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Recipe: AA Edit 1.2
Created by LociOiling 2 1
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Name: AA Edit 1.2
ID: 102274
Created on: Tue, 12/27/2016 - 21:26
Updated on: Tue, 12/27/2016 - 21:26
Description:

AA Edit 1.2 is based on SS Edit 1.2. It displays the proteins amino sequence using 1-character codes. For puzzles with "mutable" segments, it applies any updates entered to the protein.



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LociOiling's picture
User offline. Last seen 2 hours 24 min ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
long-awaited (?) companion to SS Edit

AA Edit 1.2 displays the primary structure of the protein as a sequence of single-character amino acid codes. The sequence can be copied and pasted using the normal keyboard shortcuts. (For example, on Windows, ctrl-c for copy, and ctrl-v for paste.)

For proteins which contain "mutable" segments, a new sequence can be pasted into the "AASeq" box. When you click the "change" button, the recipe attempts to mutate each segment to the new value entered.

The recipe does not attempt to change non-mutable segments. It does not change any segments where the current amino acid is the same as the new amino acid. It does not change any segments where the new amino acid code is not one of the 20 amino acids recognized by Foldit.

In puzzles with ligands, the ligand may be represented by one or more segments which return amino acid type "unk" instead of one of the normal codes. The recipe changes "unk" to "x" for display purposes. Since "x" is also not one of the recognized Foldit codes, it's ignored when the change is applied.

The "change" button is not displayed for proteins with no mutable segments, and any changes to the AASeq box are ignored in this case.

The general behavior of this recipe is similar to the companion recipe, SS Edit 1.2. If the input sequence is shorter than the length of the protein, the segments at the end of the protein are left unchanged. If the input sequence is longer than the protein, the extra portion of the input is ignored.

A new sequence can be pasted in its entirety by clicking to the left of the first character of the displayed sequence, then typing ctrl-v or the equivalent "paste" shortcut in your environment.

Alternately, you can clear the input field (via ctrl-x or the equivalent) then copy and paste the new sequence on a "blank slate".

The recipe also references the "select all" shortcut (ctrl-a or the equivalent). In general, this does not seem necessary in a Foldit textbox. For example, clicking anywhere the textbox and typing ctrl-c copies the entire contents of the textbox. Clicking anywhere in the textbox and typing ctrl-x clears the entire textbox. Use "select all" if your environment exhibits different behavior. Thanks to Bertro for pointing out the nuances of copy-and-paste in Foldit.

See also print protein 2.4 for a recipe which captures more information about the protein.

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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