# single-tile crystal DAO-O tile
#
#  Uses the same crossover motif as junction36E.script,
#  but constructs everything from just two ds regions,
#  using "nick".
#
set hush info off
set WCAdfirst on
close
#
#  create the initial ds regions
#
#  even input: sticky complement                    sticky
generate d d b CGATCAcacgatccgtcctcgactcatttgcctgcggtagtgGAGTGA
modify unit twist g 1:2 1:16 +1.7
modify unit twist g 1:17 1:17 -2
modify unit twist g 1:18 1:32 -1.87
modify unit twist g 1:33 1:33 -2
modify unit twist g 1:34 1:48 +1.7
rotorig 1 3 -107.1
rotorig 1 3 -251.35
trans 1 0 0 -71.4
write pdb Stop
close
#
# even output: sticky                               sticky complement
generate d d b GAGTGAgacagtagcctgctatcttatggcgtccagaatgacCGATCA
modify unit twist g 1:2 1:16  -.9
modify unit twist g 1:17 1:17 -2
modify unit twist g 1:18 1:32 +1.6
modify unit twist g 1:33 1:33 -2
modify unit twist g 1:34 1:48 -.9
rotorig 1 3 -99.3
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 1:2:32
nick 1:2:6
nick 1:1:32
nick 1:1:6
load pdb na Sbot
nick 2:2:16
nick 2:2:6
nick 2:1:16
nick 2:1:6

#
#  create crossover phosphates
#
link 2:2 1:6
modify phos phi 1:16:2 1:16:2 -120
link 1:5 2:3
modify phos phi 2:17:1 2:17:1 -120
link 1:2 2:5
modify phos phi 2:32:2 2:32:2 -120
link 2:4 1:3
modify phos phi 1:33:1 1:33:1 -120
#
#  bring good stuff into mol #1, sticky end complements -> mol #2
#     (thus bogus warnings)
#
move chain 2:4 1
move chain 2:2 1
move chain 1:3 2
move chain 1:1 2
delete mol 2
#
#  Make it so rotorig 1 1 180 is aligned with original 
#
trans 1 0 0 1.7
rotorig 1 3 90
rotorig 1 1 -90
rotorig 1 3 180
rotorig 1 2 180
#
write pdb DAO-O.pdb
#


# set colors for tile diagram
set background white
set color m1:1:*:* blue
set color m1:2:*:* cyan
set color m1:3:*:* green
set color m1:4:*:* yellow
set color m1:5:*:* red