Here's how to read a Stereo-Lithographic file (.STL). STL files are a simple list of XYZ coordinates of vertices. They are geometry. If, for whatever reason, you want to import some shape, like a torus, or even and molecular surface you can! First you need that .stl.To save a .stl file in PMV, simply goto File--> Write--> Write STL. Or if you want some foreign shape use your 3D modelling program like Google SketchUp or Maya to save an stl.
1. Open Vision.
3. a Drag down the 'Read STL ASCII' node from the 'deprecated' list in to the blank canvas area.
b Drag down the 'PMV Viewer' node from the PMV tab under the PMV list.
c Double-click the 'Read STL ASCII' node and load your STL file.
d Connect the two nodes by dragging a line from the bottom blue circle of 'Read STL ASCII' to the top red box of 'PMV Viewer'.
Now, that torus or whatever should be present in the viewer.
BONUS #1: This geometry will be listed in the DejaVu GUI.
BONUS #2: You can connect the torus to a pdb by binding the geometry to the molecule under '3D Graphics'--> 'Bind Geometry to Molecule'. Then you can color that torus by atom type proximity just as you would any other surface.