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Joined: 05/19/2008
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The last changes on 23 November are not really clear, or beneficial... for me at least.

The coloring of the side chains hide the actual value of how bad or good they are, being ochre or blue, regardless any view option changes. Before, the palette from green to red told us a lot about whether they are good or not.
Now, flipping side-chains to gain more point is random. Before, we had some hints from the coloring.

About the back bone coloring: If I turn off relative score coloring, the backbone is all green, side chains are ochre and blue... What shall I do?
When I turn on relative score coloring, only one place is highlighted red, the rest is green. but that very red place I can do nothing about after 50 rebuilds and wiggles, so I'd like to move on, but where to, when the rest is GREEN, all GREEN.

It is like folding in the dark. If that was the point, you achieved it big time.


Joined: 05/19/2008
Groups: None
I forgot to mention, that

I forgot to mention, that the fraction gauge I am missing very much. Could we get it back please?
The distance between a point to another is not ONE unit. There are smaller distances i'd like to know about.

Thank you.

Bozonik's picture
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Joined: 10/27/2008
Groups: xkcd
With the fraction gauge did

With the fraction gauge did you mean the progress bar? (you can now get decimal scores if you go to the General Options menu).

I quite like the blue/yellow representation but I know what you mean with the all green bar one red thing, I have the same on 108 at the moment. One long way forward is to go into note mode and right click on the sidechains - brings up a little bit of info about their scoring.

axcho's picture
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Joined: 12/18/2007
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color scheme will be fixed soon

Sorry about the poor color choices in the last big update. I've since reverted the backbone colors back to the classic green->brown->red, and that change should be up by Sunday.

We're keeping the sidechains colored for hydrophobic/hydrophilic. You can still tell how well the sidechain is doing by the color of the backbone segment it's attached to. In the original color scheme, that backbone color was just copied onto the sidechain, so there is no information actually lost when the sidechains are colored orange and blue.

Let me know what you think after Sunday. Thanks!


Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, Boehringer Ingelheim, RosettaCommons