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Migi's picture
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I think it would be a massive help if we'd have some kind of "wobble" option in the wiggle tool, which casts random forces on the parts that are being wiggled. This would make the protein start shaking around (only slightly of course), so it would never get "locked" in an instable fold, because it would get nudged out of such a fold.

It could be a tool on its own, but I think it would be a better if it were an option inside the wiggle tool, controlled by a slider that goes from 0% (default, works the way wiggle does right now) to 100% (very shaky, probably unfolding the protein).

This would require some extra gui, but apart from that I think it's easy to program, and it would certainly be worth the effort: we wouldn't have to nudge/wiggle/nudge/wiggle/... anymore! We could wiggle and slowly decrease the wobble value from say 50% to 0% and have a pretty stable protein in seconds!

Joined: 05/26/2008
Groups: Hold My Beer
I like that idea.. sounds

I like that idea.. sounds good, you should post it as a suggestion under the feedback option up top

Migi's picture
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Temperature

Thanks Steven, I've posted it as a "feature request", hoping this may one day come true... :-)

After having read http://en.wikipedia.org/wiki/Temperature#Overview (especially the image on the right), we could as well give the option the name "Temperature", which would be a lot more intuitive than just "wobble tool".

If we call it temperature, we could make the gui for it very shiny and easy to use: a thermometer on the left becomes visible when you are wiggling the molecule. It goes from 0°K (0 degrees Kelvin, aka as cold as possible, would act the same as wiggle does now), to some more or less realistic value. When you start wiggling, the thermometer indicates 0°K but you can click anywhere on it to make the temperature go up or down to where you clicked.

This would not only be (very) useful while folding, it would also develop our intuition and understanding of the relationship between protein folds and temperature, and why we die if our blood is too hot (proteins unfolding), and about a thousand other things!

Migi's picture
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Temperature

(edit) Sorry for the quadruple post...

Migi's picture
User offline. Last seen 5 years 27 weeks ago. Offline
Joined: 12/06/2008
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Temperature

(edit) Darn 500 Server Errors

Migi's picture
User offline. Last seen 5 years 27 weeks ago. Offline
Joined: 12/06/2008
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Temperature

(edit) Please remove these messages...

Joined: 06/10/2008
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This is what wiggle already

This is what wiggle already does. It gets stuck because it is hitting a local maximum.

Joined: 05/10/2008
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Wobble Tool

I like the idea. I already mostly fold my proteins by just repeatedly nudging them slightly then wiggling them to find stable configurations by trial and error (especially as your score gets really high and you start looking for fractions of points). Automating this tedious process would be really helpful.

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