binding_pocket_predictions/predict_tyk2/visualizations/tyk2.pdb.pml

        from pymol import cmd,stored
        
        set depth_cue, 1
        set fog_start, 0.4
        
        set_color b_col, [36,36,85]
        set_color t_col, [10,10,10]
        set bg_rgb_bottom, b_col
        set bg_rgb_top, t_col      
        set bg_gradient
        
        set  spec_power  =  200
        set  spec_refl   =  0
        
        load "data/tyk2.pdb", protein
        create ligands, protein and organic
        select xlig, protein and organic
        delete xlig
        
        hide everything, all
        
        color white, elem c
        color bluewhite, protein
        #show_as cartoon, protein
        show surface, protein
        #set transparency, 0.15
        
        show sticks, ligands
        set stick_color, magenta
        
        
        
        
        # SAS points
 
        load "data/tyk2.pdb_points.pdb.gz", points
        hide nonbonded, points
        show nb_spheres, points
        set sphere_scale, 0.2, points
        cmd.spectrum("b", "green_red", selection="points", minimum=0, maximum=0.7)
        
        
        stored.list=[]
        cmd.iterate("(resn STP)","stored.list.append(resi)")    # read info about residues STP
        lastSTP=stored.list[-1] # get the index of the last residue
        hide lines, resn STP
        
        cmd.select("rest", "resn STP and resi 0")
        
        for my_index in range(1,int(lastSTP)+1): cmd.select("pocket"+str(my_index), "resn STP and resi "+str(my_index))
        for my_index in range(1,int(lastSTP)+1): cmd.show("spheres","pocket"+str(my_index))
        for my_index in range(1,int(lastSTP)+1): cmd.set("sphere_scale","0.4","pocket"+str(my_index))
        for my_index in range(1,int(lastSTP)+1): cmd.set("sphere_transparency","0.1","pocket"+str(my_index))
        
        
        
