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Recipe: Rav3n_pl DRW v3.2.1
Created by Rav3n_pl 102 1128
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Name: Rav3n_pl DRW v3.2.1
ID: 28877
Created on: Wed, 05/25/2011 - 16:28
Updated on: Sun, 07/31/2011 - 11:16

Deep Rebuild Worst. Script is finding and rebuilding worst scorin parts of protein.

Best For


Joined: 06/17/2010

+ignoring "reference" score part on finding worst.

Reference indicating amino acid type and is always the same. Sometimes "red" area is just because aa type, not that it can be improved.

Defaults are:
- area 2 to 4 segments
- up to 17 worst parts to rebuild
- break and search new bad parts on points
- 15 rebuild tries + shake to stabilize
- fast stabilize
- fuze only if points after stabilize
- work in all-loop mode (structure is saved at start if need)

Script is scoring each rebuild by partial and total score. It is finding up to 7 poses to stabilize. If stabilize yield points it runs fuze.

Script is using slots 3-10, where best position is in slot 3.

Script can be set on many ways, all is described at end.

1. 'drw' - need 'minLen' and 'maxLen'; finding worst scores by len betwen that 2
2. 'fj' - need 'len'; searching len then cutting in pieces 2->len and rebuilds pieces
3. 'all' - need 'minLen' and 'maxLen'; rebuilding ENTIRE prorein (from min to max) like in WalkinRebuild script
4. 'simple' - need 'len'; find and rebuild worst scoring parts of that lenght
5. 'areas' - need secondary structure set and 'true' on at least one of structure

Happy rebuilding :)

Joined: 06/17/2010

+ fixed double stabilizing on same position
+ amount of searched bad areas are increasing by 1 each loop

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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