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Recipe: Loop explorer 3.01
Created by spvincent 41 23
Your rating: None Average: 4.7 (6 votes)


Name: Loop explorer 3.01
ID: 101630
Created on: Sun, 11/22/2015 - 18:09
Updated on: Mon, 11/23/2015 - 02:09

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spvincent's picture
User offline. Last seen 4 hours 2 min ago. Offline
Joined: 12/07/2007
Groups: Contenders
(Change from 3.0 : on

(Change from 3.0 : on termination load results in Quicksave slots for easy access via Undo as suggested by Bruno)

Repeatedly rebuilds, shakes and wiggles a selected area (not necessarily a loop, the name's a bit misleading); storing the most promising results in Quicksave slots.

This script is not intended to improve your score in itself, although it may have that happy side effect. Its intended use is to explore new configurations of an existing region, which can then be loaded, inspected, and the rebuilder of your choice used to hammer away at the new loop and hopefully produce a better score.

This script never terminates. It's up to the user to stop it after a bit and examine the poses in Quicksave slots 11 and 12 which are loaded on termination prior to restoring the current best pose. Suggest taking the best-looking (not necessarily the higher scoring) of these two poses and proceed from there.

Min residue: max residue

Used to define the area (not necessarily a loop, despite the name of the script) to be rebuilt. A likely candidate would be one 8-12 residues in length with an appearance that displeases you or which you have cause to think may be stuck in a local minimum.

Post rebuild

Specifies the action(s) to be taken after a rebuild. The default is a Shake/Wiggle but other action sequences are provided: they allow the usual trade off between speed and accuracy.

Rebuild threshold

The idea is to reject rebuilds that are too similar to the original. If the score after a rebuild is less than the original score by this value or lower than the rebuild will be rejected. ( "bt" will be printed in the output ). Not entirely sure how well this will works in practise but it struck me as a nice feature when writing the script. Drag slider to zero to effectively remove this feature.

Score type

If set to 2, toggles filters off except when determining the score. For better performance on slow design puzzles.

Joined: 02/08/2012
Groups: None
Wishfull Thinking

I wish after rebuild, it would start off with CI=0.01

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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, Boehringer Ingelheim, RosettaCommons