Recipe: Snow Flea Bonding

created by brow42

Profile

• Name: Snow Flea Bonding
• ID: 42892
• Shared with: Public
• Parent: None
• Children: None
• Created on: July 11, 2012 at 14:51 PM UTC
• Updated on: July 11, 2012 at 14:51 PM UTC
• Description:

  Snow Flea h-bond pattern based on the first few I found. (Spoiler!)

Code

--[[
  * Snow Flea bonder
  * Original Author Brow42 Jun 28 2012

  * Based on the few h-bonds I had,
  * make all the other bonds in the
  * same pattern.
--]]

str = 1          -- strength of bands
bondlen = 3.0    -- about the length of the bond (possibly a little shorter)
-- comment out to set goal length to actual length

--band.DeleteAll()

--[[
Band a Sheet args:

  Segment with red atom (oxygen, acceptor, last atom in segment)
  Segment with blue atom (nitrogen, donor, first atom in segment)
  Number of bonds to make
  Stride of red strand
  Stride of blue strand
--]]
function BandSheet(red,blue,n,d1,d2)
    local i
    rc, err = pcall(
        function() -- extra debugging to catch segment-out-of-bound errors
            for i = 1,n do
                j = band.AddBetweenSegments(blue,red,1,4)
                if j == 0 then error("Couldn't make band") end -- not sure if this would ever happen
                band.SetGoalLength(j,bondlen and bondlen or band.GetLength(j))
                band.SetStrength(j,str)
                red,blue = red+d1,blue+d2
            end
        end
    )
    if rc == false then error (err..string.format(' red: %d blue: %d i: %d n: %d',red,blue,i,n)) end
end

--   9 sheets between 7 strands
-- args are: red atom seg, blue atom seg, # of bonds, red direction, blue direction
BandSheet(71,45,4,3,3)
BandSheet(44,15,4,3,3)
BandSheet(67,73,3,-3,3)
BandSheet(37,46,4,-3,3)
BandSheet(10,16,3,-3,3)
BandSheet(46,67,3,3,-3)
BandSheet(16,37,4,3,-3)
BandSheet(68,39,4,-3,-3)
BandSheet(38,12,4,-3,-3)

-- 2 disulfide bridges
i = band.GetCount()
band.AddBetweenSegments(1,28,6,6)
band.AddBetweenSegments(13,43,6,6)
band.SetStrength(i,str)
band.SetStrength(i+1,str)
band.SetGoalLength(i,bondlen and 2.05 or band.GetLength(i))
band.SetGoalLength(i+1,bondlen and 2.05 or band.GetLength(i+1))

Comments

[brow42]

Snow Flea is 75% over, but it's pretty hard and maybe some of you have given up. I knew what I wanted to make but even knowing that I still couldn't do it because I couldn't keep track of which atoms bonded; I lose them every time I moved the puzzle.

After lining up all the sidechains, part of my puzzle seemed bonded correctly. Extending those bonds to adjacent strands, like sheets, determined where all the other bonds should go. This script bands all the bonding atoms together. It also bands the cysteine bridges.

As a bonus, I found that the bands made the glycines flip over really quickly, unlike manual banding or my glycine flipper recipe.

The script has one option: if you comment out the band length, it will set the band to the current distance, effectively locking the atoms in place. This will help the structure survive rebuilds.

If you don't want to know what (I think) the puzzle looks like don't run this script!

I hope none of you think I'm making the puzzle too easy (and making you rank down) but this was a pretty hard puzzle.