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Recipe: Rebuild-Remix Selection 2.51
Created by Serca 142 97
4.583335
Your rating: None Average: 4.6 (12 votes)

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Name: Rebuild-Remix Selection 2.51
ID: 103403
Created on: Mon, 04/13/2020 - 14:53
Updated on: Wed, 06/17/2020 - 08:43
Description:

Allows to Remix or Rebuild selections. You may choose between high quality and fast speed execution.



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Serca's picture
User offline. Last seen 2 weeks 4 days ago. Offline
Joined: 02/03/2020
Groups: Go Science
Please report any bugs and ideas

Original Interface users don't worry: it allows you to make a selection of any length with a dialog on script start.

Joined: 09/29/2016
Groups: Gargleblasters
Note: to potential users...

By "make a selection", it is not via mouse click, but by a Slider Option where you pick (ie your 'select') the Start and End segment numbers that you want to be worked on.

To find those numbers out, hover mouse over the first (Start) segment you want it to work on, and press the Tab key. In that window that pops up, the number at the top is the Start number. Move mouse to second segment, press Tab again, and that is your End number. :)

Also be aware that any puzzle that has a Locked target protein, will be unable to be remixed, but those segments are still part of the numbers. So, using puzzle 1824 as an example, if you run the recipe and let it go without changing anything, the defaults will be segments that can't move (therefore, cannot be remixed). In that puzzle 1-92 are Locked, where only 93-154 are what we can use.

Serca's picture
User offline. Last seen 2 weeks 4 days ago. Offline
Joined: 02/03/2020
Groups: Go Science
Thank you Formula350. You are

Thank you Formula350.

You are right, Remix tool in Foldit don't works near the protein ends and cuts, because it needs some amino acid angles with its neighbors. Use Rebuild instead, it usually gives more points. Remix is good on searching solutions in the real protein database.

Serca's picture
User offline. Last seen 2 weeks 4 days ago. Offline
Joined: 02/03/2020
Groups: Go Science
Scenarios

If you have to rebuild the long 30 resudues loop, make 2-3 selections that overlap each other and run this script.
Typical rebuild length it likes is about 10-15 residues. To get higher quality on larger loops, increase "Solutions to search" value in option window. That increases the amount of total Rebuild solutions generated or Remix slots used.
"Slots to fuze" allows you to choose how much of them to fuze. On solutions to search of 36, i usually set this option to 6.

"Turbo Mode" tells this script to skip the fuzing stage while choosing best Rebuild solution. It accepts the solution that has the best backbone score (all the subscores excluding the non-clashing score). Next selection Rebuild is starting than.
When all selections are Rebuild that way there is the Fuze to check for score improvement.

"Full protein Rebuild" is a great alternative to classical overnight DRW scripts. Use it with "Infinite execution" option enabled to loop protein Rubild until stopped.
It uses sliders from Selection1 to set overlap and selection length.

Have fun.

Serca's picture
User offline. Last seen 2 weeks 4 days ago. Offline
Joined: 02/03/2020
Groups: Go Science
Protein end stage

On the final stage, when protein is packed very tight and backbone is well optimized, there is a lot of clashing score from sidechains we cannot ignore. So it is better to use high "Slots to fuze" value to fuze most of the rebuild solutions generated.

In that case I run this recipe with the short rebuild length (3) with "Slots to fuze" slider set to half of the "Solutions to search" value.
So setting it to about 8-10 and even more gives some points usually.

marsfan's picture
User offline. Last seen 1 day 2 hours ago. Offline
Joined: 12/18/2015
Groups: None
Increase number of allowed remixes

Currently this script only allows for working with up to 36 rebuild/remix values. While this works great for rebuild, remix is a good bit faster, and it is possible to have more than 36 possible rebuild combinations. Could this max range on the first two sliders be increased further to account for this?

Serca's picture
User offline. Last seen 2 weeks 4 days ago. Offline
Joined: 02/03/2020
Groups: Go Science
Max is 98

Yes, it is possible. Maximal number of rebuilds are 98 (100-2 service slots).
You can change it yourself changing '36' to '98' at line 34 (script version 2.5):

ask.maxRebuildCount = dialog.AddSlider("Solutions to search",15,1,36,0)

36 is set as max by default just for better slider handling on typical value range of 10-35 rebuild slots.

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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