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Recipe: Zero Length Bands v 2.0.1 -- Brow42
Created by brow42 131 82
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Name: Zero Length Bands v 2.0.1 -- Brow42
ID: 37147
Created on: Fri, 01/06/2012 - 16:35
Updated on: Mon, 01/28/2013 - 06:18
Description:

Creates zero-length bands on the backbone and sidechains, best for QTTN or guided puzzles. Can also randomize backbone to break frozen proteins.



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brow42's picture
User offline. Last seen 1 day 2 min ago. Offline
Joined: 09/19/2011
Groups: None
Zero Length Band description

This recipe is meant to assist with QTTN or other guided puzzles. You can band all the backbone and/or all the sidechains to their current position. You still have to drag the other ends where you want them.

Alternatively you can use the U-Turn detector which bands U-turns...this helps keep the protein exploding or wandering off without restricting the wiggle. Only loops will be detected as U-Turns, so be sure to mark your helices.

The atom slider picks the side chain atom, default is the 1st carbon on the sidechain (glycine doesn't have one).

The random slider is experimental, it will BREAK your protein, hopefully unfreezing it, but fixable by a fuze.

The U-Turn slider relaxes the detection so you can find where a U-turn connects two sheets that aren't level.

Range is 0,1, or 2 numbers to select segments.

Updated on Jan 7, to make randomize actually work.

Defaults:
option.backbone = true-- Lock down the backbone
option.sidechains = false-- Best option for QTTN
option.uturn = false -- Lock what seems like U-Turns
option.bandstr = 3.0
option.random = 0.0
option.uradius = 6.5
option.sidechainatom = 1
option.range = {} -- only segments in this range will be banded { low, high }

brow42's picture
User offline. Last seen 1 day 2 min ago. Offline
Joined: 09/19/2011
Groups: None
Version 2.0

Not huge changes to the operation, but the menus have been expanded. The script now offers many ways to to select which segments are banded. Some menu options have been moved to a second menu panel. (The reset to defaults button has been removed).

By default, all segments will be banded. Setting options restricts which segments are banded...only segments that meet all the restrictions will be banded.

Options are:

Range list: either individual segments or ranges of segments.
Structures: Loops, Sheets, or Helices (default all 3 if blank)
Either only Frozen/Locked, or Not Frozen or Locked (default is both)
Selected
U-Turn detection
Every Nth segment (now with an offset so it doesn't have to start at 1).

The script will warn you if nothing will be banded because of restrictions.

The randomize, FINALLY, seems to work (before it was always length 0).

spmm's picture
User offline. Last seen 5 hours 6 min ago. Offline
Joined: 08/05/2010
Groups: Void Crushers
only bands loops?

Not sure why but it only seems to band loops now

spmm's picture
User offline. Last seen 5 hours 6 min ago. Offline
Joined: 08/05/2010
Groups: Void Crushers
my mistake just can't see them

not visible if on the backbone of a helix

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