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Recipe: Walkin Rebuild v4.0.4
Created by Rav3n_pl 60 2063
Your rating: None Average: 5 (8 votes)
Used 3547 times with an average impact of -667 points.


Name: Walkin Rebuild v4.0.4
ID: 8634
Created on: Tue, 08/17/2010 - 16:37
Updated on: Sat, 08/28/2010 - 17:07

Rebuilding form point to point. Now have shpered (faster) rebuild stabilizer and LWS option.

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Joined: 06/17/2010
changes and usage

Walkin Rebuild v3
- walks form point to point and rebuilds structure.
- can work in allloop or structure mode

Some changes in rebuild algo inspired by Nerro`s script :)

Usage on start of script, if any argument set to nil it becomes default

start segment - default = 1
end segment - default = end of protein
minimum length - default = 1
maximum length - default = 5
all loop - default = false

Joined: 06/17/2010

Changed max rebuild tries to 5 (sometimes looks like "stuck" on helix or sheet).
Try change to all-loop in script.

Joined: 08/09/2010
Possible bug

I noticed when using the script the score reset to after an unsuccessful rebuild was below my maximum score, even though the maximum was set moments earlier by the script. So either the script was missing a momentary maximum or there was some bug with resetting the score.

Joined: 06/17/2010

Rewrite :]

ReBuild(sSeg, eSeg, backward, minLen, maxLen, maxiters, loopmode, sphere, lws, bf)
sSeg- start segment to rebuild
eSeg- end segment to rebuild
backward- start from end
minLen- minimum sgmnts len to rebuild (may be even 1)
maxLen- maximum len to rebuild (over 7 seems useless)
maxiters- maximum tries to rebuild
loopmode- work in all-loop mode
sphere- sphere size for shake/wiggle after rebuild
lws- LWS sphere around (min gain 2pts, not LWSing totally)
bf- BlueFuze sphere around

Now it try first done rebuild. If no gain after rebuild moving to next len/position.

Should catch all possible points :D

Looks better in new interface (normal not showing selected segments).

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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