Marvin 5.2.2 on Leopard 10.5.7 - Cannot See Menus

In MarvinSpace, when I click on a menu, the top two menu items (which layer on the menubar and toolbar display areas) are clearly seen and can be selected. All other menuitems in the menulist below that cannot be seen and cannot be selected. This happens for ALL menus. These are on top of the dark MarvinSpace MoleculeViewer window. New iMac 24" with 3+GHz core duo processor, 4GB Ram and 1TB HD. 

This is critical bug issue and has made MarvinSpace unusable for us. 

MarvinSpace 5.2.2 on  Tiger 10.4.11 installed. The menuitems can be seen. However, the moleculeviewer window has a light grey background and does not load any molecules. Nothing happens when I try to load a molecule from pdb or a small molecule created in MarvinSketch. I had reported this issue for earlier versions of Marvin (4.x). There, my troubleshooting indicated that MSpace was still looking for a very old java jogl library that has since been deprecated, although it is not supposed to use it- MBeans does not contain that old jogl lib. I do not know if the same bug is preventing MSpace 522 on Tiger. 

Dear Anil,

 

This problem was reported earlier, see http://www.chemaxon.com/forum/ftopic4677.html

Could you also post the result of "java -version" and "mspace -v"?

The problem with Tiger seems to be a JOGL initialization issue. As requested in http://www.chemaxon.com/forum/ftopic3808.html could you try to delete the whole /Users/a_user_name/.chemaxon/lib/jogl_1.1.0-rc2/ directory? Also could you check if our public examples ( http://www.chemaxon.com/marvin/examples/applets/space/index.html ) work on Tiger?

Regards,

Gabor

 

java -version -->

Java version 1.5.0_16

Java(tm) 2 Runtime Environment, Standard Edition (build 1.5.0_16_b06-284)

Java HotSpot (tm) Client VM (build 1.5.0_16-133), mixed mode, sharing. 

 

mspace -v --> Command not found. I tried which mspace - gave no location. Tried executing from /, from ~ and from /Applications/. 

The mspace script is located in the "bin" subdirectory of Marvin Beans / JChem package.

If you used Marvin Beans installer, in default, Marvin was placed into the "/Applications/ChemAxon/MarvinBeans" directory. By JChem, the location is "/Application/ChemAxon/JChem". Unless you have choosen another target directory by installation, the path of mspace will be

/Applications/ChemAxon/MarvinBeans/bin/mspace

or

/Applications/ChemAxon/JChem/bin/mspace

 

Hi Tamas,

First- thanks to all you folks for providing this suite of programs.  

I'm getting the same issue on running the program as ruizao (http://www.chemaxon.com/forum/ftopic4677.html) and adiwan1- the menus disappear into the black background and the help text runs off screen (not wrapped).  I'll add my info.

Mac OSX 10.5.7, macbook pro, 2.4 GHz, 4G memory

output from java -version:

java version "1.5.0_19"

Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_19-b02-304)

Java HotSpot(TM) Client VM (build 1.5.0_19-137, mixed mode, sharing)

97-86-169-133:~ jrt$ 

 

output from mspace -v

Native directory is /Users/jrt/.chemaxon/lib/jogl_1.1.0-rc2

NativeLibLoader disabled.

Jogl libraries have been loaded.

JOGL specification version 1.1.0-rc2

JOGL implementation version 1.1.0-rc2

JOGL implementation vendor Sun Microsystems, Inc.

sun.java2d.noddraw: true

jogl.GLContext.noopt: true

Using AWT thread for performing OpenGL work in javax.media.opengl implementation

OpenGL Renderer = NVIDIA GeForce 8600M GT OpenGL Engine

OpenGL Version = 2.0 NVIDIA-1.5.44

OpenGL Vendor = NVIDIA Corporation

 

 

I deleted .chemaxon/lib/jogl_1.1.0-rc2/ but it makes no difference with the marvinspace menus when run stand-alone.

I ran the public applets at: http://www.chemaxon.com/marvin/examples/applets/space/index.html  

#1, #2,  4, 6, 7 and 8 (including menus) seem to work ok also, but #8 does not show the property grid.

#3 (colotypes) crashes- but only crashes (with an initialization error) if I view it (runs fine), then go back to the examples page, then view #3 again.  I sent a report , but here are the details are below(sorry it's so long). 

#5 crashes Safari every time.

In Firefox, all the demos work, all the menus show up, no crashes, but in  #5 the windows  move over the firefox menu bars when I scroll through.  

Thanks,

Jason

details from #3:

java.lang.RuntimeException: Exception in GL initialization: GL is already initialized

at chemaxon.marvin.space.GraphicScene.init(GraphicScene.java:1421)

at com.sun.opengl.impl.GLDrawableHelper.init(GLDrawableHelper.java:72)

at javax.media.opengl.GLCanvas$InitAction.run(GLCanvas.java:271)

at com.sun.opengl.impl.GLDrawableHelper.invokeGL(GLDrawableHelper.java:189)

at javax.media.opengl.GLCanvas.maybeDoSingleThreadedWorkaround(GLCanvas.java:265)

at javax.media.opengl.GLCanvas.display(GLCanvas.java:130)

at chemaxon.marvin.space.GraphicScene.paint(GraphicScene.java:1724)

at javax.swing.JComponent.paintChildren(JComponent.java:843)

at javax.swing.JComponent.paint(JComponent.java:1015)

at javax.swing.JComponent.paintChildren(JComponent.java:843)

at javax.swing.JComponent.paint(JComponent.java:1015)

at javax.swing.JLayeredPane.paint(JLayeredPane.java:559)

at javax.swing.JComponent.paintChildren(JComponent.java:843)

at javax.swing.JComponent.paint(JComponent.java:1015)

at java.awt.GraphicsCallback$PaintCallback.run(GraphicsCallback.java:34)

at sun.awt.SunGraphicsCallback.runOneComponent(SunGraphicsCallback.java:60)

at sun.awt.SunGraphicsCallback.runComponents(SunGraphicsCallback.java:97)

at java.awt.Container.paint(Container.java:1722)

at sun.awt.RepaintArea.paintComponent(RepaintArea.java:276)

at sun.awt.RepaintArea.paint(RepaintArea.java:241)

at apple.awt.ComponentModel.handleEvent(ComponentModel.java:268)

at java.awt.Component.dispatchEventImpl(Component.java:4144)

at java.awt.Container.dispatchEventImpl(Container.java:2068)

at java.awt.Component.dispatchEvent(Component.java:3903)

at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)

at java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:269)

at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:190)

at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:184)

at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:176)

at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)

 

 

Dear Jason,

Thanks for the detailed report. We will notify you in this (and the other referred) topic when  progress is made on this issue.

 

Regards,

Gabor

Hi Gabor,

Thanks for looking into it.

For what it's worth, I ran archived Marvin Space programs- all the 5.x.x versions show the same behavior.  The 4.1.14 compile shows all the menus.

So, for now, I've just got both versions installed and run 5.x for Sketch and 4.x for Space.

Cheers,

Jason

Dear Jason,

 

Sorry again for this bug. Thanks for the hint.

 

Regards,

Gabor