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Recipe: Quickfix 3.0
Created by spvincent 66 56
4.64706
Your rating: None Average: 4.6 (34 votes)

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Name: Quickfix 3.0
ID: 100031
Created on: Thu, 10/02/2014 - 02:06
Updated on: Thu, 10/02/2014 - 02:06
Description:

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spvincent's picture
User offline. Last seen 3 hours 18 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 shape. 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.

Changes since 2.0

Incorporates elements from MicroIdealize
More efficient and frequent use of Shake and Mutate.
Allows protection of sheets and helices from rebuild.

Generally these changes enable faster recovery.

Joined: 03/08/2012
Groups: None
Quickfix 3.0 hanging in rb

Hi,
rebuild seems to hang and repeating the same three rebuild areas again and again

example
rb 47-50
rb 23-26
rb 22-25

rb 47-50
rb 23-26
rb 22-25

rb 47-50
rb 23-26
rb 22-25

thanks for soon correction

regards

Joined: 09/24/2012
Groups: Go Science
suggestion

it's really a great recipe.

tvdl handled this kind of problem (always repeating the same zones) by allowing user to skip a number of worst zones.

I suggest something like, for several zones, a kind of list of "alreadydone". This "alreadydone" would be true only during 1 or several loops, so that the recipe still can come back to these zones after other zones were managed.
(the recipe is quite gaining when returning to worst segments several times - they should not be skipped forever)

Joined: 08/06/2010
Groups: Contenders
Love the recipe but...

could you add a deselect all in the cleanup routine?

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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, Microsoft, Adobe, RosettaCommons