Yes, you can use Blender to prepare figures for your next paper and the results for sure will look different than the ones obtained with a standard software (hemoglobin [1HBG] as example below)… But given amount of work and really steep learning curve (at least for somebody who tries that for the very first time), I would not recommend Blender that much… 
UPDATE: if you look for a way to import a PDB file into Blender, some instructions are at the bottom of this page.
That’s a neat figure. A lot of the figures in my PhD thesis were done in FormZ .. definitely made a difference
Thanks Deepak.
FormZ? I didn’t have a chance to try, but its interface looks way cleaner than Blender’s. Can you share some details (like how to get PDB file inside; I’ve spent more time on importing the structure than on rendering)?
Lights,camera,action ! Once upon a time there lived an hemoglobin in a land called far far way :).
This was a very long time ago … and I didn’t do the images, my wife did.
What I did was open up the structures in a visualizer capable of VRML export. The VRML was then imported into FormZ and material, shadows, shapes, etc were added there. Cool applications - rendering a proton channel, showing off potential ion binding sites, etc.
Thanks Deepak, I did try VRML, however Blender understands only version 1.0… Will look further.
Pedro, if you have a scenario I can start rendering next pictures
. I’m not into animations, but a comic? Why not? 