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Recipe: AA Copy Paste Compare v 1.1.1 -- Brow42
Created by brow42 79 387
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Name: AA Copy Paste Compare v 1.1.1 -- Brow42
ID: 38147
Created on: Wed, 02/01/2012 - 22:23
Updated on: Sun, 09/23/2012 - 03:03
Description:

Read and set the primary and secondary structure in a copy/paste friendly dialog. Also can list changes you made.



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brow42's picture
User offline. Last seen 1 week 1 day ago. Offline
Joined: 09/19/2011
Groups: None
Good for Sharing, de Novo Freestyle

This script makes it easy to read or set the primary structure (amino acid sequence) and secondary structure (loop, helix, sheet) using dialogs. Now, instead of making a script for each puzzle to set the structure, you can just paste it into the dialog box.

Uses:

Reading SS from SAM predictions or FASTA file. The devs usually provide a SS prediction in the comments of each puzzle. Note that sometimes they want you to guess the SS, so don't use external sources.

Setting the initial state of a denovo freestyle or design puzzle. Very painful to do by hand, and annoying to script it.

Keeping track of all the changes you've made to a protein is hard. This will find the differences between your current protein, and another saved protein in a save slot or different reset. It will find mutations, insertions, deletions, and SS changes.

Once you've found your differences, you can share them with other players, and they can paste them in!

Output is both a string of letters, and letter-number or letter-range notation.

Warnings:

This was a huge script to write spread over many weeks. I'm releasing it now so that you can use it with the current flu design puzzle.

Looping through resets assumes that each reset is already threaded with a unique score.

The Compare function was written last and has seen the least testing.

The Compare function will detect insertions, deletions, and mutations, but only mutations are possible in Lua. You must do the insertions/deletions by hand, and then the script can do the mutations.

Bug Reports and Suggestions:

Please PM or post below bugs or obviously wrong answers. Use the 'Read' Function to give me PS and SS of your initial protein, and also what you were trying to write, or compare against.

Beta Notice:

The script will nag you to update until I release version 1.0.

dnevill's picture
User offline. Last seen 2 years 15 weeks ago. Offline
Joined: 05/12/2008
Groups: None
Very handy to restore my SSs

Very handy to restore my SSs after rav3n_pl's DRW or the like.

brow42's picture
User offline. Last seen 1 week 1 day ago. Offline
Joined: 09/19/2011
Groups: None
Patch 1.1 Comparing

Patch 1.1: Added a dialog to present the results of comparing the current structure to a saved structure. Previously it put the results into the read dialog, which was confusing. Remember you can copy text right out of dialog boxes.

Added a check box to reverse the roles of current and saved structure. Normally it prints the changes needed to go from the saved structure to the current structure. When checked, it gives the changes needed to from the current structure to saved structure.

Good for comparing SAM predictions with server folds or CASP provided fold.

brow42's picture
User offline. Last seen 1 week 1 day ago. Offline
Joined: 09/19/2011
Groups: None
Patch 1.1.1

A syntax error in reporting the changes between one primary sequence and another. It only appears if the edit list contains insertions and deletions. I've fixed this.

I'm not convinced its giving the shortest edit list. Also, players may want a pure substitution list instead. Expect an update in the near future.

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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