My molecules have just been sold / Fatty Acid Synthase is a centerfold
June 5, 2007 11:27 AM Subscribe
Molecule of the Month - a feature of biophysics weblog Biocurious. Don't neglect the more links under each entry.
DNA topoisomerase is not the molecule of the month!!?? Gee, the humanity!
posted by dov3 at 11:48 AM on June 5, 2007
posted by dov3 at 11:48 AM on June 5, 2007
This is really cool. Like, the coolest thing I've seen on MeFi in a while.
posted by klangklangston at 12:08 PM on June 5, 2007
posted by klangklangston at 12:08 PM on June 5, 2007
My favorite molecule is CH3CH2OH.
posted by Pope Guilty at 12:21 PM on June 5, 2007
posted by Pope Guilty at 12:21 PM on June 5, 2007
There's a very real risk of learning a bundle following that link.
posted by Catfry at 12:43 PM on June 5, 2007
posted by Catfry at 12:43 PM on June 5, 2007
Dangit, I need to stop posting instead of Previewing!
Coming from a biochemistry background and now working in IT, I miss learning about and knowing how things worked on the molecular level. Three years out of college, and I feel like I've forgot damn near everything I learned. This site rocks. Interesting reading for the biochemist on me to refresh a little on what I learned without reliving nightmares by looking at my text books.
posted by jmd82 at 12:50 PM on June 5, 2007
Coming from a biochemistry background and now working in IT, I miss learning about and knowing how things worked on the molecular level. Three years out of college, and I feel like I've forgot damn near everything I learned. This site rocks. Interesting reading for the biochemist on me to refresh a little on what I learned without reliving nightmares by looking at my text books.
posted by jmd82 at 12:50 PM on June 5, 2007
I want to meet some bi-curious biocurious folks. Great site!
posted by WolfDaddy at 12:53 PM on June 5, 2007
posted by WolfDaddy at 12:53 PM on June 5, 2007
Beautifully designed site. What would be the name for the type of rendering down on the molecules? It looks like a cut-out/watercolor/rotoscope hybrid.
posted by geoff. at 1:11 PM on June 5, 2007
posted by geoff. at 1:11 PM on June 5, 2007
These molecules also discussed here, the incredibly deep protein data bank (PDB). The full archive of molecules of the month--several years' worth--is here. You can download cartesian coordinates of every atom* in these proteins. All told the PDB has over 45,000 structures available. A superb resource (for biophysicists and the like).
*not actually every atom, but damn close
On preview, Pope Guilty will be needing some of this.
posted by Joe Invisible at 1:11 PM on June 5, 2007
*not actually every atom, but damn close
On preview, Pope Guilty will be needing some of this.
posted by Joe Invisible at 1:11 PM on June 5, 2007
geoff. writes "What would be the name for the type of rendering down on the molecules? It looks like a cut-out/watercolor/rotoscope hybrid."
I'm not 100% sure, but these look like simple "space-filling models". That term only describes how the atoms and bonds between the atoms are shown, however. These images are all rendered, as Joe Invisible describes, from files describing the three-dimensional coordinates of the atoms in the molecules. The exact look of the images is dependent on the program that does the rendering (and the settings that the user gives this program). It looks like these were all done with RasMol, which is freely available. If you'd like, you can play around with this program (or Protein Explorer, which is easier to use) and with some PDB files (in Joe Invisible's links) to see what kind of images can be produced.
posted by mr_roboto at 1:30 PM on June 5, 2007
I'm not 100% sure, but these look like simple "space-filling models". That term only describes how the atoms and bonds between the atoms are shown, however. These images are all rendered, as Joe Invisible describes, from files describing the three-dimensional coordinates of the atoms in the molecules. The exact look of the images is dependent on the program that does the rendering (and the settings that the user gives this program). It looks like these were all done with RasMol, which is freely available. If you'd like, you can play around with this program (or Protein Explorer, which is easier to use) and with some PDB files (in Joe Invisible's links) to see what kind of images can be produced.
posted by mr_roboto at 1:30 PM on June 5, 2007
Most of those images are by David S. Goodsell.
His style of illustration is instantly recognizable and much clearer than what is often seen. Unnecessary detail that would just obscure has been removed or toned down using pastel colors. It's a wonderful example of how good pedagogy doesn't just dump raw unfiltered information on students, but pre-digests it to elucidate how it hooks together.
Goodsell is the author of several wonderful books that showcase his talents as an illustrator, scientist, and educator:
Bionanotechnology: Lessons from Nature
Our Molecular Nature: The Body's Motors, Machines and Messages
The Machinery of Life
(regrettably, the paperback edition, at least, has the illustrations in black-and-white)
I asked him once how he generated his models, and he replied that he uses custom-written software. However, on his webpage he has a list of resources for illustrators ... and in particular a link to a page by Nick Woolridge about producing somewhat similar results.
posted by nickp at 7:08 PM on June 5, 2007
On preview, Pope Guilty will be needing some of this.
Thanks for looking out!
posted by Pope Guilty at 4:33 AM on June 6, 2007
Thanks for looking out!
posted by Pope Guilty at 4:33 AM on June 6, 2007
David writes the MOM features for the PDB, and then lets everyone use his images/text for whatever they want. The stylized images are a hack of a computer program.
You can read an interview with him about this feature at the PDB site. You can also check out a PDF of 80 molecules drawn to scale by David here. He also has some paintings to sell...
posted by armacy at 6:23 PM on June 6, 2007
You can read an interview with him about this feature at the PDB site. You can also check out a PDF of 80 molecules drawn to scale by David here. He also has some paintings to sell...
posted by armacy at 6:23 PM on June 6, 2007
Great site, Wolfdog, and the page title here made me snort laughing.
Plutor, I was so excited to see a huge archive of equations ... damn.
posted by olecranon at 10:13 PM on June 6, 2007
Plutor, I was so excited to see a huge archive of equations ... damn.
posted by olecranon at 10:13 PM on June 6, 2007
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