - 6038 - processMouseEvent javax.swing.JComponent - 3260 - processMouseEvent java.awt.Component - 5803 - processEvent java.awt.Container - 2058 - processEvent java.awt.Component - 4410 - dispatchEventImpl java.awt.Container - 2116 - dispatchEventImpl java.awt.Component - 4240 - dispatchEvent java.awt.LightweightDispatcher - 4322 - retargetMouseEvent java.awt.LightweightDispatcher - 3986 - processMouseEvent java.awt.LightweightDispatcher - 3916 - dispatchEvent java.awt.Container - 2102 - dispatchEventImpl java.awt.Component - 4240 - dispatchEvent java.awt.EventQueue - 599 - dispatchEvent java.awt.EventDispatchThread - 273 - pumpOneEventForFilters java.awt.EventDispatchThread - 183 - pumpEventsForFilter java.awt.EventDispatchThread - 173 - pumpEventsForHierarchy java.awt.EventDispatchThread - 168 - pumpEvents java.awt.EventDispatchThread - 160 - pumpEvents java.awt.EventDispatchThread - 121 - run error opening string java.lang.StringIndexOutOfBoundsException: String index out of range: 70Von: "H. Paul Benton" <[EMAIL PROTECTED]> An: jmol-users@lists.sourceforge.net Betreff: Re: [Jmol-users] loading jmol file from open babel Datum: Mon, 22 Jan 2007 17:08:42 -0800 |
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