issues with xyz and pdb in molconvert

Hi,


if i convert the following molecules into xyz or pdb with molconvert 4.1.11


I get some molecules (either with empty coordinates in case of xyz) or


in case of pdb files I can not open them with MArvin again (I can open some of them in other programs but sometimes they are correct sometimes they are wrong).





in case of the following sucrose conformers the xyz conversion


fails totally and the file (if opened again in MarvinView has


wrong bond connections). At least one would expect that Marvin would


read its own generated XYZ files. I think XYZ is a trouble maker.





For PDB conversion Marvin can not perform any calculation on these molecules.





[H]C1C[C@@H]2C[C@@H]1c3ccccc3C2


[H]C1C[C@H]2C[C@@H]1c3ccccc3C2


[H]C1C[C@@H]2C[C@H]1c3ccccc3C2


[H]C1C[C@H]2C[C@H]1c3ccccc3C2





and





OC[C@@H]1O[C@](CO)(O[C@@H]2O[C@@H](CO)[C@@H](O)[C@@H](O)[C@@H]2O)[C@H](O)[C@@H]1O


OC[C@@H]1O[C@](CO)(O[C@@H]2O[C@H](CO)[C@H](O)[C@@H](O)[C@@H]2O)[C@H](O)[C@@H]1O


OC[C@@H]1O[C@](CO)(O[C@@H]2O[C@@H](CO)[C@H](O)[C@@H](O)[C@@H]2O)[C@H](O)[C@@H]1O


OC[C@@H]1O[C@](CO)(O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]2O)[C@H](O)[C@@H]1O


OC[C@@H]1O[C@](CO)(O[C@@H]2O[C@@H](CO)[C@@H](O)[C@H](O)[C@@H]2O)[C@H](O)[C@@H]1O


OC[C@@H]1O[C@](CO)(O[C@@H]2O[C@H](CO)[C@H](O)[C@H](O)[C@@H]2O)[C@H](O)[C@@H]1O


OC[C@@H]1O[C@](CO)(O[C@@H]2O[C@@H](CO)[C@H](O)[C@H](O)[C@@H]2O)[C@H](O)[C@@H]1O


OC[C@@H]1O[C@@](CO)(O[C@H]2O[C@H](CO)[C@@H](O)[C@@H](O)[C@H]2O)[C@H](O)[C@@H]1O


OC[C@@H]1O[C@@](CO)(O[C@H]2O[C@@H](CO)[C@@H](O)[C@@H](O)[C@H]2O)[C@H](O)[C@@H]1O


OC[C@@H]1O[C@@](CO)(O[C@H]2O[C@H](CO)[C@H](O)[C@@H](O)[C@H]2O)[C@H](O)[C@@H]1O


OC[C@@H]1O[C@@](CO)(O[C@H]2O[C@@H](CO)[C@H](O)[C@@H](O)[C@H]2O)[C@H](O)[C@@H]1O


OC[C@@H]1O[C@@](CO)(O[C@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)[C@H](O)[C@@H]1O


OC[C@@H]1O[C@@](CO)(O[C@H]2O[C@@H](CO)[C@@H](O)[C@H](O)[C@H]2O)[C@H](O)[C@@H]1O


OC[C@@H]1O[C@@](CO)(O[C@H]2O[C@H](CO)[C@H](O)[C@H](O)[C@H]2O)[C@H](O)[C@@H]1O


OC[C@@H]1O[C@@](CO)(O[C@H]2O[C@@H](CO)[C@H](O)[C@H](O)[C@H]2O)[C@H](O)[C@@H]1O


OC[C@@H]1O[C@@](CO)(O[C@H]2O[C@H](CO)[C@@H](O)[C@@H](O)[C@@H]2O)[C@H](O)[C@@H]1O


OC[C@@H]1O[C@@](CO)(O[C@H]2O[C@@H](CO)[C@@H](O)[C@@H](O)[C@@H]2O)[C@H](O)[C@@H]1O


OC[C@@H]1O[C@@](CO)(O[C@H]2O[C@H](CO)[C@H](O)[C@@H](O)[C@@H]2O)[C@H](O)[C@@H]1O


OC[C@@H]1O[C@@](CO)(O[C@H]2O[C@@H](CO)[C@H](O)[C@@H](O)[C@@H]2O)[C@H](O)[C@@H]1O


OC[C@@H]1O[C@@](CO)(O[C@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]2O)[C@H](O)[C@@H]1O


