Temperature tool?

Case number:845813-813187
Topic:Game: Tools
Opened by:Migi
Opened on:Thursday, January 8, 2009 - 19:01
Last modified:Friday, January 6, 2012 - 01:16

I've posted this idea on the forums at first, but Steven Pletsch suggested that this would be a better place to post it. So I did :p

I will try to summarize it a little:
The suggestion is for a new "Temperature" option while you are wiggling the protein. The user can set the temperature to either 0°K (no effect) or any other temperature he likes, which results in random forces cast on the wiggled parts. The hotter, the stronger those forces. This would automatically "nudge" proteins out of unstable folds and would replace the current nudge/wiggle/nudge/wiggle strategy.

You can read the whole idea here:

(Thu, 01/08/2009 - 19:01  |  6 comments)

Migi's picture
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By the way, I know some programming and, if necessary, I could help converting the idea into code.

I don't think that this would be hard to program, it's just some random forces and a new gui, and maybe some altering of the tutorials. Most of the work would probably go into fine-tuning.

xiando's picture
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Great idea. I'm in total agreement with adding this tool. I don't know that it would *replace the current techniques, but it would definitely be a great tool, and it *could conceivably result in exactly what you predict..

I had suggested a tool called "jiggle" early on that I guess is similar, in that its purpose was to perturb the protein's selected - like rebuild or isolated wiggling - residues with a quasi random vibration to the protein's residues, except that yours is thermally driven, whereas the older and more inaccurate suggestion was an injected mechanical vibration..

Yours is a more scientifically accurate description and is, I believe, accounted for in the equations of motion in molecular systems, since thermal energy is where all the natural jostling comes from anyway.

Joined: 05/30/2008
Groups: Contenders

I agree and think this would be a very useful tool, although I think it would take a long time to really learn how to properly use the tool.

I think some useful information that would help us narrow down the range at which we should maintain the temperature would be the temperature of the environment where the protein is assembled, i.e. 310K for human proteins.

Migi's picture
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Nudge then wiggle, repeated over and over again, finalized by locking and doing the same to isolated parts. Not much intuition required.


Trying to think intuitively what the shape of a protein should be, fold it that way and let the computer run the mindless tasks. Try things, see what works and what doesn't work. Develop your understanding of proteins. Use it to help science.

The brain processes about 100 TeraFLOPS per second. Even if we use only 1% of that to play the game, this is still a 1998 supercomputer. Don't waste it on brainless nudge-wiggle cycles.

"Don't use cannon to kill mosquito."
 - Confucius.


We need more tools. Tools that automate the tiresome parts and let us play the actual game: experimenting, creating new strategies, etc. However, the problem with tools is that they can easily clutter the nice user interface or the user friendliness. But this Temperature tool would be very easy-to-use, it would fit in nicely in the GUI and it would most importantly be intuitive, make sense and be extremely useful.

So, once again, if you need any help with coding or making tutorial levels for this, just ask!

(PS: Xiando's argument that tools cause API crud is true, so I edited this from "want more tools!" to "want this tool!", because that's what I'm really trying to say)

axcho's picture
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When we implement the flexible inventory system for managing tools, we will be able to start creating the various new tools that are being suggested. This temperature/jiggle tool sounds like a good idea.

Joined: 06/17/2010



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