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e.g. this gorgeous image of DNA Helicase:

DNA Helicase

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While I don't know what is used, David Goodsell should know it, as he is responsible for this, as far as I can see. Write him a friendly email, my best guess is that he will tell you. And please tell us (you can answer your own questions), I am curious, too. –  Chris Jul 2 at 16:34

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Those (really cool) pictures are created by David Goodsell using custom-written software.

From an interview to the artist:

PDB: How do you create the illustrations?

Goodsell: Most of the pictures are created with a computer program that I developed back when I was doing postdoctoral work with Dr. Art Olson here at The Scripps Research Institute. I've been using this style of illustration--with flat colors and black outlines--for about 10 years now. I like the way that this style simplifies the molecule, giving a feeling for the overall shape and form of the molecule, but at the same time you can still see all the individual atoms. On the last page of each Molecule of the Month--"Exploring the Structure"--I always use RasMol, to give visitors an idea of the kinds of pictures that they can create themselves with off-the-shelf software.

There are good tools around if you want to replicate that look. Although it may take a bit of tweaking (and possibly programming) I would surely give PyMOL and Bioblender a try.

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I found QuteMol got me closest to Goodsell's look :) –  nornagon Jul 5 at 4:36
    
@nornagon: nice, I did not know about QueteMol! –  nico Jul 5 at 9:33

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