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Recipe: Quickfix 1.1
Created by spvincent 39 32
4.5
Your rating: None Average: 4.5 (16 votes)

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Name: Quickfix 1.1
ID: 44264
Created on: Thu, 09/27/2012 - 19:22
Updated on: Thu, 09/27/2012 - 19:22
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spvincent's picture
User offline. Last seen 2 days 15 hours ago. Offline
Joined: 12/07/2007
Groups: Contenders
Description

The purpose of this script is to repair a very low scoring solution; such as might be produced after fixing cut points or doing a register shift. It use a combination of local wiggles, rebuilds, and side chain wiggles to improve the score from -478094 (or whatever) to something respectable like 9000 or so while maintaining the general structure of the protein.

The script doesn't terminate: quit when it doesn't seem to producing points at a reasonable rate. By that time the protein should be in a state where you can wiggle without it blowing apart.

1.1 : added workaround for initial scores < 1e6

Joined: 05/28/2012
More selected wiggle

This would probably go a lot quicker if you did multiple wiggle areas at once. I know when i manually select all the cut-points and wiggle them all at the same time the score increase sooo much. maybe if you could pick like 5 or 10 of the worst areas to local wiggle at the same time.

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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, RosettaCommons