        set_color pcol1 = [0.361,0.576,0.902]
select surf_pocket1, protein and id [5473,5822,5823,5824,5827,4716,5465,5474,5070,5071,5850,5851,5975,5438,4728,4731,4722,4725,5988,5992,5995,4761,4764,4702,4704,4709,4712,4703,4706,4707,5416,4763,5053,5069,5054,5435,5437,4721,4749,4714,4729,5490,5820,6329,5821,5799,5812,5834,5810,6122,6128,6131,5798,5833,5835,5530,6367,6132,6380,6403,6404,6088,6086,6094,6098,6100,6103] 
set surface_color,  pcol1, surf_pocket1 
set_color pcol2 = [0.278,0.388,0.702]
select surf_pocket2, protein and id [627,571,572,573,608,609,623,605,629,794,1245,803,1213,1184,2181,2182,2188,2196,2198,2194,2199,811,836,798,1236,1239,1243,1244,1246,1284,2162,2180,1287,2178] 
set surface_color,  pcol2, surf_pocket2 
set_color pcol3 = [0.361,0.427,0.902]
select surf_pocket3, protein and id [8128,8129,8130,8208,8210,8115,8101,8109,7120,7735,7709,7176,7178,7179,7304,7757,7760,7754,7122,7123,7124,7117,7118,7126,7136,7121,7762,7789,8213,8217,8215,7731,7734,7714,7569,8207] 
set surface_color,  pcol3, surf_pocket3 
set_color pcol4 = [0.286,0.278,0.702]
select surf_pocket4, protein and id [3588,4432,4433,3587,3579,3570,3578,3761,3526,3528,3360,3367,526,529,3400,3363,3478,3480,3503,3506,3500,421,515,519,523,524,496,521,3499,3494,3495,3758,3760,3764,3792,3802,495,3773,390,392,3399,3397,3407] 
set surface_color,  pcol4, surf_pocket4 
set_color pcol5 = [0.443,0.361,0.902]
select surf_pocket5, protein and id [7211,7263,7077,7231,7074,7075,7250,5424,5422,5423,7293,7209,5418,5430,5445,5030,5034,5033,5037,5040,5029,5011,5322,5323,7094,7265] 
set surface_color,  pcol5, surf_pocket5 
set_color pcol6 = [0.404,0.278,0.702]
select surf_pocket6, protein and id [8197,8196,8145,8146,8153,8180,7578,7577,7718,7723,7711,7713,7719,5253,5254,5718,7743,7744,5753,5754,5751,5255,5716,7536,7539,3023,3025,3026,3154,3159,3147,3150,3165,3166,3167,3163,2969,3027,7540,7541,7542] 
set surface_color,  pcol6, surf_pocket6 
set_color pcol7 = [0.592,0.361,0.902]
select surf_pocket7, protein and id [7280,7282,7283,7284,7285,7216,7218,7220,6976,6978,2309,2310,7235,7237,7238,7272,2307,2308,2300,5272,7270,7274,7268,5269,5271,7016,7018,6991,6988,7005,3184,3183,2283,2286,3164,3171,6977,6990] 
set surface_color,  pcol7, surf_pocket7 
set_color pcol8 = [0.518,0.278,0.702]
select surf_pocket8, protein and id [4547,6213,6217,4544,6006,6214,6216,6015,6009,6014,5218,5782,5777,5771,5774,5775,5789,5790,5791,6194,5989,5161,5188,5191,5193,5160,6003,6004,6021,5192,6016,6018,6017,5187,5189,5194,5200] 
set surface_color,  pcol8, surf_pocket8 
set_color pcol9 = [0.741,0.361,0.902]
select surf_pocket9, protein and id [4353,4233,4352,4349,4231,4232,4368,4367,6724,3557,3550,3552,3556,4176,4179,4180,3728,4204,4205,4206,4207,4354] 
set surface_color,  pcol9, surf_pocket9 
set_color pcol10 = [0.635,0.278,0.702]
select surf_pocket10, protein and id [3535,3406,4373,6805,6813,3415,6777,6778,6660,3536,3426,3429,3512,3533,3452,6744,6738,6730,6721,4390,6740] 
set surface_color,  pcol10, surf_pocket10 
set_color pcol11 = [0.890,0.361,0.902]
select surf_pocket11, protein and id [2273,6990,6992,2965,7519,7521,7524,2977,3183,3150,3167,3182,2959,2974,2274,2980,2982,7576,7573,7592,3184,7596,6999,7595,6991,7583,7585,7575] 
set surface_color,  pcol11, surf_pocket11 
set_color pcol12 = [0.702,0.278,0.647]
select surf_pocket12, protein and id [1936,1937,1934,1928,1931,1964,1458,1459,1460,1491,1480,1490,2074,1482,1492,2013,2014,2075,2076,2077,1484,1516,1974] 
set surface_color,  pcol12, surf_pocket12 
set_color pcol13 = [0.902,0.361,0.757]
select surf_pocket13, protein and id [2247,2241,2244,3221,3108,3219,3106,2341,2346,2348,3102,3101,3087,3092,3079,2235,2459,2461,2266,3205,3207,2345] 
set surface_color,  pcol13, surf_pocket13 
set_color pcol14 = [0.702,0.278,0.533]
select surf_pocket14, protein and id [8406,8379,8376,8865,8866,8374,8841,8470,8504,8506,8473,8479,8346,8363,8476,8070,8391,8393,8442,8440] 
set surface_color,  pcol14, surf_pocket14 
set_color pcol15 = [0.902,0.361,0.608]
select surf_pocket15, protein and id [1016,993,4411,1028,1031,4455,989,4457,4408,4410,970,972,9309,4482,4494,4495,4497,4474,987,990,1094] 
set surface_color,  pcol15, surf_pocket15 
set_color pcol16 = [0.702,0.278,0.416]
select surf_pocket16, protein and id [8544,8554,8555,9196,9198,9200,8557,8579,8549,8551,8545,8547,7999,8003,9205,9202,9213,9218,9219,9221] 
set surface_color,  pcol16, surf_pocket16 
set_color pcol17 = [0.902,0.361,0.459]
select surf_pocket17, protein and id [1223,1261,1263,1264,1680,1681,1221,1226,1501,1502,1227,1533,1534,1204,1203,1205,1229,1228,235] 
set surface_color,  pcol17, surf_pocket17 
set_color pcol18 = [0.702,0.278,0.298]
select surf_pocket18, protein and id [4112,4114,4115,4116,4117,4119,4121,4095,4108,4255,4257,4246,4248,4252,4253,4224,4241,4243,4325,4258] 
set surface_color,  pcol18, surf_pocket18 
set_color pcol19 = [0.902,0.412,0.361]
select surf_pocket19, protein and id [3173,3174,5656,5662,5667,2293,2294,2296,2291,2290,2292,2297,5926,6794,5687,3175,5655,5657,5663,5639,2295,5661,5281,5282,5669] 
set surface_color,  pcol19, surf_pocket19 
set_color pcol20 = [0.702,0.376,0.278]
select surf_pocket20, protein and id [7147,8232,7410,7411,7390,8253,8365,8366,8367,7377,7378,8070,8393,8240,8362,8363,7391,8372,8377,7157,7159] 
set surface_color,  pcol20, surf_pocket20 
set_color pcol21 = [0.902,0.561,0.361]
select surf_pocket21, protein and id [964,958,967,1091,1094,1063,1067,1090,952,875,1096,1031,1032,972,969,9277,1040] 
set surface_color,  pcol21, surf_pocket21 
set_color pcol22 = [0.702,0.494,0.278]
select surf_pocket22, protein and id [3275,645,668,616,3255,3257,3258,621,638,669,670,747,748,599,581] 
set surface_color,  pcol22, surf_pocket22 
set_color pcol23 = [0.902,0.710,0.361]
select surf_pocket23, protein and id [1392,1420,1423,1424,1425,1433,1828,1802,1867,1829] 
set surface_color,  pcol23, surf_pocket23 
set_color pcol24 = [0.702,0.608,0.278]
select surf_pocket24, protein and id [884,886,1153,1155,888,1149,1151,1152,1154,1156,889,2033,2068,1098,1100,1116,1128,1129] 
set surface_color,  pcol24, surf_pocket24 
set_color pcol25 = [0.902,0.859,0.361]
select surf_pocket25, protein and id [3781,3787,3795,3774,3841,3843,3604,3593,3605,3999,3780,3638,3753,3754,3997,3998,3796] 
set surface_color,  pcol25, surf_pocket25 
set_color pcol26 = [0.675,0.702,0.278]
select surf_pocket26, protein and id [585,798,774,776,571,608,609,1236,1237,1239,1243,1268,1270,1269,1272] 
set surface_color,  pcol26, surf_pocket26 
   
        
        deselect
        
        orient