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Recipe: Idealize 3.0
Created by spvincent 42 51
4.714285
Your rating: None Average: 4.7 (56 votes)

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Name: Idealize 3.0
ID: 100708
Created on: Sat, 02/21/2015 - 02:47
Updated on: Sat, 02/21/2015 - 02:47
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spvincent's picture
User offline. Last seen 6 days 18 hours ago. Offline
Joined: 12/07/2007
Groups: Contenders
A quick-running script that

A quick-running script that idealizes secondary structure elements. Useful after running a rebuild script.

The principal change since 2.0 is to add a mode for Slow Filters

Algorithm outline

For each secondary structure element
    Idealize
    If the score drop is significant
         Wiggle Sidechains
    end
    Wiggle
    Record any gain
end

It does helices, sheets, then loops: mostly out of a general sense that it's better not to go through the protein in a linear way.

Min residue, Max residue

Only structures that lie at least partially within this range will be processed: by default the entire protein is used.

Score type

Default is Normal. Normal/Slow Filters is for slow design/symmetry puzzles (for such puzzles the score type defaults to this mode): it sets slow filters off apart from scoring.

Joined: 02/24/2015
Groups: None
Thanks

This worked really well for me, thank you!

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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