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Recipe: Helix twister 2.0 (NC)
Created by spvincent 47 31
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Name: Helix twister 2.0 (NC)
ID: 48501
Created on: Tue, 03/11/2014 - 18:06
Updated on: Tue, 03/11/2014 - 18:06
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spvincent's picture
User offline. Last seen 7 hours 37 min ago. Offline
Joined: 12/07/2007
Groups: Contenders
This is an attempt to mimic

This is an attempt to mimic some of the functionality of the tweak tool using bands. It doesn't take long to run and often produces a few points in the endgame but doesn't seem to be a big point getter.

Changes since 1.0: generally made more NC friendly: suggest using at MWP. Also eliminated some useless options and needless complexity.

Algorithm outline

For each helix
    Bracket it with loops of the specified size
    For each residue of the helix, create a band from the alpha carbon into empty space parallel to the backbone (more or less: not sure if I've understood the spherical coordinate system correctly)
    Wiggle a region making up the helix plus spacers on other side.
    Wiggle
    Delete bands
    Shake or mutate
    Wiggle sidechains 
    Wiggle
    Record any improvements as appropriate
end

Repeat in other direction (clockwise/anticlockwise)

Parameters

Loop spacer

Just as when using the Tweak tool you have to bracket a sheet or helix with loop segments; so you can do something similar here.

Target loss

On banded wiggle, aim to lose this amount of points. Band strength will be adjusted if its wildly off but it won't make extraordinary efforts to get

Helix list

All selected by default

Mutate not shake

For design puzzles only. If set will replace Shake after banded wiggle by Mutate as indicated in the algorithm outline above.

Clockwise

Whether a clockwise twist is done first or an anti-clockwise one. Kind of unnecessary.

Check conditions met

When set, will only accept a score improvement if all conditions are met. For puzzles where some restrictions are imposed.

Keep trying

Repeats everything indefinitely with minor random changes to band length and band strength.

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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