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Recipe: DRW v3.4 Disulfides (3.4.2)
Created by brow42 79 387
4.369565
Your rating: None Average: 4.4 (46 votes)

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Name: DRW v3.4 Disulfides (3.4.2)
ID: 42502
Created on: Sat, 06/16/2012 - 12:44
Updated on: Sun, 07/22/2012 - 21:24
Description:

Deep Rebuild Worst. Script is finding and rebuilding worst scorin parts of protein. Never breaks disulfide bonds



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brow42's picture
User offline. Last seen 1 week 1 day ago. Offline
Joined: 09/19/2011
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New option to save bridges

This is a somewhat hacked version of DRW to preserve disulfide bridges. Hopefully Rav3n will clean it up and make it standard in all his scripts (hint!)

To use, set savebridges to true (default in this version)

If savebridges is true, and there is a cysteine in your rebuild range that starts out bonded to another cysteine, then the script will reject any rebuilds that break that bond. It will do extra rebuilds (9 instead of 3) per slot to find one that preserves the bond. If the bond breaks during qstab or fuze, the result isn't saved. If the best solution breaks the bond, it is ignored just as if the score had not increased.

It's a little hackish with all the if statements...a better way might be to change the save functions. I'll leave that decision up to Rav3n.

brow42's picture
User offline. Last seen 1 week 1 day ago. Offline
Joined: 09/19/2011
Groups: None
Patch 3.4.1

Fixed a bug with variable extra_rebuilds...it's supposed to do extra rebuilds for each rebuild attempt but wasn't being initialized properly, leading to infinite rebuilding if a rebuild fails.

brow42's picture
User offline. Last seen 1 week 1 day ago. Offline
Joined: 09/19/2011
Groups: None
patch 3.4.2

A bug was allowing rebuilds to break bonds (which would be rejected in qstab or fuze), instead of doing extra rebuilds to find a non-breaking rebuild. It now does the extra rebuilds (9 total) per slot to find a non-breaking rebuild.

New option, globalbridge, if true, makes the script count all the bridges, so that it can catch them being broken during qstab/fuze. If not set, then it uses old behavior of only watching the rebuild segments.

Bridge counting now runs over a list of cysteines instead of checking all 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, RosettaCommons