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Recipe: MicroIdealize 4.0
Created by spvincent 42 51
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Name: MicroIdealize 4.0
ID: 102027
Created on: Sat, 04/30/2016 - 17:20
Updated on: Sat, 04/30/2016 - 17:20
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spvincent's picture
User offline. Last seen 4 days 22 hours ago. Offline
Joined: 12/07/2007
Groups: Contenders
Added a "Worst First" option

Added a "Worst First" option which is enabled by default. If checked, segment sequences are sorted according to the sum of their ideality scores and the worst ones are processed first. This enables you to run the script and kill it after a few iterations (typically 10) when the script is no longer producing gains in the reasonable expectation that the script has gained whatever points is going to.

Algorithm outline

For each section (default length 3) in the selected range (default = whole protein)
    Isolate that section with cut points (prevents the structure from blowing apart)
    Idealize the section
    Close cutpoints
    Wiggle
Joined: 06/30/2016
Groups: Go Science
Thank you so much, this

Thank you so much, this recipe is fantastic.
I was reluctant to use cuts when aligning / setting up proteins because I never seemed to be able to solve the ideality issues without it blowing up, but not anymore!

Joined: 09/24/2012
Groups: Go Science
What are the score types?

in the options "Score type" 1 or 2

LociOiling's picture
User offline. Last seen 6 hours 50 min ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
"score type" setting

Score type 1 is normal scoring for puzzles without filters.

Score type 2 is for puzzles with filters. Score type 2 means filters are disabled during wiggle, but enabled before current.GetEnergyScore is called.

Score type 2 is selected by default if the recipe detects a filter bonus.

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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, Microsoft, Adobe, RosettaCommons