# RC molecule
#
#  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...
#
set hush info off
set WCAdfirst on
close
#
#  create the initial ds regions
#
#   hairpin end  arm        core         arm   hairpin end
#              ++++++++================++++++++
generate d d b GTTTGAGGACGCTATGAACATCCAGGTACTCG
modify unit twist g 1:2 1:8 +1.7
modify unit twist g 1:9 1:9 -2
modify unit twist g 1:10 1:24 -1.87
modify unit twist g 1:25 1:25 -2
modify unit twist g 1:26 1:32 +1.7
rotorig 1 3 -72.85
trans 1 0 0 -54.4
write pdb Stop
close
#
#              sticky   arm       core         arm   sticky complement
#              -------+++++++================+++++++-------
generate d d b TCCGACGCTCGGCAGGTGTCTCTGCTTAGGACGAATGCGTCGGA
modify unit twist g 1:2 1:14  -.9
modify unit twist g 1:15 1:15 -2
modify unit twist g 1:16 1:30 +1.6
modify unit twist g 1:31 1:31 -2
modify unit twist g 1:32 1:44 -.9
rotorig 1 3 -279.3
trans 1 19 0 -74.8
write pdb Sbot
close
#
#  add nicks for crossovers and for sticky ends
#
load pdb na Stop
nick 1:2:24
nick 1:1:24
load pdb na Sbot
nick 2:2:37
nick 2:2:14
nick 2:1:37
nick 2:1:14
#
#  create crossover phosphates
#
link 2:1 1:4
modify phos phi 1:8:2 1:8:2 -120
link 1:3 2:2
modify phos phi 2:15:1 2:15:1 -120
link 1:1 2:4
modify phos phi 2:30:2 2:30:2 -120
link 2:3 1:2
modify phos phi 1:25:1 1:25:1 -120
#
# add hairpin loop to top and bottom of Stop
#   note: move chains into m1 so it doesn't disappear
#
load pdb na Htttt.pdb
rotorig 3 1 180
trans 3 0 0 51
rotorig 3 3 60
move chain 2:3 1
link 1:3 3:1
modify phos phi 3:1:1 3:1:1 -210
link 1:3 1:2
modify phos phi 1:32:2 1:32:2 -210
#
load pdb na Htttt.pdb
rotorig 3 3 -60
trans 3 0 0 -54.4
link 2:1 3:1
modify phos phi 3:1:1 3:1:1 -210
move chain 2:1 1
link 1:3 1:1
modify phos phi 1:1:1 1:1:1 -210
#
#  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
#
#  bring good stuff into mol #1, sticky end complements -> mol #2
#
delete mol 2
#
write pdb RC.pdb
#
set usr 255 255 0
set background white
set thick *:*:*
set color m1:1:* usr
set color m1:2:* orange
#