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Recipe: Local Mutate 3.0
Created by spvincent 32 28
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Name: Local Mutate 3.0
ID: 103229
Created on: Mon, 01/13/2020 - 13:36
Updated on: Mon, 01/13/2020 - 21:36
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spvincent's picture
User offline. Last seen 13 hours 26 min ago. Offline
Joined: 12/07/2007
Groups: Contenders
Fairly minor update, changing

Fairly minor update, changing a few parameters so that the defaults work well under most circumstances. I've found this a most useful midgame script.

A script similar in style to Rav Mutate, intended for design puzzles.

Algorithm outline

For each amino acid
Set the Clash Importance to something low
Select everything in the immediate neighbourhood of that residue
Mutate
Set the CI to 1 and select the whole protein
Wiggle
Record any improvement
end

Dialog settings

Min residue, Max residue

The range to be mutated : by default the whole protein.

Delta residue

Processing each residue in turn is inefficient: the selection in each case will be largely duplicated. This setting indicates the difference between successive residues. For example, if the min and max residues above are 1 and 100 respectively and the delta value is 5, then residues will be processed in the order 1,5,10,15,etc.....2,6,11 and so on.

Clash importance

The value during the initial mutate. Something that reduces the energy score by about 200 seems about right (the median reduction is printed out at the end of the script)

Modify count

Determines how many amino acids will be mutated at each step. They will be the closest (as measured by the distance between alpha carbons) to the residue being processed. Fewer means faster processi8ng.

Score type

If set to 2, filters are toggled on to determine the score only: other operations such as wiggle are done with filters off. If set to 1 (default), the initial filter setting will be used throughout.

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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