The latest incarnation of Loop Rebuild: hope people find it useful. It was working nicely before NC came along and I was all set to release it then: seems to work reasonably now but a lot of testing needs to be redone.

Given a number of rebuilds, which is the best one to use? Not necessarily the best-scoring one, or even the best-scoring one at low CI (see http://proteinoftheday.wordpress.com ), or the best -scoring after shake, but probably the best-scoring after shake and wiggle, which is what's going on here. Since Shake and wiggle are computationally expensive, considerable effort is made to work only with the relevant sub-section of the protein.

Best used at high WP.

Algorithm outline

For each section to rebuild
   For each rebuild (defined by N Rebuilds)
      Rebuild once
      Set selection to that defined by Inner sphere
      Shake
      Wiggle for a fixed number of iterations
   end
   
   For each pose corresponding to the two best scores above
      Set selection to that defined by Outer sphere
      Wiggle adaptively in the NC-approved way
   end

   Take the best pose from the two above
   Set selection to that defined by Outer sphere
   Shake (or Mutate if a design puzzle and that option chosen)
   Wiggle again if the Shake or Mutate gained anything.

   If we've gained an overall improvement
      Shake at low CI
      Wiggle at normal CI
      Record overall improvement
  end

end

Dialog settings

Rebuild Length

How big a section to rebuild. Values from 4 to 6 are typically most useful.

Min residue, Max residue

The range to be rebuilt: by default the entire protein. These values can be usefully changed to whatever region of the protein you're working on: it's often desirable to set them to the start and end of a loop you're working on.

Loops only

When set, only loops will be rebuilt, although a single non-loop residue is allowed, This effectively means that the end residue of a helix or sheet will be treated as a loop for rebuild purposes.

Convert to Loops

Meaningful if and only if Loops nnly above is unchecked. If checked, non-loops will be converted to loops before rebuilding: if not the secondary structure will be maintained.

So for example, if you had a helix from 35-40 and you wished to rebuild it as a helix with, say , a loop spacer 2 residues wide on either end, suitable settings would be:

Rebuild Length 10
Min residue 33
Max residue 42
Loops only unchecked
Convert to loops unchecked

Number of rebuilds

How many rebuilds to attempt. The default is a bit of a compromise: too small a value means that not enough poses will be created: too many and there's a high probability of ending up working on a pose which is extremely similar to the starting structure.

Inner Sphere,Outer Sphere

Radii that define the spheres surrounding the rebuilt region: used to restrict the number of segments that need to be wiggled/shaken as a speed optimization.

I think the default values may be a little conservative and it would be safe to reduce them slightly.

Mutate not shake

This checkbox will appear if and only if the puzzle contains mutable residues. If set, the side chain wiggle in the algorithm will be replaced by a mutate.

Check conditions met:

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