OC[C@@H]1O[C@@](CO)(O[C@H]2O[C@@H](CO)[C@@H](O)[C@H](O)[C@@H]2O)[C@H](O)[C@@H]1O


OC[C@@H]1O[C@@](CO)(O[C@H]2O[C@H](CO)[C@H](O)[C@H](O)[C@@H]2O)[C@H](O)[C@@H]1O


OC[C@@H]1O[C@@](CO)(O[C@H]2O[C@@H](CO)[C@H](O)[C@H](O)[C@@H]2O)[C@H](O)[C@@H]1O


OC[C@@H]1O[C@@](CO)(O[C@@H]2O[C@H](CO)[C@@H](O)[C@@H](O)[C@H]2O)[C@H](O)[C@@H]1O





Also if I call molconvert for xyz conversion I get the following error


Z:\sucrose>molconvert xyz *.mol


Exception in thread "main" java.lang.NoClassDefFoundError: xyz





If I open some of the attached moleculs I can an null pointer


exception.


Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException


at chemaxon.marvin.view.swing.TableOptions.updateFields(TableOptions.java:118)


at chemaxon.marvin.view.swing.TableOptions.updateFields(TableOptions.java:159)


at chemaxon.marvin.View$7.propertyChange(View.java:324)


at java.beans.PropertyChangeSupport.firePropertyChange(Unknown Source)


at java.beans.PropertyChangeSupport.firePropertyChange(Unknown Source)


at java.awt.Component.firePropertyChange(Unknown Source)


at chemaxon.marvin.beans.MarvinPane.propertyChange(MarvinPane.java:218)


at java.beans.PropertyChangeSupport.firePropertyChange(Unknown Source)


at java.beans.PropertyChangeSupport.firePropertyChange(Unknown Source)


at chemaxon.marvin.common.swing.MolPanel.setFile(MolPanel.java:2229)


at chemaxon.marvin.view.swing.modules.ViewDnD.callback(ViewDnD.java:166)


at chemaxon.marvin.common.swing.DnD.drop(DnD.java:193)


at java.awt.dnd.DropTarget.drop(Unknown Source)


at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(Unknown Source)


at sun.awt.dnd.SunDropTargetContextPeer.access$800(Unknown Source)


at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(Unknown Source)


at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(Unknown Source)


at sun.awt.dnd.SunDropTargetEvent.dispatch(Unknown Source)


at java.awt.Component.dispatchEventImpl(Unknown Source)


at java.awt.Container.dispatchEventImpl(Unknown Source)


at java.awt.Component.dispatchEvent(Unknown Source)


at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)


at java.awt.LightweightDispatcher.processDropTargetEvent(Unknown Source)


at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)


at java.awt.Container.dispatchEventImpl(Unknown Source)


at java.awt.Window.dispatchEventImpl(Unknown Source)


at java.awt.Component.dispatchEvent(Unknown Source)


at java.awt.EventQueue.dispatchEvent(Unknown Source)


at java.awt.EventDispatchThread.pumpOneEventForHierarchy(Unknown Source)


at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)


at java.awt.EventDispatchThread.pumpEvents(Unknown Source)


at java.awt.EventDispatchThread.pumpEvents(Unknown Source)


at java.awt.EventDispatchThread.run(Unknown Source)








Tobias

I could not reproduce the mentioned errors with Marvin 4.1.11.


Are you sure that you run Marvin 4.1.11?


There was a NoClassDefFoundError by xyz export in an alpha release of Marvin 5.0. Are you sure if there is no other MarvinBeans.jar (or jchem.jar) in your system classpath?


Please check the version of the running molconvert.


The command line help of molconvert prints the version number of the application. (Call molconvert script without parameter.)


You should see something like this:

Code:

Molecule File Converter, version 4.1.11, (C) 1999-2007 ChemAxon Ltd. Usage: molconvert [options] outformat[:export-opts] [files...] Converts the specified files to another format. ...