# RB 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
#
#  lower helix (toward corner tile):
#    sticky complement  arm      core          arm   hairpin end
#              -------+++++++================++++++++
generate d d b AGGCTGCCAACTCCTGCTCAAGATGTTCGTCCTATCGC
modify unit twist g 1:2 1:14 +1.7
modify unit twist g 1:15 1:15 -2
modify unit twist g 1:16 1:30 -1.87
modify unit twist g 1:31 1:31 -2
modify unit twist g 1:32 1:38 +1.7
rotorig 1 3 -287.05
trans 1 0 0 -74.8
write pdb Stop
close
#
#  upper helix (away from corner tile, with output)
#       short sticky  arm         core       arm   sticky complement
#              -----++++++++================+++++++-------
generate d d b CATACCTTACCGTCCAGTGTAGCATAACCTGCGAAGCGTCGGA
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 1:43 -.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 1:2:24
nick 1:1:30
nick 1:1:7
load pdb na Sbot
nick 2:2:38
nick 2:2:14
nick 2:1:36
nick 2:1:13
#
#  create crossover phosphates
#
link 2:1 1:5
modify phos phi 1:14:2 1:14:2 -120
link 1:4 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 1:31:1 1:31:1 -120
#
# add hairpin loop to top of Stop
#
load pdb na Htttt.pdb
rotorig 3 1 180
trans 3 0 0 51
rotorig 3 3 60
link 2:3 3:1
modify phos phi 3:1:1 3:1:1 -210
link 2:3 1:3
modify phos phi 1:38:2 1:38:2 -210
#
#  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 1:1
#
#  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
#
delete mol 2
#
write pdb RB.pdb
#
set usr 255 255 0
set background white
set thick *:*:*
set color m1:1:*:* usr
set color m1:2:*:* orange
set color m1:3:*:* grey
#