Problem to generate 3D view of Methane

The attached pic shows what I get when I try to display Methane in Marvin Space in Ball-Stick notation. Is there a fix for this? What am I missing.

I am using Marvin 6.2.0 on a Ubuntu 12.04 64bit system with OpenJDK6

Hi,

It seem, it is a cleaning issue. (MarvinSpace does 3D clean on molecule load.)

Here is a workaround until I get response from the people who are responsible for that module:

- Open the structure in MarvinSketch.

- Do a 3D clean, the Cleaning Method should be 'Fine with Hydrogenize'

- Save the structure

- Load this modified file in MarvinSpace.

 

Regards,

Andras

 

Thanks for the help. Following your procedure it works. Playing around with the cleaning I found out that a 2D cleaning works as well.