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What does fivemack do all day?
Nov. 24th, 2006 06:19 pmHere are some pretty pictures of proteins and electron density which I generated today.
http://www.globalphasing.com/~twomack/radx/
They have little to do with what I actually do all day, but quite a lot of that is commercially sensitive, and quite a lot of it is deeply esoteric of interest only to crystallographers, and quite a lot of it is throughly boring and involves debugging reams of shell-script, and once you've removed those three parts there's little left.
The sticks are protein structure (green is carbon, red is oxygen, blue is nitrogen, orange is sulphur); Didier Nurizzo at the ERSF laboratory in Grenoble measured by X-ray diffraction the amplitudes of the Fourier components of the electron density in a crystal of the protein thaumatin, Global Phasing's software figured out the distribution of the electron density in space and the placement of the atoms within the electron density, starting from a model of thaumatin measured in a different-shaped crystal by someone else ten years ago, and the green chicken-wire clouds represent the portion of the electron density that our refined model of the atom placement doesn't explain.
Specifically, we measured electron density before and after radiation damage, and then fitted a model where a bit of the protein we'd expect to fall off with radiation exposure wasn't present; so you'd expect to see a bean-shaped blob at the end of the horizontal green stick in the centre of each image with 'ASP' or 'GLU' in the left column ('TYR' was for a different experiment, and is here mostly because the phenyl group looks nice), and you'd expect the blob to look skinnier in the right-hand image where the radiation has made the bit of protein fall off -- in fact, I was expecting the blob to go from bean-shaped and attached to the stick to medicine-capsule-shaped and separated from the stick, but that doesn't seem to have happened.
http://www.globalphasing.com/~twomack/radx/
They have little to do with what I actually do all day, but quite a lot of that is commercially sensitive, and quite a lot of it is deeply esoteric of interest only to crystallographers, and quite a lot of it is throughly boring and involves debugging reams of shell-script, and once you've removed those three parts there's little left.
The sticks are protein structure (green is carbon, red is oxygen, blue is nitrogen, orange is sulphur); Didier Nurizzo at the ERSF laboratory in Grenoble measured by X-ray diffraction the amplitudes of the Fourier components of the electron density in a crystal of the protein thaumatin, Global Phasing's software figured out the distribution of the electron density in space and the placement of the atoms within the electron density, starting from a model of thaumatin measured in a different-shaped crystal by someone else ten years ago, and the green chicken-wire clouds represent the portion of the electron density that our refined model of the atom placement doesn't explain.
Specifically, we measured electron density before and after radiation damage, and then fitted a model where a bit of the protein we'd expect to fall off with radiation exposure wasn't present; so you'd expect to see a bean-shaped blob at the end of the horizontal green stick in the centre of each image with 'ASP' or 'GLU' in the left column ('TYR' was for a different experiment, and is here mostly because the phenyl group looks nice), and you'd expect the blob to look skinnier in the right-hand image where the radiation has made the bit of protein fall off -- in fact, I was expecting the blob to go from bean-shaped and attached to the stick to medicine-capsule-shaped and separated from the stick, but that doesn't seem to have happened.
