#this first part is for Ecoli from the Cate paper
reinitialize
fetch 4V4H
hide all
show cartoon, chain AA
show cartoon, chain AU
color gray, chain AA
color red, chain AU
#binding sites primary in dark blue, secondary in light blue
show spheres, /4V4H/A/AA/A`794
color blue, /4V4H/A/AA/A`794
show spheres, /4V4H/A/AA/G`926
color blue, /4V4H/A/AA/G`926
show dots, /4V4H/A/AA/A`792
color lightblue, /4V4H/A/AA/A`792
show dots, /4V4H/A/AA/A`1499
color lightblue, /4V4H/A/AA/A`1499
show dots, /4V4H/A/AA/G`1505
color lightblue, /4V4H/A/AA/G`1505
show dots, /4V4H/A/AA/U`1506
color lightblue, /4V4H/A/AA/U`1506
sele /4V4H/AD/AA/KSG`1601
#then manually clicked the A next to select (for action), then preset, then ligand
#the above steps should make KSG show up

set_view (\
     0.420035332,   -0.732767820,    0.535370588,\
    -0.903723359,   -0.283917546,    0.320430815,\
    -0.082800806,   -0.618419111,   -0.781473339,\
     0.000011355,   -0.000007816, -157.203308105,\
    86.363372803,   33.183898926,  -41.713066101,\
   145.469314575,  168.896835327,  -20.000000000 )

ray 2000,1000
png C:\Users\hanna\OneDrive\Desktop\ksg4.png

set_view (\
     0.961485505,    0.168188870,    0.217390031,\
    -0.246542305,    0.178116277,    0.952623844,\
     0.121500798,   -0.969528854,    0.212722361,\
    -0.000138864,   -0.000086963, -305.555541992,\
    64.483039856,  -91.732711792,  -61.295814514,\
    45.200958252,  565.984558105,  -20.000000000 )
    ray 2000,1000
    png C:\Users\hanna\OneDrive\Desktop\ksg_new.png


#for showing bS21 to ASD interactions
reinitialize
fetch 6O7K
hide all
show licorice, chain g
show cartoon, chain 2
color gray, chain g
color red, chain 2
color green, /6O7K/C/g/C`1539
show licorice, /6O7K/P/2/ARG`17
distance (/6O7K/C/g/C`1539/OP1), (/6O7K/P/2/ARG`17/NH1)
hide label
set dash_color, yellow
set dash_width, 3
set dash_gap, 0.3
show licorice, /6O7K/C/g/A`794
color blue, /6O7K/C/g/A`794
show licorice, /6O7K/C/g/G`926
color blue, /6O7K/C/g/G`926
show licorice, /6O7K/C/g/A`792
color lightblue, /6O7K/C/g/A`792
show licorice, /6O7K/C/g/A`1499
color lightblue, /6O7K/C/g/A`1499
show licorice, /6O7K/C/g/G`1505
color lightblue, /6O7K/C/g/G`1505
show licorice, /6O7K/C/g/U`1506
color lightblue, /6O7K/C/g/U`1506
ray 2000, 1000
png C:\Users\hanna\OneDrive\Desktop\ksg_ASD.png


##this is for showing secondary binding site of ksg in thermus, the Fucini paper. Because it's in Thermus and there's no bS21, I'm mapping it in the same E.coli structure as earlier
reinitialize
fetch 4V4H
hide all
show cartoon, chain AA
show cartoon, chain AU
color gray, chain AA
color red, chain AU
show cartoon, chain AG
color forest, chain AG
show spheres, /4V4H/A/AA/G`693
color blue, /4V4H/A/AA/G`693
show spheres, /4V4H/A/AA/U`788
color blue, /4V4H/A/AA/U`788
show spheres, /4V4H/A/AA/U`789
color blue, /4V4H/A/AA/U`789
show spheres, /4V4H/F/AG/GLY`81
color lightblue, /4V4H/F/AG/GLY`81
show spheres, /4V4H/F/AG/GLY`80
color lightblue, /4V4H/F/AG/GLY`80
set_view (\
     0.689836740,   -0.625592232,   -0.364362091,\
    -0.546665788,   -0.780075490,    0.304367930,\
    -0.474639982,   -0.010781765,   -0.880113125,\
     0.000030238,   -0.000023156, -354.087005615,\
   145.207275391,   17.382362366,   70.542190552,\
    93.751762390,  614.535217285,  -20.000000000 )
  ray 2000, 1000
  png C:\Users\hanna\OneDrive\Desktop\ksg_secondary_1.png

  set_view (\
     0.753609300,    0.065869763,    0.654012442,\
     0.008624922,   -0.995870233,    0.090360306,\
     0.657265425,   -0.062456362,   -0.751065433,\
    -0.000045806,    0.000130161, -354.109619141,\
    21.411970139,   49.603214264,   23.356481552,\
    93.751762390,  614.535217285,  -20.000000000 )
ray 2000, 1000
png C:\Users\hanna\OneDrive\Desktop\ksg_secondary_2.png

#map both sites on one image
reinitialize
fetch 4V4H
hide all
show cartoon, chain AA
show cartoon, chain AU
color gray, chain AA
color red, chain AU
show cartoon, chain AG
color forest, chain AG
show spheres, /4V4H/A/AA/G`693
color lightblue, /4V4H/A/AA/G`693
show spheres, /4V4H/A/AA/U`788
color lightblue, /4V4H/A/AA/U`788
show spheres, /4V4H/A/AA/U`789
color lightblue, /4V4H/A/AA/U`789
show spheres, /4V4H/F/AG/GLY`81
color lightblue, /4V4H/F/AG/GLY`81
show spheres, /4V4H/F/AG/GLY`80
color lightblue, /4V4H/F/AG/GLY`80
show spheres, /4V4H/A/AA/A`794
color blue, /4V4H/A/AA/A`794
show spheres, /4V4H/A/AA/G`926
color blue, /4V4H/A/AA/G`926
show dots, /4V4H/A/AA/A`792
color blue, /4V4H/A/AA/A`792
show dots, /4V4H/A/AA/A`1499
color blue, /4V4H/A/AA/A`1499
show dots, /4V4H/A/AA/G`1505
color blue, /4V4H/A/AA/G`1505
show dots, /4V4H/A/AA/U`1506
color blue, /4V4H/A/AA/U`1506
set_view (\
     0.972363830,   -0.229439735,    0.043144010,\
     0.055354580,    0.406110436,    0.912145257,\
    -0.226804435,   -0.884550691,    0.407587707,\
    -0.000432525,    0.000028089, -336.641632080,\
    91.281036377,  -50.825271606,  -70.677795410,\
    76.265983582,  597.049987793,  -20.000000000 )
ray 2000, 1000
png C:\Users\hanna\OneDrive\Desktop\ksg_both_1.png
set_view (\
     0.831917405,    0.063770011,    0.551219046,\
    -0.553772986,    0.158581972,    0.817426503,\
    -0.035286099,   -0.985283315,    0.167240396,\
    -0.000234663,   -0.000110183, -286.885314941,\
    48.934501648,  -35.635307312,  -45.488159180,\
    26.511301041,  547.295349121,  -20.000000000 )

ray 2000, 1000
png C:\Users\hanna\OneDrive\Desktop\ksg_both_2.png
