Recently I have been playing around with VMD and the included Tachyon ray trace engine. Once you get used to the weird selection algebra in VMD and accustomed to tcl scripting, it is truly incredible easy to use the Tachyon engine to generates publication grade renders.
I can’t help wondering about how perfect a combination PyMol’s user interface together with the Tachyon engine would be. As an example: If you want to get a specific view in VMD, to use in your script, you have to write out 3 different matrices and then use output from them as input for the same three matrix settings in your script. VMD does support something called a view_matrix which basically gives you the matrices you want, BUT you are not allowed to set the view_matrix, instead you have to set each individual matrix on its own. This is just annoying. In Pymol you just write get_view and copy the view matrix into your script, done.
Anyway, here are some of the renders and an example script for generating the pictures behind the GIF (also, the GIF creating commands are included at the end, but they have been commented out):
The above script should generate the images needed to make the below GIF, as long as the map file (emd_3802.mrc) and the PDB file (5OF4.pdb) are present in the same directory as where you run the script form. NB: The images was normalized in ImageMagick before being converted to a GIF.
Example of one the frames from the GIF, in higher res.
Render of F-actin model where I just show different model representations.
Render of the cryo-EM map of the C.elegans 80S ribosome.
Below is shown a mix of two types of material in the same render. Tachyon is especially good for creating the Goodsell look.