Error when searching in Protein (pdb) structure table.

User 2f67f74af0

26-03-2009 17:47:36

Hi every one

I'm having problem searching in a table of pdb structures. The table is created using JChemManager. I had some issues when importing pdb files due to memeory. After increasing memory I was able to import files one at a time.

Now when I do search I get a popup window saying (Error in module clean2D)

The stack Trace is:

Code:

ava.lang.OutOfMemoryError: Java heap space

    at chemaxon.struc.CGraph.regenCtabs(Unknown Source)

    at chemaxon.struc.CGraph.getCtab(Unknown Source)

    at chemaxon.struc.CGraph.findFrags(Unknown Source)

    at chemaxon.marvin.modules.Clean2D.a(Unknown Source)

    at chemaxon.marvin.modules.Clean2D.modfunc(Unknown Source)

    at chemaxon.struc.MoleculeGraph.clean(Unknown Source)

    at chemaxon.struc.Molecule.clean(Unknown Source)

    at chemaxon.struc.MoleculeGraph.clean(Unknown Source)

    at chemaxon.marvin.common.swing.MolPanel.molLoaded(Unknown Source)

    at chemaxon.marvin.view.swing.ViewPanel.molLoaded(Unknown Source)

    at chemaxon.marvin.view.swing.ViewPanel.molLoaderFinished(Unknown Source)

    at chemaxon.marvin.util.MolLoader.run(Unknown Source)

    at java.awt.event.InvocationEvent.dispatch(Unknown Source)

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

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

    at java.awt.EventDispatchThread.pumpEventsForFilter(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)

It's complaining about Java heap space, but even when I increase that I got the same error.

The table now have only 26 records (structures)

Thank you.

--Saif

ChemAxon a3d59b832c

27-03-2009 12:09:17

Hi Saif,

Please note that JChem and Marvin were designed for handling small molecules.

Nevertheless, it can handle large molecules like proteins as well, and there is a chance that it can perform well with those.

The fact that 2D cleaning is used by the applet suggests to me that you pass the cd_smiles column for display. Instead of that, I recommend the cd_structure column, which contains the original PDB source with (3D) coordinates.

Let us know if that helps.

Regards,

Szabolcs