# Single-tile crystal DAE-O unit
#
set hush info off
set WCAdfirst on
close
#
#  create the initial ds regions
#
#  even input: sticky comp                                    sticky
generate d d b AGGTACcgagtttcgtccaacggtccagaacggctgtccactgagagTGATCG
modify unit twist g 1:2 1:16 +.78
modify unit twist g 1:17 1:17 -2
modify unit twist g 1:18 1:37 +.5
modify unit twist g 1:38 1:38 -2
modify unit twist g 1:39 1:53 +.78
rotorig 1 3 -104.34
rotorig 1 3 88
trans 1 0 0 -71.4
write pdb Stop
close
#
# even output: sticky complement                              sticky
generate d d b GTACCTgacgatgacctgcttcggttactgtttagcctgctctactgCGATCA
modify unit twist g 1:2 1:16  +.78
modify unit twist g 1:17 1:17 -2
modify unit twist g 1:18 1:37 +.25
modify unit twist g 1:38 1:38 -2
modify unit twist g 1:39 1:53  +.78
rotorig 1 3 -104.34
rotorig 1 3 126
trans 1 -19.5 0 -71.4
write pdb Sbot
close
#
#  add nicks for crossovers and for sticky ends
#
load pdb na Stop
nick 1:2:6
nick 1:1:37
nick 1:1:24
nick 1:1:16
nick 1:1:6
load pdb na Sbot
nick 2:2:37
nick 2:2:16
nick 2:2:6
nick 2:1:6
#
#  create crossover phosphates
#
link 1:2 2:6
modify phos phi 2:16:2 2:16:2 -120
link 2:5 1:3
modify phos phi 1:17:1 1:17:1 -120
link 1:3 2:5
modify phos phi 2:37:2 2:37:2 -120
link 2:4 1:4
modify phos phi 1:38:1 1:38:1 -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 1:4 2
move chain 1:1 2
#
delete mol 2
#
#  Make it so rotorig 1 1 180 is aligned with original 
#
trans 1 0 0 -17
rotorig 1 3 90
rotorig 1 1 -90
rotorig 1 3 180
rotorig 1 2 180
#
write pdb DAE-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