Bob has set up a new interface between the data model and the
Jmol renderer, which allows him to define other types of export too. One of this is a
POV-Ray export, which allows creating of high quality images for paper. Jmol has had POV-Ray export for a long time now, but never included the secondary structures or other more recent visual featues.
PyMOL is well-known for its POV-Ray feature, and often used to create publication quality protein prints. The script command to create a POV-Ray input file takes the output image size as parameters:
write povray 400 600 # width 400, height 600
Here's a screenshot of a protein with surface:

And here a MO of water:

Note the shading. More examples are available
here.
Those images look really good. I am hoping to add more improvements to the POV-Ray support in Avogadro. It is good to see the surfaces and orbitals being displayed in such a nice way.
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