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Recipe: Local Quake 3.0
Created by spvincent 59 35
Your rating: None Average: 4.8 (4 votes)


Name: Local Quake 3.0
ID: 41305
Created on: Thu, 05/03/2012 - 15:57
Updated on: Thu, 05/03/2012 - 15:57

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spvincent's picture
User offline. Last seen 19 hours 52 min ago. Offline
Joined: 12/07/2007
Groups: Contenders

Changes since 2.5:

Mostly small.

1) Removed irritating warning messages caused by no-longer-used wiggle and shake accuracy controls.

2) Won't band to frozen or locked segments. That and the mutate option (see below) make it usable for design puzzles.

3) Tidies up better after quitting.

Algorithm outline:

1) Pick a couple of amino acids
2) From each of the above two amino acids, create bands to its nearest neighbours (see the script for how it selects these residues)
3) Wiggle
4) Delete bands and shake
5) Wiggle and hope for an improvement from the starting score

Doesn't do any fuzing and generally tries to optimize for speed.

Notes on dialog settings:

Target reduction: The band strength is set so that after creating the bands, wiggle will occur until the score drops by approximately this amount. Supreme precision is not attempted here: the script readjusts band strength based on whether the wiggle in the previous quake overshot or undershot this value.

Max bands: From each centre.

Max band length: No bands longer than this length will be created. To aid in localizing the effects of the Quake.

Second offset: Quake 'centres' will be this far apart along the protein. A value of 0 is allowed and will result in a single centre. The default value of 3 seems to work well: because the number of residues in a helix turn is 3.6 this means that in the case of a helix both quake centres will be on approximately the same side and less likely to mangle it: a bit of a general problem with Quake-style scripts.

Change after: Default 10. After this number of quakes without any improvement in the score, change the value of second offset to something random.

Inverse scale: If true (default), then inversely scale the band strength with length: in other words long bands will be weaker. The idea is to help localize the effects of the quake.

Mutate not shake: This checkbox will appear if and only if the puzzle contains mutable residues. If set, the shake in the algorithm will be replaced by a mutate.

marie_s's picture
User offline. Last seen 1 year 33 weeks ago. Offline
Joined: 05/18/2008
Groups: None
this recipe stops on small puzzles

if less than 37 working segments like symmetry hub test

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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