Recipe: Cysteine Tagger - LO

created by LociOiling

Profile

• Name: Cysteine Tagger - LO
• ID: 47126
• Shared with: Public
• Parent: None
• Children:
  • Glycines Tagger - PR step by step LO
  • Glycine Tagger - AK
  • Cysteine Tagger - freeze
• Created on: October 24, 2013 at 21:42 PM UTC
• Updated on: October 24, 2013 at 21:42 PM UTC
• Description:

  Adds a segment note to any cysteines found. Existing notes are preserved.

Code

--[[ 
  * Cysteine Tagger
  * Original Author: LociOiling
  * Version 1.0 October 24, 2013
  * Thanks to brow42!

  * This recipe sets a note for each cysteine in the puzzle.
  * For example, "C15" indicates a cysteine in segment 15. 
  * The idea is to help visualize possible disulfide bonds.
  
  * The segment note is concatenated in front of any existing notes.
  * create the bonds.

]]--

version = '1.0'
title = 'Cysteine Tagger v'..version

nSeg = structure.GetCount()
nSeg2 = nSeg
while structure.GetSecondaryStructure ( nSeg2 ) == "M" do nSeg2 = nSeg2 - 1 end

print ( title )
print ( "number of segments = ", nSeg2 )

cFound = 0

for ii = 1, nSeg2 do
    if structure.GetAminoAcid ( ii ) == "c" then
        cFound = cFound + 1
        segNote = structure.GetNote ( ii )
        if segNote == nil then segNote = "" end
        segTag = "C"..ii
        if string.len ( segNote ) > 0 then
            if string.find ( segNote, segTag ) ~= 1  then
                segNote = segTag.." "..segNote
            end
        else
            segNote = segTag..segNote
        end
        structure.SetNote ( ii, segNote )
        print ( "Cys found at segment ", ii )
    end
end
print ( cFound, "cysteines found" )

Comments

[LociOiling]

Recent changes to the foldit client have made segment notes a lot more usable.

This recipe adds segment note for every cysteine found. For example, "C15" indicates a cysteine in segment 15. The goal is to help visualize the location of possible disulfide bridges.

Any existing notes are preserved, with the cysteine note placed in front. Also, the recipe does not add duplicate notes.

Use the Note Remover recipe to delete all notes.

Thanks to brow42, this receipe occurred to me while tinkering with the Bridge Wiggle recipe.

[LociOiling]

If you're using the original interface, the "3" key toggles note mode. You can still run scripts in note mode, but you can't add bands or do much else. You need to switch back to pull mode (via "1"), structure mode ("2"), or design mode ("4") to actually tinker with the protein.

If you're using the newer selection interface, the "1" key toggles display of segment notes. You can tinker as needed while notes are displayed.

[BeImmie]

Tremendously helpful, thank you. I'm sick of doing this manually.