# First try at "modeling" Sierpinski RCxy tiles  (constructed by Shaun Lee)
#
# Follows the approach from SierCorner.script, constructing
# everything from two ds regions, using "nick."
#
set hush info off
set WCAdfirst on
close
#
# create initial ds regions
#
#             hairpin end                       connects to bridge piece
generate d d b gtttgaggacgctatgaacatccaggtactcgttgaa
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 1:37 +1.7
rotorig 1 3 -72.85
trans 1 0 0 -54.4
write pdb RCxybot1
close
#
#           sticky end                                  sticky end
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 1:31 1:44 -.9
rotorig 1 3 -279.3
trans 1 19 0 -74.8
write pdb RCxytop
close
#
# add nicks for crossovers and for sticky ends
#
load pdb na RCxybot1
nick 1:2:29
nick 1:1:24
load pdb na RCxytop
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 2:20:2 2:20:2 -120
link 2:3 1:2
modify phos phi 1:25:1 1:25:1 -120
#
# add hairpin loop to one side of bot
#
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
#
move chain 2:2 1
delete mol 2
write pdb RCxyComplex1
close
#
# create the other side
#
#             hairpin end                       bridge piece
generate d d b gtttgaggacgctatgaacatccacctcaaactgcaacttac
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 1:42 +1.7
rotorig 1 3 -72.85
trans 1 0 0 -54.4
write pdb RCxybot2
close
#
# add nicks for crossovers and for sticky ends
#
load pdb na RCxybot2
nick 1:2:34
nick 1:1:24
load pdb na RCxytop
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 one side of bot
#
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
#
move chain 2:2 1
delete mol 2
write pdb RCxyComplex2
close


#
# load both complexes.  Form double complex
#
load pdb na RCxyComplex1
rotate 1 3 -90
rotate 1 1 -90
load pdb na RCxyComplex2
trans 2 0 149 -22
rotate 2 3 -90
rotate 2 1 90
#
link 1:3 2:1
link 1:1 2:2
move chain 2:1 1
#
write pdb RCxy.pdb
#
set usr 255 255 0
set background white
set thick *:*:*
set color m1:4:* blue
set color m1:2:* blue
set color m1:3:* usr
set color m1:1:* orange
set zoom .5