Changing material properties

Click on button off the Toolbar to open DejaVu GUI. DejaVu uses scene-graph to organize objects in the scene and you can use the GUI to control different properties of the objects. Click on + to navigate object hierarchy and select MSMS-MOL geometry. To change opacity of the surface, click on Front button next to Material. This opens Front Material Editor shown below where you can control opacity by moving Opacity slider. You can also alter front polygon mode by clicking on Font button next  to Polygon mode and selecting one of the options (point, line, outlined, etc. ).