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Recipe: Loop Turn-Twist 1.0
Created by brow42 78 351
3.2
Your rating: None Average: 3.2 (5 votes)

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Name: Loop Turn-Twist 1.0
ID: 39500
Created on: Mon, 03/12/2012 - 08:41
Updated on: Wed, 07/18/2012 - 19:52
Description:

Twists and Rotates segments. Like sheet rotation, but also twists, and works on loops and around U-turns. Experimental, doesn't always work. Maybe you can figure out why?



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brow42's picture
User offline. Last seen 2 days 10 hours ago. Offline
Joined: 09/19/2011
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For rotating/twisting/untwisting sheets, twists around corners

This script will turn and/or twist a region of the protein. Unlike the tweak tool, it work on loops, not just sheets, and it can make a twist, not just straighten, and you can pick which end rotates, or both.

A good use is to continue the turn/twist around U-turns at the end of a sheet. Think of a rolled up towel, how if you rotate one end, it all wants to rotate.

The script has a built in undo function, so you can back up if you turn/twist too far, or in the wrong direction. There are 25 undo slots.

Rotation is defined by the "Right Hand Rule". If your right thumb points along the protein towards higher segment numbers, RIGHT rotation is the direction your fingers curl. Rotation rotates the entire region the same way; twist rotates the ends of the region in opposite directions. If you combine rotation and twist of the same strength, then you can make one end of the region be pinned.

A help panel explains all this. Or, you can just guess, and if it's wrong, hit the built-in undo button and reverse your settings.

It doesn't always work...maybe it's not strong enough, or maybe in a mostly folded protein, all the packed sidechains lock it in place...or maybe there are problems with the coordinate system. This recipe is experimental. I'm posting it so that you can try it out on Snow Flea Antifreeze protein, which has twisted sheets. I've added lots of knobs. Short regions seem best.

Version 0.1 beta will expire July 15 2012. At that time I'll add in any suggested improvements or bug fixes and release it as 1.0.

brow42's picture
User offline. Last seen 2 days 10 hours ago. Offline
Joined: 09/19/2011
Groups: None
Update

Removed beta status.

It seems the reason some times things won't twist is clashing by very large sidechains. They won't rotate through other sidechains/backbones.

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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