binding_pocket_predictions/predict_slc6a19/visualizations/slc6a19.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/slc6a19.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/slc6a19.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 [444,445,448,3812,3815,3816,443,1003,1005,485,406,430,434,441,436,1028,3107,3786,2154,3821,3849,486,2139,2140,2141,3818,3820,3822,3834,3092,3098,3099,3102,3108,3094,3097,473,475,478,3751,3792,4339,4341,4342,4375,3831,4376,2100,2102,2103,2129,2132,2098,4398] 
set surface_color,  pcol1, surf_pocket1 
set_color pcol2 = [0.278,0.361,0.702]
select surf_pocket2, protein and id [3918,3943,3914,3942,3985,4250,3976,3978,48,3944,3945,3946,4284,3908,3910,3911,3912,4249,4251,4254,4261,4285,4730,4728,4732,4733,4735,4738,4758,848,849,861,846,850,3984,862,870] 
set surface_color,  pcol2, surf_pocket2 
set_color pcol3 = [0.373,0.361,0.902]
select surf_pocket3, protein and id [1415,4527,4531,4539,4526,4528,3075,1368,1339,1344,2614,4438,4440,4542,4544,4439,3109,3110,3144,1367,1414,1417,3085,3143,3087,2582,3178,3089,3092,3094,3095,3097,3083,3081,3751] 
set surface_color,  pcol3, surf_pocket3 
set_color pcol4 = [0.380,0.278,0.702]
select surf_pocket4, protein and id [2293,2302,778,4939,243,246,4941,3453,4954,4946,4950,3478,3485,250,252,253,2305,3571,3573,4957,3477,1705,4959] 
set surface_color,  pcol4, surf_pocket4 
set_color pcol5 = [0.600,0.361,0.902]
select surf_pocket5, protein and id [3808,3675,3807,3698,961,4679,4671,962,3774,3778,4649,3699] 
set surface_color,  pcol5, surf_pocket5 
set_color pcol6 = [0.557,0.278,0.702]
select surf_pocket6, protein and id [4350,4352,4353,4383,3829,3831,3857,4371,4629,4654,4656,4659,4664,4370,4372,4378,4415,4414,4626,4628,4631,3856,4683,3888,4706,4685,4686,4714,3855,4312] 
set surface_color,  pcol6, surf_pocket6 
set_color pcol7 = [0.831,0.361,0.902]
select surf_pocket7, protein and id [4299,4301,603,2119,2121,2125,594,4269,4295,4292,2114,2094,2115,2117,2133,4327] 
set surface_color,  pcol7, surf_pocket7 
set_color pcol8 = [0.702,0.278,0.667]
select surf_pocket8, protein and id [2187,384,2216,390,394,378,3411,3412,1002,3381,1005,405,2240] 
set surface_color,  pcol8, surf_pocket8 
set_color pcol9 = [0.902,0.361,0.741]
select surf_pocket9, protein and id [1797,3341,3349,3369,3339,1790,1787,1791,1650,1685] 
set surface_color,  pcol9, surf_pocket9 
set_color pcol10 = [0.702,0.278,0.486]
select surf_pocket10, protein and id [947,930,3468,922,3469,3621,3640,3613,3618,3622,949,953,951,952,954,3676] 
set surface_color,  pcol10, surf_pocket10 
set_color pcol11 = [0.902,0.361,0.514]
select surf_pocket11, protein and id [1072,1619,1115,1117,1651,3342,3343,1106,3340,3341,3339] 
set surface_color,  pcol11, surf_pocket11 
set_color pcol12 = [0.702,0.278,0.310]
select surf_pocket12, protein and id [4284,4305,4308,4310,4312,3905,3907,3908,3909,3910,3918,3886,3887] 
set surface_color,  pcol12, surf_pocket12 
set_color pcol13 = [0.902,0.435,0.361]
select surf_pocket13, protein and id [647,618,617,2396,2397,4160,4162,4163,4164,4177,2424,2426] 
set surface_color,  pcol13, surf_pocket13 
set_color pcol14 = [0.702,0.427,0.278]
select surf_pocket14, protein and id [3160,2515,3324] 
set surface_color,  pcol14, surf_pocket14 
set_color pcol15 = [0.902,0.667,0.361]
select surf_pocket15, protein and id [520,519,2002,2003,2000,2027,2028,497,2037,2040,3065,3067,2043] 
set surface_color,  pcol15, surf_pocket15 
set_color pcol16 = [0.702,0.608,0.278]
select surf_pocket16, protein and id [942,3419,971,972] 
set surface_color,  pcol16, surf_pocket16 
set_color pcol17 = [0.902,0.894,0.361]
select surf_pocket17, protein and id [3124,3118,3159,3161,422,427,421,425] 
set surface_color,  pcol17, surf_pocket17 
   
        
        deselect
        
        orient