Recipe: 674 jpred structs

created by gramps

Profile

• Name: 674 jpred structs
• ID: 45367
• Shared with: Public
• Parent: None
• Children:
  • 678 jpred structs
• Created on: February 14, 2013 at 17:14 PM UTC
• Updated on: February 14, 2013 at 17:14 PM UTC
• Description:

  yields majority structs prediction running jpred versus puzzle 674 AA sequence

Code

newprog = "674 jpred structs"
--
-- autogenerated code

local Struct_Types = {
["L"] = "Loop",
["E"] = "Sheet",
["H"] = "Helix",
["M"] = "Ligand" }

function Make_All_Loop()
  selection.SelectAll()
  structure.SetSecondaryStructureSelected("L")
  print("everything has been changed to a loop")
  selection.DeselectAll()
end -- function Make_All_Loop

function Restore_One_Stuct(s_start,s_end,s_type)
selection.SelectRange(s_start,s_end)
print(Struct_Types[s_type].."("..s_start..","..s_end..")")
structure.SetSecondaryStructureSelected(s_type)
selection.DeselectAll()
end -- function Restore_One_Stuct

function Restore_Structs()
  Restore_One_Stuct(1,11,"L")
  Restore_One_Stuct(12,18,"E")
  Restore_One_Stuct(19,27,"L")
  Restore_One_Stuct(28,29,"E")
  Restore_One_Stuct(30,39,"H")
  Restore_One_Stuct(40,44,"L")
  Restore_One_Stuct(45,53,"H")
  Restore_One_Stuct(54,69,"L")
  Restore_One_Stuct(70,70,"E")
  Restore_One_Stuct(71,84,"L")
  Restore_One_Stuct(85,88,"E")
  Restore_One_Stuct(89,92,"L")
  Restore_One_Stuct(93,95,"E")
  Restore_One_Stuct(96,100,"L")
  Restore_One_Stuct(101,108,"E")
  Restore_One_Stuct(109,113,"L")
  Restore_One_Stuct(114,124,"E")
  Restore_One_Stuct(125,130,"L")
  Restore_One_Stuct(131,135,"E")
  Restore_One_Stuct(136,141,"L")
  Restore_One_Stuct(142,147,"E")
  Restore_One_Stuct(148,148,"L")
  Restore_One_Stuct(149,156,"H")
  Restore_One_Stuct(157,158,"L")
end -- function Restore_Structs

print("begin ",newprog)

if structure.GetCount() == 	158	 then -- num segs match
  Make_All_Loop()
  Restore_Structs()
else -- print warning line
  print("segment number mismatch -- no action taken")
end

print("end ",newprog)

Comments

[gramps]

begin 674 jpred structs
everything has been changed to a loop
Loop(1,11)
Sheet(12,18)
Loop(19,27)
Sheet(28,29)
Helix(30,39)
Loop(40,44)
Helix(45,53)
Loop(54,69)
Sheet(70,70)
Loop(71,84)
Sheet(85,88)
Loop(89,92)
Sheet(93,95)
Loop(96,100)
Sheet(101,108)
Loop(109,113)
Sheet(114,124)
Loop(125,130)
Sheet(131,135)
Loop(136,141)
Sheet(142,147)
Loop(148,148)
Helix(149,156)
Loop(157,158)
end 674 jpred structs

puzzle 674 page:
https://fold.it/portal/node/994456

jpred run for 674 AA sequence (up for about 48 hours):
http://www.compbio.dundee.ac.uk/www-jpred/results/jp_R3_9nZa/jp_R3_9nZa.results.html
http://www.compbio.dundee.ac.uk/www-jpred/results/jp_R3_9nZa/jp_R3_9nZa.html

public Recipe: Jpred helper V1.0 (gets AA string for jpred input):
http://fold.it/portal/recipe/44826

[gramps]

should have added "-11" everywhere and let the $%#@ computer do the subtractions

[gramps]

that relates to the 678 recipe of course, long day