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Recipe: Toolbox - selection interface
Created by MurloW 172 80
Your rating: None Average: 4.7 (12 votes)


Name: Toolbox - selection interface
ID: 101820
Created on: Wed, 01/27/2016 - 03:09
Updated on: Sun, 02/07/2016 - 20:57

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MurloW's picture
User offline. Last seen 2 weeks 12 hours ago. Offline
Joined: 11/21/2012
Toolbox includes:

-A Rebuilder, Rainbow whole structure or Selected residues only;
-a Cut and Wiggle routine, selected residues only or worst backbone scores and all loops;
-an Idealize routine, selected residues only or whole structure variable length with the option to use cutpoints;
-a Rotamer Tester, selected residues only (recommended, you're better off with AcidTweak/Mutators when not targetting specific segs) or all polar residues (hydrophilics + TYR & TRYP), tries all rotamers of current sidechain and local wiggles;
-and bruteforce polar AAs, while testing their rotamers (very lengthy, up to ~30mins/residue), if you pick the right residues this will do wonders for finding HBonds,
e.g.: a network is <75% satisfied -> select promising nearby residues (and/or those already contributing to the network) and run;
-Contact Bander, bands all contacts with a heat >=0.75 and runs WorkExBands;
-Work Existing Bands, randomly disables/enables bands and quakes the structure (needs user created bands, more bands = more profit);
-BandFuze, creates random bands and quakes the structure. Updated/revised, same functionality.
If multiple Actions are checked they will happen in consecutive order, top to bottom, as displayed in the dialog (unless loop forever negates this).
A single pull of Contact Bander and/or Quick Quake happen around the same time as qStab/fuze, after the rebuild/cuts/idealize stabilization wiggles.
Contact Bander, Work Exist. Bands and BandFuze loop forever until cancelled.
If 'Disable filters during operations' is unchecked, recipe will not touch the filters and leave them as is,
this can be used to run the recipe with only 1 filter enabled, or to keep any filter bonus from locking up the structure, etc.
If it is checked, all filters will be enabled to check score, and disabled during any and all other operations.
Has no effect on puzzles without filters, just ignore the option.

MurloW's picture
User offline. Last seen 2 weeks 12 hours ago. Offline
Joined: 11/21/2012

2 bugfixes: rebuild length on rr not working right and occasional missed points from shock bands.

sorry about that.

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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