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Recipe: Helix Rebuild 4.0
Created by spvincent 40 12
Your rating: None Average: 4.3 (26 votes)


Name: Helix Rebuild 4.0
ID: 48811
Created on: Mon, 04/07/2014 - 13:42
Updated on: Mon, 04/07/2014 - 20:42

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spvincent's picture
User offline. Last seen 12 hours 38 min ago. Offline
Joined: 12/07/2007
Groups: Contenders
This script is probably most

This script is probably most usefully used in the early/middle game (although the chess analogy can be pushed too far). Best used at Low Wiggle Power I think: the script never terminates.

Algorithm outline

For each helix
    For however many rebuilds specified
        Bracket it with a loop on either end
        Rebuild once
        Shake and wiggle briefly
        Record score
    Take two best poses from above
    Wiggle each
    Take the best scoring of those two, shake and wiggle.
    Nudge if appropriate
    Record any gain

Selection is restricted to the local vicinity of the helix for the sake of efficiency.
See values of inner_cylinder_radius and outer_cylinder_radius, which are probably unnecessarily conservative.

Loop spacer

Specifies the length of the loops at either end of the helix. The greater the value, the more freedom there is for the helix to adopt new configurations but the less likely you are to get small refinements.

Helix List

Initially all are selected. Helices with locked or frozen backbones will not appear in this list: frozen sidechains are allowable though.


How many times to rebuild each helix

Mutate not shake

For puzzles with mutable residues only

Check conditions met:

If set, check that conditions are met before accepting any improvement. For puzzles with RMSD conditions, etc.

Joined: 11/08/2011
Groups: Gargleblasters
I really like turning off the

I really like turning off the blue fuze option just to see if the rebuild is going to give good points. Then I can either go with that rebuild or rebuild with the fuze from the last best.

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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