Marvin Visualize H bonds Display Conformers

User 85fa3b3118

25-05-2012 10:20:53

Dear Sir,

I received this error code when I check the Visualize H
Bonds in Display Conformers.

java.lang.NullPointerException

    at chemaxon.calculations.HBondViewer.e(Unknown Source)

    at chemaxon.calculations.HBondViewer.c(Unknown Source)

    at chemaxon.calculations.HBondViewer.calcDACouples(Unknown
Source)

    at chemaxon.marvin.calculations.ConformerPlugin.a(Unknown
Source)

    at
chemaxon.marvin.calculations.ConformerPlugin.run(Unknown
Source)

    at
chemaxon.marvin.plugin.CalculatorPluginManager.a(Unknown
Source)

    at
chemaxon.marvin.plugin.CalculatorPluginManager.a(Unknown
Source)

    at
chemaxon.marvin.plugin.CalculatorPluginManager.a(Unknown
Source)

    at
chemaxon.marvin.plugin.CalculatorPluginManager.callback(Unknown
Source)

    at chemaxon.marvin.plugin.PluginManager.callback(Unknown
Source)

    at chemaxon.marvin.common.swing.MolPanel$6.run(Unknown
Source)

What happens?

It's a bug in your .app or from Java?

Thanks

User 85fa3b3118

28-05-2012 10:54:14

I think that it's a big bug, because the techincal suport say no words in reply.

User 25d107bd42

28-05-2012 12:23:10

Hi,

some days ago we found the same problem, see attached screen shot "Bug in newer Marvin versions".

But remembering that earlier Marvin versions have been able to show H-bonds I tried to use this option in these earlier versions (My desktop has 17 versions running - back to version 2.10.4 )

And I found the newest MarvinSketch version being able to show H-bonds was version 5.6.0.2.

All younger versions have the bug and don't show conformers when "Visualize H-bonds" is activated.

As a Java programmer I have the suspicion once more: There is a problem with the "swing" objects and its methods. Is version 5.6.0.2 also using "swing" ?

Best regards, Hans-Ulrich

BTW: The conformer tool of Marvin is not able to calculate and to show correct H-bonds in acetylacetone. There should be a structure having H inside a planar six membered ring ...O=C-C=C-O-H...

ChemAxon e08c317633

30-05-2012 11:15:17

We can reproduce the error, and we will fix it. The fix can be expected in Marvin 5.10.x (1 <= x <= 10).

I moved the topic to "Structure based predictions: Calculation Plugins & Chemical Terms" forum.

Zsolt

User 25d107bd42

13-06-2012 17:53:12

Hi Marvin developers,

having now 5.10.0 it works ! Thank you for fixing the bug.

It calculated 28 conformers for this example acetylaceton.

Best regards, Hans-Ulrich