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Joined: 05/10/2008
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Maybe I don't understand something about how the rebuild tool is supposed to be used. When I run it, the purple tube bounces around wildly, and when I stop it, the protein remains totally unchanged. No matter how different the purple tube looks when I stop it, it seems to have absolutely no effect on the structure.

Am I trying to use it in an invalid situation? Should the protein structure always change to match the purple template?

Jwb52z's picture
User offline. Last seen 28 weeks 6 days ago. Offline
Joined: 05/11/2008
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Here's how it works:

You have to use one or a series of rubberbands on the piece you want to rebuild to get it to work. The rubberband or series of them guides the rebuild and pulls the rebuild where you want it to go. It is not like wiggle as it is not based upon energy, just position. After you find the position you want, you must stop it quickly or it will change on you. Then, when you get the right structure you want, you have to go back to shake and wiggle to redo your score. I hope this was helpful.

Angus's picture
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Joined: 06/04/2008
Groups: Beta Folders
Why aren't these types of

Why aren't these types of things documented?

What good is a tool with no instructions on how to use it?

Joined: 05/10/2008
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Very helpful, thanks!

Thanks, Jwb52z - works like a charm!

feet1st's picture
User offline. Last seen 7 years 4 weeks ago. Offline
Joined: 01/25/2008
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I made a video of rebuild

If you'd like to see it, I posted a video on how to use the rebuild tool. It is described in this thread.

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
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