binding_pocket_predictions/predict_inhbe/visualizations/inhbe.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/inhbe.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/inhbe.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 [1362,1360,1941,1942,1945,2172,1377,1950,1960,1963,2169,1879,1883,1866,1867,1881,1882,1224,1232,1353,1359,1364,1365,1348,1355,300,1349,262,264,289,263,267,268,287,288,286,293,295,296,246,265,245,1239] 
set surface_color,  pcol1, surf_pocket1 
set_color pcol2 = [0.416,0.278,0.702]
select surf_pocket2, protein and id [1400,905,906,909,1837,2684,1838,1841,1763,2144,2159,2668,1934,2496,2681,2499,2678,2680,2682,2143,1862,1952,1953] 
set surface_color,  pcol2, surf_pocket2 
set_color pcol3 = [0.902,0.361,0.878]
select surf_pocket3, protein and id [2701,2705,2704,1917,1915,1916,2232,2341,2241,2242,2310,2250,2269,2248,2698,2265,2268,2278] 
set surface_color,  pcol3, surf_pocket3 
set_color pcol4 = [0.702,0.278,0.380]
select surf_pocket4, protein and id [716,717,718,1696,1693,701,1697,1675,1695,1317,1656,973,977] 
set surface_color,  pcol4, surf_pocket4 
set_color pcol5 = [0.902,0.620,0.361]
select surf_pocket5, protein and id [2250,2269,2248,1917,1915,1916,2695,2698] 
set surface_color,  pcol5, surf_pocket5 
   
        
        deselect
        
        orient