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Recipe: Jolter 2.0
Created by spvincent 42 21
Your rating: None Average: 4.4 (40 votes)


Name: Jolter 2.0
ID: 101947
Created on: Sat, 03/12/2016 - 12:30
Updated on: Sat, 03/12/2016 - 20:30

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spvincent's picture
User offline. Last seen 35 min 24 sec ago. Offline
Joined: 12/07/2007
Groups: Contenders
Jolter is a rebuild script

Jolter is a rebuild script that's designed, as the name suggests, to jolt the protein out of a local minimum (that's the intent anyway), although it does seem very useful as a general purpose rebuild script to use in the middle game.

It successively rebuilds alternate structural elements in the protein, being prepared to accept a small loss in score after the usual quota of shakes and wiggles that normally follow a rebuild (gains are also accepted, needless to say).

The script never terminates: it's best run overnight or at least for a couple of hours. After cancelling the script you can start from the existing position, or, since the score meanders up and down when running the script, reset best.

Algorithm outline

Get list of secondary structure elements (helix, sheet, loop)

For each element (going alternately)
Repeat 4 times (default value of N rebuilds below)
Rebuild element
Shake/Wiggle etc (Post Rebuild below)

Take best scoring position from above
Wiggle at low CI/wiggle
If score is better than the current score minus the rejection threshold then
make this the new current position


Min residue: max residue

Used to define the region of the protein to be rebuilt. Any secondary structure element that lies at least partially within this region will be processed.

Additionally, an element that contains a residue with a frozen backbone will not be processed.

Further control over which elements are to be rebuilt is provided by the Rebuild helices (etc) checkboxes below.

N Rebuilds

How many times to rebuild each structure. Reducing this value may result in a more structurally diverse result, albeit at the likely expense of a poorer score.

Post Rebuild

The actions to be taken after each rebuild, The default value for non-design puzzles is (Shake/Wiggle/Shake/Wiggle) but for design puzzles number the default action is (Shake/Wiggle/Mutate/Wiggle).

Rejection threshold

This is an optimization to prevent unnecessary processing being done subsequent to rebuilds which are clearly going nowhere. If Post Rebuild above is set to either of the last two positions, then, after the first Shake/Wiggle, further processing is only done if the score is lower than that of the current starting pose by less than the Rejection Threshold.

The default value of 200 works quite well but at script termination, some performance data is printed out to aid in determining a good value for this parameter. Of the rebuilds that were processed (i.e.passed this threshold test), the best gains from the subsequent Shake (or Mutate)/ Wiggle are printed. If these values are close to the rejection threshold, then the threshold should probably be increases: on the other hand if they are all much lower the rejection threshold can probably be safely reduced.

Maximum loss

Specifies how big a loss in score is permissible. The larger the value the greater the change in structure that will be allowed at the possible expense of score.

Setting this to zero means that only gains will be permitted.

Rebuild helices, Rebuild sheets, Rebuild loops

Control over which structural elements to rebuild

Helix spacer, Sheet spacer, Loop spacer

When rebuilding, specifies the length of a spacer at either end of the structural element that will be included in the rebuild. So if the value of Helix spacer were 3, then when working on a helix from 63 to 75, the actual rebuild length would be 60 to 78.

Score type

If set to 2, toggles filters off except when determining the score. For better performance on slow design puzzles.

Joined: 03/08/2012
Groups: None
Working Score decreasing

I noticed, that the Working Score is sometimes decreasing
see picture

gitwut's picture
User offline. Last seen 2 years 48 weeks ago. Offline
Joined: 05/18/2012
Groups: Contenders
As described

Yes, Stephen mentions that it accepts lowered scores (you can control acceptable losses via slider at start of the script). It backtracks when attempting to break out of a minimum.

Joined: 09/24/2012
Groups: Go Science
Suggestion for Sketchbook puzzles

I made a private 2.1 version only by allowing gain in the "accepted loss" slider.

The gain (negative loss) works like a minimum point per iteration: it saves moves, which is great for sketchbox puzzles.

I suggest you to make an official 2.1 or 2.0.1 version like this.

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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