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Recipe: Helix Twister 1.0
Created by spvincent 42 32
4.603775
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Name: Helix Twister 1.0
ID: 47646
Created on: Tue, 12/31/2013 - 16:39
Updated on: Tue, 12/31/2013 - 16:39
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spvincent's picture
User offline. Last seen 14 hours 17 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.

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.

Band length

Adjust to taste but the default value seems to be reasonable.

Band strength

Ditto.

Helix list

All selected by default

Co-twist

If set to true, twists a helix together with the nearest selected helix. Seemed like a good idea at the time but not sure how useful it really is: I haven't seen gain from it.

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