I am impressed by the illustrations for the Protein Data Bank ‘Molecule of the month’, e.g. the gorgeous image of DNA Helicase below. Does anyone know how they were made or how one might create something similar?
(source: rcsb.org)
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$\begingroup$ 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. $\endgroup$– Chris ♦Jul 2, 2014 at 16:34
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2 Answers
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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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$\begingroup$ @nornagon: nice, I did not know about QueteMol! $\endgroup$– nicoJul 5, 2014 at 9:33
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$\begingroup$ "I always use RasMol, to give visitors an idea of the kinds of pictures that they can create". Oh no they can't! Rasmol does not run on Mac OS X. But you can use Jmol instead, which has a command for saving high res png files that you can actually drag back into the application and modify further. $\endgroup$– DavidFeb 22, 2019 at 23:50
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$\begingroup$ @David there are Mac OS X binaries for RasMol, although I have never tried them. rasmol.org/software/RasMol_2.7.3.MAC/index.html $\endgroup$– nicoMar 2, 2019 at 12:17
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$\begingroup$ @nico — Not quite. They are Unix binaries that will run under an X-windowing environment. It requires you to set up Unix directories and move stuff there. I tried it years ago and it was a real pain compared with the Mac OS9 version. Now a user would have to install XQuartz before they started. For practical purposes it's dead. One feature of JSmol is that it supports all RasMol console commands, so if you are used to RasMol... $\endgroup$– DavidMar 2, 2019 at 14:33
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I don’t actually consider these pictures either “gorgeous” or “cool” — they are not to my taste — and I’m not really sure that the question is about biology, but as it has resurfaced after almost 5 years I thought I’d give an answer which explained how one might create something similar, rather than how they were actually made.
The original 3D-graphics program used was RasMol, but as that only runs on Windows, hasn’t been updated for years, and has no viable web version, I would suggest using JMol/JSMol instead. You can either download the application and work with it as described in my answer to a previous question. Alternatively you can just find a web page with a JSMol window (such as a page used in my own teaching material) and use that with the Console available from the JSMol logo. So what I do is:
- Get the PDB file I want to work with from the Protein Data Bank.
- Drag it into the JMol window when the molecule loads in wireframe mode as in (A), below.
- Give a series of commands such as the following to get a spacefilling image (B) in colours other than CPK (you can specify the colours of the chains if you wish) and without the shiny light patches, which are fine for standard images, but will cause problems. The beauty of JMol is you can generate high resolution images which you can drag back into a JMol window and work on again later (as long as you haven’t edited them).
restrict protein
wireframe off
select protein
spacefill on
colour chains
set specular off
write pngj 2000 2000 "my.png"
Next you need access to decent bitmap graphics application. If you are in a University someone will have a copy of Photoshop (old versions are fine), but otherwise you will have to make do with what you can find. I am almost certain that the original artist would have developed the style he uses with Photoshop. He says he wrote a program himself to automate it, but he could just have well used a Photoshop script (Action) in my opinion. Any, for occasional use, just do it interactively.
The first thing to do is to get the outlines on the spheres and make the the colours flat. The former is done with a filter that finds the edges, and the latter by posterizing (reducing the number of colours in the image). I used a filter called ‘Poster Edges’ to produce C. There are sliders which allow you to change the intensity of the edges and degree of posterizing.
Finally to reproduce the rather washed out feel of the colours I used the ‘Exposure’ tool (Image > Adjustments > Exposure), but I could have used curves (Image > Adjustments > Curves) or, no doubt, other options.
And there you have the final image in D. It doesn't have quite the same posterization as the DNA Helicase illustrated in the question, but if you really wanted that you could experiment.
