# Paul's SEs DAE-E unit
#
set hush info off
set WCAdfirst on
close
#
#  create the initial ds regions
#
#  even input: sticky                                   sticky
generate d d b cagacagtttcgtccaacggtccagaacggctgtccactgagaggta
modify unit twist g 1:2 1:13 +.78
modify unit twist g 1:14 1:14 -2
modify unit twist g 1:15 1:34 +.5
modify unit twist g 1:35 1:35 -2
modify unit twist g 1:36 1:47 +.78
rotorig 1 3 88
trans 1 0 0 -71.4
write pdb Stop
close
#
# even output: sticky complement             sticky complement
generate d d b aggtacgatgacctgcttcggttactgtttagcctgctctaccagac
modify unit twist g 1:2 1:13  +.78
modify unit twist g 1:14 1:14 -2
modify unit twist g 1:15 1:34 +.25
modify unit twist g 1:35 1:35 -2
modify unit twist g 1:36 1:47  +.78
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 1:2:42
nick 1:2:5
nick 1:1:34
nick 1:1:21
nick 1:1:13
load pdb na Sbot
nick 2:2:34
nick 2:2:13
nick 2:1:42
nick 2:1:5
#
#  create crossover phosphates
#
link 1:1 2:6
modify phos phi 2:13:2 2:13:2 -120
link 2:5 1:2
modify phos phi 1:14:1 1:14:1 -120
link 1:2 2:5
modify phos phi 2:34:2 2:34:2 -120
link 2:4 1:3
modify phos phi 1:35:1 1:35:1 -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 1:5 2
move chain 1:3 2
#
#  Make it so rotorig 1 1 180 is aligned with original 
#     (note bug death if delete first)
#
trans 1 0 0 -17
rotorig 1 3 90
rotorig 1 1 -90
rotorig 1 3 180
rotorig 1 2 180
#
delete mol 2
#
write pdb DAE-E_SE.pdb
#


#highlight DAE crossover points & nick
set background black
set color m1:*:*:* black
set color m1:1:13-14:* white
set color m1:2:1:*     red
set color m1:2:42:*    red
set color m1:2:13-14:* white
set color m1:2:34-35:* white
set color m1:4:13-14:* white


# 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