binding_pocket_predictions/predict_slc30a8/visualizations/slc30a8.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/slc30a8.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/slc30a8.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 [790,792,771,772,1421,769,1444,1424,1426,1760,1762,1789,1792,1233,1764,1259,1230,1256,1766,1767,1771,1759,1761,797,800,815,817,818,1734,1733,1736,819,820,821,1395,1397,1398,1399,1791,1361,1362,1363,1368,1288,1291,1342,1344,1351,1932,1933,1961,1264] 
set surface_color,  pcol1, surf_pocket1 
set_color pcol2 = [0.329,0.278,0.702]
select surf_pocket2, protein and id [536,967,968,970,972,971,973,504,505,506,532,534,2401,2424,1075,1076,1077,2425,2423,979,1102,1639,1645,939,2398,2402,2405,2410,2413,2415,2416,528] 
set surface_color,  pcol2, surf_pocket2 
set_color pcol3 = [0.698,0.361,0.902]
select surf_pocket3, protein and id [2596,2597,434,416,419,431,2686,2690,433,435,2687,2623] 
set surface_color,  pcol3, surf_pocket3 
set_color pcol4 = [0.702,0.278,0.639]
select surf_pocket4, protein and id [552,554,1644,1638,1663,1634,1636,594,1534,1660,1662,1621,1633,1546] 
set surface_color,  pcol4, surf_pocket4 
set_color pcol5 = [0.902,0.361,0.545]
select surf_pocket5, protein and id [1736,1204,1206,852,1711,844,1173,1178,1177,1214] 
set surface_color,  pcol5, surf_pocket5 
set_color pcol6 = [0.702,0.353,0.278]
select surf_pocket6, protein and id [1119,1120,928,930,1090,1093,1114,900,922,924,1143,1092,962] 
set surface_color,  pcol6, surf_pocket6 
set_color pcol7 = [0.902,0.729,0.361]
select surf_pocket7, protein and id [839,844,1169,1171,870,872,865,866,867,868,869] 
set surface_color,  pcol7, surf_pocket7 
   
        
        deselect
        
        orient