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Recipe: Mutate No Wiggle 1.3.1 -- Brow42
Created by brow42 77 529
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Name: Mutate No Wiggle 1.3.1 -- Brow42
ID: 100042
Created on: Fri, 10/03/2014 - 03:48
Updated on: Mon, 11/30/2015 - 08:48
Description:

Brute Force Mutator, but doesn't wiggle, stabilize, or fuze. Keeps best AA for each spot. Good for slow design puzzles. Has options for restricting mutations. 1.2.1 bans alanines. 1.3 re-allows p,g,a for loops.



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brow42's picture
User offline. Last seen 3 days 5 hours ago. Offline
Joined: 09/19/2011
Groups: None
Some questions you might have

Q: What's the point of this script?

A: Back when the fragment filter could not be turned off, it took seconds to do ANYTHING. Now that you can turn it off, you might be better off using a brute force mutator like Rav3n's or the mutations built into TvdL's EDRW. However, I think this is the only public script that lets you easily select what to mutate to. I specifically wrote it because I did not want to create or remove cysteines from a puzzle that had cystine bridges. The creation of prolines wherever I had a kink (that I would later want removed) was always an annoyance to me.

Q: This script freezes up my screen!

A: It seems Foldit's graphics can get overloaded if it has to do too much at once. It has to do a redraw every time you mutate. The new pause instructions at the bottom put the script into a loop that does nothing to let the screen catch up. But it runs fastest if you minimize, this turns the GUI off completely (unless you force it to always run in the options somewhere)

Q: If I turn on the delay loop, the script runs FASTER!

A: INORITE?

Q: The puzzle penalizes glycines. I told it not to mutate to glycines. It left them in!

A: To change the puzzle over to only using approved amino acids, click the Remove residues (not in mutation list or keep list) box. Note that your score will probably go down when it mutates these away.

Q: I clicked the remove box and the glycine is still there!

A: The script has to actually be able to mutate the segment. So, if you restricted the aminos to hydrophilic, but said preserve hydrophobicity, then it won't do anything. Also Foldit might itself prevent mutations via the infamous layer mutation filter. Or it might be locked. Or you listed it in the "don't change list".

Changelog:

* Version 1.02 -- Republished under new id
*
* Version 1.1 Oct 31 2014 Brow42
*
* Added pause to allow GUI to function. Added timing info
* Added option to remove unwanted residues (from Googol30)
* Added trap for User Cancel

brow42's picture
User offline. Last seen 3 days 5 hours ago. Offline
Joined: 09/19/2011
Groups: None
Updated for 1087

It will now mutate locked segments if the devs have marked them as mutable. This is required for puzzle 1087. You do not need to update if you have LociOling's 1.1.1.

Skippysk8s's picture
User offline. Last seen 19 hours 5 min ago. Offline
Joined: 06/06/2013
Groups: Gargleblasters
glycines

I didn't open this script or puzzle yet, though I worked the dev prev versions. Note that if there is too little space you get a glycine -- nothing else will fit. So you might want to check and see if the glycines are showing up across from large tail AAs, like the aromatics

brow42's picture
User offline. Last seen 3 days 5 hours ago. Offline
Joined: 09/19/2011
Groups: None
Version 1.2

I've added shortcut checkbox to the front panel to only mutate hydrophillics, for bonding. I've moved all the AA type selection checkboxes to another panel. The help button also appears on this panel. Panel contents will change if you used one of the shortcut checkboxes or used the custom AA list. Added some more user input error checking.

Skippysk8s is absolutely correct about the glycines. My script only optimizes one AA at a time, so if nothing else will fit, it will insert a glycine or alanine. The built-in mutator (and scripts that use it) can mutate in a cloud, changing more than one at a time. They can replace the big-small pair with two medium-size AAs.

You should exclude glycines on the AA selection page if you don't want any created.

Joined: 04/11/2013
Thank you

Thanks Brow

Thanks for responding so quickly to this request. You really have something good going on here :)

Porky

Joined: 09/24/2012
Groups: Go Science
bug report

line 501 calling "find" a nil value

options limied allowed list of AA and remove not allowed

brow42's picture
User offline. Last seen 3 days 5 hours ago. Offline
Joined: 09/19/2011
Groups: None
Fixed

Thank you for catching that. I did a search to make sure there weren't any more instances of that mistake.

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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, Microsoft, Adobe, RosettaCommons