spvincent Lv 1
Changes since 5.2
1) Added threshold value for post-rebuild threshold improvements at low CI.
2) Alternate score functions
The default settings work pretty well if you don't want to be bothered reading this.
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.
Tested and best used at Auto 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
if initial score minus current score is less than threshold value
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.
Wiggle at low CI
Wiggle
If we've gained an overall improvement
Shake at low CI
Wiggle at normal CI
Record overall improvement
end
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.
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.
Post wiggle threshold
An optimization used to prevent doing unnecessary shake/mutates. If the score after the best rebuild/shake/wiggle (as described in the algorithm) is below the best by more than this amount, then skip the subsequent fuze-like processing as an overall gain is unlikely,
The default value works quite well: it might be worth lowering it to say 10 for endgame running or raising it yo 60 or aso at the beginning, particular for dimer puzzles where overall scores are greater than usual.
Score type
Allows different scoring functions to be used - the values are:
1) Normal. Self-explanatory: the value as described by the program. Most of the time this is what you'll want
2) Exploration score. Oerhaps one day there will be another exploration puzzle.
3) Energy score. Design puzzles without those filters.
4) Hiding. Just use the hiding component of the score
5) Bonding. Just use the bonding component of the score
In the last two cases, no fuzing will be done, irrespective of the threshold value.
Check conditions met
If set, check that conditions are met before accepting any improvement. For puzzles with RMSD conditions, etc.
After each rebuild sequence, up to three numbers are printed.
The first is the difference between the starting score and the best score after a rebuild/shake/wiggle sequence.
The second, which will only be shown if the number above plus the threshold value is greater than zero, shows the gain from the subsequent Shake/Wiggle/Wiggle at Low CI/Wiggle
sequence. Watching this value provides a clue as to what value to set the threshold slider: ideally the slider should be set to the maximum likely gain value .
The third, which will only be shown if the previous processes resulted in an overall gain, is the gain from doing the final Shake at low CI/Wiggle sequence.
