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# R00N sequences
#
# 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 cataccgatccgtcctcgactcatttgcctgcggtagagtga
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
#
# even output: sticky sticky complement
generate d d b caagacagtagcctgctatcttatggcgtccagaatggagat
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
#
delete mol 2
#
write pdb DAO-E_R00N.pdb
#
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