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Recipe: Helix Rebuild 5.1
Created by spvincent 36 13
Your rating: None Average: 4.6 (66 votes)


Name: Helix Rebuild 5.1
ID: 100725
Created on: Mon, 02/23/2015 - 18:24
Updated on: Tue, 02/24/2015 - 02:24

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Joined: 12/07/2007
Groups: Contenders
As 5.0 but fixed some

As 5.0 but fixed some problems related to Secondary structure (thanks LociOiling)

This script is probably most useful in the early/middle game (although the chess analogy can be pushed too far). Best used at Low or Auto 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 pose, shake (optionally mutate) and wiggle.
    If the score looks as if it might result in a new best
        Wiggle at Low CI
        If score is better than the current best  
            Shake at Low CI
        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

Post wiggle threshold

Threshold that specifies the maximum allowable difference between the score after shake/wiggle and the best score to allow before proceeding with the mini-fuses. An optimization: the default value is perhaps a bit permissive.

Check conditions met

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

Score type

Default is Normal. Normal/Slow Filters is for slow design/symmetry puzzles (for such puzzles the score type defaults to this mode): it toggles slow filters apart from scoring.

When running, the script will print out from one to three values after each helix rebuild set. The first value, which is usually negative, shows the difference between the score after Shake(or Mutate)/Wiggle and the best current score. This could be used to fine tune the threshold value above. The second value (which will only happen if the first value is numerically below the threshold value) will show the gain from LowCI Wiggle/Wiggle. The third value, if present, shows the gain, if any, from Low CI Shake/WiggleL in this case there will be a score improvement.

Joined: 08/18/2015
Groups: None
Thank you

Thank you for sharing this. I am still new at this, and this looks like it will help.

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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