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Recipe: Quickfix 2.0
Created by spvincent 33 28
4.727275
Your rating: None Average: 4.7 (22 votes)

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Name: Quickfix 2.0
ID: 47725
Created on: Fri, 01/10/2014 - 19:20
Updated on: Sat, 01/11/2014 - 03:20
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spvincent's picture
User offline. Last seen 14 hours 51 min ago. Offline
Joined: 12/07/2007
Groups: Contenders
Quickfix is not intended to

Quickfix is not intended to improve the score, although it might have that happy side effect. Rather; the script is designed to rapidly recover from extremely low scores such as those that occur after actions like cut point closure and register shifts, while making no more than minimal changes to the protein. Eventually the score should rise to a value where it's safe to kill the script and subsequent wiggling won't cause the protein to fly apart.

The default values work pretty well: still some notes may be helpful.

Pass 1

Looks for adjacent residues which have a combined backbone score less than a threshold value (default -2000): then applies a quick local wiggle. Particularly intended to help tidy up after cut point closure. Very quick so might as well always leave it on.

At the start of the script, anything frozen will be unfrozen and all bands will be disabled. On killing the script bands will be restored and the pose set to that corresponding to the most recent improvement.

Pass 2

First, wiggles sidechains. Then looks at the total scores of all 3-residue segments; selecting the worst and local wiggling it. If said local wiggle doesn't improve the score, try rebuilding that section a few times: then take the best-scoring result and local wiggle.

Repeat all the above (taking care not to hammer away unsuccessfully on one section should that prove intractable), until the total improvement for three consecutive tries is less than some threshold (default=1000), whereupon things move on to Pass 3 (if selected).

Pass 3

Similar to Pass 2 except it local wiggles/rebuilds the worst-scoring 4-residue section (as opposed to 3). Rebuilds if the gain from local wiggle is less than a certain threshold (default=100) Also at intervals does a Shake (or Mutate: see below). Does not terminate: it's up to the user to kill the script, whereupon the highest scoring solution made is restored.

Leave sheets alone

In Passes 2 and 3, don't work on sections that include a sheet (so they don't get mangled)

Mutate not shake

For design puzzles only. If checked, substitutes a mutate for a shake in Pass 3. Often better but Mutate can be quite slow.

Joined: 09/24/2012
Groups: Go Science
Thanks spvincent

Very useful after hand folding !

Joined: 04/15/2012
Groups: Beta Folders
Yes, this will be helpful. So

Yes, this will be helpful. So long taking eons trying to recover from a very low score. :)

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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