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Recipe: SS Edit 2.0.1
Created by LociOiling 8 1
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Name: SS Edit 2.0.1
ID: 103294
Created on: Tue, 03/10/2020 - 13:13
Updated on: Thu, 04/16/2020 - 20:28
Description:

Displays the current secondary structure. The displayed value can be cut or copied and a new value pasted in. Clicking the "Change" button applies the displayed value to the protein. Click "Exit" when any changes are complete. Version 1.1 disables filters during the change and avoid crashes by not attempting to set ligand type "M". Version 1.2 disables undo stack pushes to allow one-key undo. Version 2.0 handles each chain separately, similar to AA Edit 2.0. Version 2.0.1 is a quick fix for proline at the N terminal.



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LociOiling's picture
User offline. Last seen 3 hours 21 min ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
now with chain detection

SS Edit 2.0 lets you copy and paste the protein's secondary structure.

Similar to AA Edit 2.0 this version of SS Edit presents each chain of the protein separately. This is handy for binder puzzles like the coronavirus series, where there's a locked target and a designable binder which are separate chains.

When you click the "Change" button, the recipe applies the contents of the "sec struct" box for a given chain to the protein. All entries are converted to upper case. Only the standard Foldit codes "L" for loop, "H" for helix, and "E" for sheet are applied to the protein. Anything else causes the entry to be skipped and the corresponding segment left unchanged.

The code "M" may appear for ligands in some puzzles, but it's normally not possible to change this code. "M" is included here as a valid input, but will probably fail when the recipe tries to apply it.

Joined: 08/24/2010
*** Thanks ***

Thanks!

Do you think you can add an "idealize" and/or "remix" component, as well as numbered segments or a way to avoid assigning to "locked" segments?

LociOiling's picture
User offline. Last seen 3 hours 21 min ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
Maybe a different recipe?

Just saw this comment...are you thinking of another recipe?

LociOiling's picture
User offline. Last seen 3 hours 21 min ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
Version 2.01 quick fix

Version 2.0.1 fixes chain detection when proline is at the N terminal. In this case, the atom count is 18, instead of 15 when proline is mid-chain. Usually the atom count increases by 2 at the N terminal.

(Edit: mid-chain count is 15.)

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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