Recipe: extruder by jeff101

created by Serca

Profile

• Name: extruder by jeff101
• ID: 109230
• Shared with: Public
• Parent: extruder
• Children:
  • extruder by jeff101 (COPY)
• Created on: October 28, 2025 at 08:21 AM UTC
• Updated on: October 28, 2025 at 08:22 AM UTC
• Description:

  fold strands 'naturally' from N-terminus to C-terminus

Code

-- extruder made 4/27/12 by jeff101.
--
-- Goal is to fold protein 'naturally' starting with the N-terminus of each strand.
-- This script assumes all strands start as widely-separated parallel linear chains 
-- with loop as their secondary structure.
--
-- startres = 1 -- use 1 for the first run, use higher numbers if restarting a cancelled run
-- startres = 17 -- tells how many residues per strand to unfreeze at the start
-- startres = 1000 -- use a very high number to start with all residues unfrozen
--
-- First get information about the protein strands.
--
tot=structure.GetCount() -- find # of residues in the protein
nstr=1 -- # of strands in the protein
starts={1} -- # beginnings of strands
ends={} -- # ends of strands
for i=2,tot do
   im=i-1
   dist=structure.GetDistance(im,i) -- find distance between residues i-1 and i 
   if dist > 5 then
      print('break between residues '..im..' and '..i)
      ends[nstr]=i-1
      nstr=nstr+1
      starts[nstr]=i
   end -- if dist
end -- for i
ends[nstr]=tot
print('for '..tot..' residues we have '..nstr..' strands')
lens=ends
--
-- Next report the endings of each strand.
--
maxlen=0
for i=1,nstr do
   lens[i]=ends[i]-starts[i]+1
   if lens[i]>maxlen then
      maxlen=lens[i] 
   end -- if lens
   print('strand '..i..' goes from residue '..starts[i]..' to '..ends[i]..' and has length '..lens[i])
end -- for i
print('the longest of the '..nstr..' strands has length '..maxlen)
local ask=dialog.CreateDialog('Extruder')
ask.Instructions = dialog.AddLabel("Set startres to the number of amino acids\non each strand you want to begin unfrozen:")
ask.Startres = dialog.AddSlider("startres:", 1, 1, maxlen, 0) -- default is 1, pick values from 1 to maxlen, 0 means use intergers only
ask.OK = dialog.AddButton("OK", 1)
dialog.Show(ask)
startres=ask.Startres.value
if startres > maxlen then
   startres = maxlen
end
print('startres='..startres)
--
-- Next fold it all.
--
freeze.FreezeAll() -- freeze it all
for j=1,maxlen do -- j is how long each unfrozen strand section is
   print('about to wiggle and shake up to '..j..' residues on each strand')
   for i=1,nstr do -- i is which strand we are doing
      nlo=starts[i]
      nhi=starts[i]+j-1
      if nhi>ends[i] then
         nhi=ends[i]
      end -- if nhi
      freeze.Unfreeze(nhi,true,true) -- unfreezing nhi each time should eventually unfreeze all parts
   end -- for i
   if j >= startres then
      conlo=0.05
      conhi=1.00
      constp=0.05
      for con=conlo,conhi,constp do
         behavior.SetClashImportance(1) -- set Clash Importance to 1    
         oldscore=current.GetScore() -- get current score
         recentbest.Save() -- save current score's pose
         selection.SelectAll() -- select everything
         structure.RebuildSelected(1) 
         behavior.SetClashImportance(con) -- set Clash Importance to con
         print('just rebuilt, now doing wiggle, shake, wiggle with con='..con..' for up to '..j..' residues per strand')
         structure.WiggleAll(5) -- wiggle unfrozen parts
         structure.ShakeSidechainsAll(2) -- shake unfrozen parts
         structure.WiggleAll(5) -- wiggle unfrozen parts
         behavior.SetClashImportance(1) -- set Clash Importance to 1
         newscore=current.GetScore()
         if newscore > oldscore then
            print('new score '..newscore..' beats '..oldscore..' so save new')
            recentbest.Save()
         else
            print('old score '..oldscore..' beats '..newscore..' so restore old')
            recentbest.Restore() -- reload oldscore's pose
         end
         behavior.SetClashImportance(con) -- set Clash Importance to con
         print('doing wiggle, shake, wiggle with con='..con..' for up to '..j..' residues per strand')
         structure.WiggleAll(5) -- wiggle unfrozen parts
         structure.ShakeSidechainsAll(2) -- shake unfrozen parts
         structure.WiggleAll(5) -- wiggle unfrozen parts
      end -- for con
   end -- if j
   if j == maxlen then
      j = maxlen-1 -- this will prevent j from ever exceeding maxlen
      -- and will keep the loop going until the script is cancelled
   end
end -- for j
print('all done now')