# S01 molecule
#
set hush info off
set WCAdfirst on
close
#
#  create the initial ds regions as blunt-end helices,
#   which will be nicked and joined at crossover points,
#   and sticky complements will be cut and deleted...
#
#  output side helix
#  sticky complement  arm         core        arm   sticky
#              -----++++++++================++++++++-----
generate d d b TCTTGGATGATGTCCTTGTAAACTTCGCCTGTTGCTCCAAGA
modify unit twist g 1:2 1:13 +1.7
modify unit twist g 1:14 1:14 -2
modify unit twist g 1:15 1:29 -1.87
modify unit twist g 1:30 1:30 -2
modify unit twist g 1:31 1:42 +1.7
rotorig 1 3 -251.35
trans 1 0 0 -71.4
write pdb Stop
close
#
#  input side helix
#             sticky  arm         core        arm   sticky complement
#              -----++++++++================++++++++-----
generate d d b AGTGAGAACGACCTGATTGCGATTAGAGTCCGTAAGCCATAC
modify unit twist g 1:2 1:13  -.9
modify unit twist g 1:14 1:14 -2
modify unit twist g 1:15 1:29 +1.6
modify unit twist g 1:30 1:30 -2
modify unit twist g 1:31 1:42 -.9
rotorig 1 3 -246.2
trans 1 19 0 -71.4
write pdb Sbot
close
#
#  add nicks for crossovers and for sticky ends
#
load pdb na Stop
nick 1:2:29
nick 1:2:5
nick 1:1:29
nick 1:1:5
load pdb na Sbot
nick 2:2:37
nick 2:2:13
nick 2:1:37
nick 2:1:13
#
#  create crossover phosphates
#
link 2:1 1:6
modify phos phi 1:13:2 1:13:2 -120
link 1:5 2:2
modify phos phi 2:14:1 2:14:1 -120
link 1:2 2:4
modify phos phi 2:29:2 2:29:2 -120
link 2:3 1:3
modify phos phi 1:30:1 1:30:1 -120
#
#  bring good stuff into mol #1, sticky end complements -> mol #2
#     (thus bogus warnings)
#
link 2:2 2:4 
move chain 2:3 1
move chain 2:1 1
link 2:1 1:3
link 2:1 1:1
#
#  Make it so rotorig 1 1 180 is aligned with original 
#     (note bug death if delete first)
#
trans 1 0 0 1.7
rotorig 1 3 90
rotorig 1 1 -90
#
delete mol 2
#
write pdb S01.pdb
#
set usr 255 255 0
set background white
set thick *:*:*
set color m1:1:*:* green
set color m1:2:*:* usr
set color m1:3:*:* red
set color m1:4:*:* blue