Hi!

I've read the FAQ and feel I have a good grasp of what it is Rosetta is doing.

However, I'd like to know more.
What do the colors mean? Does each color correspond to a particular amino acid? If so, could we get the color chart for these?

During the more detailed computation phase, I see structural details within the protein. Any chance we could get a primer on what these mean?

I don't expect (and probably don't want) you to attempt to educate us in the deep subtleties of protein chemistry. But I'm curious about what I'm seeing and I'd like to know more detail! I can look at Einstein or SETI and understand exactly what it is I'm seeing. I'd like to do the same for Rosetta.

Thanks,
Raoul

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Hi Raoul,
As far as I know, the colors are only for making the the graphic easier to look at - they help distiguish the different bits that might be in front or behind other bits.

You might be interested in some of the more recent posts in this thread.

If you go to the Rosetta homepage, and look under the "About" section at the left, there are many links to information that should give you the level of detail you seem to be after. Some of the references are WAY more scientific then I am, so just skip those that seem a little too deep.

As for the colors, I believe it simply helps you identify the start and end of the protein's backbone. If you could grab the ends and pull it straight again, you'd simply see a rainbow of colors from red through blue. This is true regardless of how many amino acids are in the protein being illustraited.

The further structural details you mention sounds like you are describing what they call the side chains.

I did find a primer on the subject here. Be sure to click on each of the four section links at the top, in addition to reading the initial page of description.

From there, if you have other specific questions, the Science Message Board would be a great place to post them.

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