Overlay variants in NOD2 alphafold model

nod2AF.py

from pymol import cmd

cmd.load("/Users/ochoa/Downloads/AF-Q9HC29-F1-model_v1.cif")

cmd.bg_color("grey95")

cmd.set_color("veryHigh", [0, 83, 214])
cmd.set_color("confident", [101, 203, 243])
cmd.set_color("low", [255, 219, 19])
cmd.set_color("veryLow", [255, 125, 69])

myspace = {'bfactors': [], 'colors': []}
cmd.iterate('(all)', 'bfactors.append(b)', space=myspace)
for i in range(len(myspace["bfactors"])):
    if myspace["bfactors"][i] >= 90:
        cmd.color("veryHigh", "id %s"%(i))
    if myspace["bfactors"][i] >= 70 and myspace["bfactors"][i] < 90:
        cmd.color("confident", "id %s"%(i))
    if myspace["bfactors"][i] >= 50 and myspace["bfactors"][i] < 70:
        cmd.color("low", "id %s"%(i))
    if myspace["bfactors"][i] < 50:
        cmd.color("veryLow", "id %s"%(i))


cmd.set_view ('''
     0.393646330,    0.902617753,   -0.174098119,\
    -0.272292942,   -0.066398188,   -0.959918439,\
    -0.878005683,    0.425276071,    0.219640806,\
     0.000002455,   -0.000060514, -288.063629150,\
    13.260636330,   -7.507136345,    7.113989830,\
   227.110061646,  349.013397217,  -20.000000000''')
cmd.scene("F0", "store")

# Common variants
cmd.set_view('''
     0.365331203,    0.919453979,    0.145344511,\
     0.527212143,   -0.075690560,   -0.846352756,\
    -0.767186105,    0.385828793,   -0.512402296,\
     0.000002455,   -0.000060514, -288.063629150,\
    13.260636330,   -7.507136345,    7.113989830,\
   227.110061646,  349.013397217,  -20.000000000 ''')
cmd.color("red", "name ca and resi 702+908")
cmd.show("spheres", "name ca and resi 702+908")
cmd.scene("Common", "store")
cmd.hide("spheres", "name ca and resi 702+908")

# #Behcet's syndrome
cmd.set_view ('''
     0.386675328,    0.922169745,    0.008488609,\
     0.156637177,   -0.056603037,   -0.986031234,\
    -0.908812225,    0.382605076,   -0.166334808,\
     0.000002455,   -0.000060514, -288.063629150,\
    13.260636330,   -7.507136345,    7.113989830,\
   227.110061646,  349.013397217,  -20.000000000''')
cmd.color("red", "name ca and resi 81+349+733+816")
cmd.show("spheres", "name ca and resi 81+349+733+816")
cmd.scene("Behcet", "store")
cmd.hide("spheres", "name ca and resi 81+349+733+816")

# # # Hinge variants
cmd.set_view ('''
     0.073372163,    0.926850855,    0.368176132,\
     0.970709980,    0.018311813,   -0.239545107,\
    -0.228766054,    0.374970824,   -0.898362696,\
     0.000002455,   -0.000060514, -288.063629150,\
    13.260636330,   -7.507136345,    7.113989830,\
   227.110061646,  349.013397217,  -20.000000000''')
cmd.color("red", "name ca and resi 334+382+383")
cmd.show("spheres", "name ca and resi 334+382+383")
cmd.scene("Hinge", "store")
cmd.hide("spheres", "name ca and resi 334+382+383")

# # # Back variants
cmd.set_view ('''
    -0.375553399,    0.917228043,    0.132829159,\
     0.353036404,    0.009065011,    0.935561597,\
     0.856921792,    0.398250222,   -0.327220917,\
     0.000002455,   -0.000060514, -288.063629150,\
    13.260636330,   -7.507136345,    7.113989830,\
   227.110061646,  349.013397217,  -20.000000000''')
cmd.color("red", "name ca and resi 469+495+496+513")
cmd.show("spheres", "name ca and resi 469+495+496+513")
cmd.scene("Back", "store")
cmd.hide("spheres", "name ca and resi 469+495+496+513")

# # #All
cmd.set_view ('''
     0.354737908,    0.890810728,    0.283912361,\
     0.482070416,    0.085916959,   -0.871900439,\
    -0.801096201,    0.446167141,   -0.398955882,\
     0.000002455,   -0.000060514, -288.063629150,\
    13.260636330,   -7.507136345,    7.113989830,\
   227.110061646,  349.013397217,  -20.000000000''')

cmd.color("red", "name ca and resi  ")
cmd.show("spheres", "name ca and resi 81+334+349+382+383+469+495+496+513+702+733+816+908")
cmd.scene("All", "store")

# ## Movie
cmd.mset("1x1200")
cmd.set("movie_loop", 0)
cmd.mview("store",  1, scene="F0")
cmd.mview("store", 240, scene="Common")
cmd.mview("store", 480, scene="Behcet")
cmd.mview("store", 720, scene="Hinge")
cmd.mview("store", 960, scene="Back")
cmd.mview("store", 1200, scene="All")


# set ray_trace_mode,  1
# set ambient, 0.4
# set reflect, 0.5
# set two_sided_lighting, on
# set antialias, 2
# set sphere_scale, 0.6, (all)
# set spec_reflect, 2 #surfaces less glossy
# set spec_power, 1000

# cmd.select("AF-Q9HC29-F1-model_v1/A/A/3")
# cmd.select( "selected","AF-Q9HC29-F1-model_v1/A/A/3")
# cmd.color("AF-Q9HC29-F1-model_v1/A/A/3", "blue")
# stored.colors = {}
# iterate all, stored.colors[chain,resi,name,b] = color

# cmd.iterate(mol, cmd.color(,))


# iterate all, print(color)

# set_color veryHigh, [0, 83, 214]
# set_color confident, [101, 203, 243]
# set_color low, [255, 219, 19]
# set_color veryLow, [255, 125, 69]

# cmd.cartoon("putty", mol)
# cmd.set("cartoon_putty_scale_min", min(bfacts),obj)
# cmd.set("cartoon_putty_scale_max", max(bfacts),obj)
# cmd.set("cartoon_putty_transform", 0,obj)
# cmd.set("cartoon_putty_radius", 100,obj)
# cmd.spectrum("b","rainbow", "%s and n. CA " %mol)

# cmd.recolor()