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Joined: 11/10/2007
Groups: Window Group

The developers have been discussing using the sidechain glow for some
protein design-related visualizations.  Now that the sidechains are colored by
whether they are hydrophobic or not, is the "Glow hydrophobic
sidechains" view option still useful?  Would it be greatly missed if
the sidechain glow were used for something else?

Joined: 11/20/2008
Groups: None
So the coloring of

So the coloring of sidechains didn't always reflect the fact they were hydrophobic or not, huh?....and with that I finally understand why there is such a thing as a hydrophobic sidechain glow in the first place!

So no, I won't miss it (never use it as I didn't see "the point" of using it)

Joined: 05/17/2008
Groups: None

Are you talking about the blue and orange glow that tells you whether or not it is hydrophobic or hydrophilic? That is extremely useful. You should run your idea of what you would like to change it to by us and then I think we could give you better feedback.

Joined: 12/14/2008

My first thought: Why bother? I never have it activated. It just makes the protein less visible.

But I came here in December, so I did never see what anjen is decribing.

Joined: 11/10/2007
Groups: Window Group
Yes, skyleriberg, I'm

Yes, skyleriberg, I'm referring to the blue and orange glow around sidechain.  At one point, the sidechains themselves were not colored the same blue and orange, but now that they are, the glow color doesn't provide any new information.  Since that is the case, we've been discussing using the glow for some other visualization.

At this point, one possibility is this: When doing design, players can mark some sidechains as able to change their amino acid type during a shake; marked sidechains could glow.

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Joined: 05/29/2008
Groups: Void Crushers
In normal view mode the

In normal view mode the glowing is pointless now, but in CPK-view mode it's still informative.

axcho's picture
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Joined: 12/18/2007
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I'm not sure what the story

I'm not sure what the story is about the Hydrophobic View mode, maybe Seth can elaborate on that?

But based on what we're thinking of using the hydrophobic glow for in design mode, we could actually still have both (black glows for autodesignable and colored glows like currently). It's just that Zoran (and perhaps others) don't like the hydrophobic glows and want to trim some fat from the interface, so to speak.

Joined: 05/17/2008
Groups: None
Take it away!

Do what you want with it. I am looking forward to design a lot. I haven't been folding much, but you can bet I will have the app up when you release this feature.


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