binding_pocket_predictions/predict_ubash3a/visualizations/ubash3a.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/ubash3a.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/ubash3a.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 [1488,1490,1532,1216,1516,1517,1553,796,804,807,1531,1551,1555,2393,1554,1526,1529,1530,905,874,896,858,861,872,875,856,1474,2392,907,833,2427,860,1822,859,838,852,888,582] 
set surface_color,  pcol1, surf_pocket1 
set_color pcol2 = [0.490,0.278,0.702]
select surf_pocket2, protein and id [1826,1828,1830,1859,1849,1860,537,1823,1829,2248,2412,2435,539,528,536,519,522,2104,410,446,448,449,2254,471,2242,2245,2246,2251,2269,2271,2247,2249,412,294,319,295,296,297,326,317,320,949,538,948,520,377,400,401,403,406] 
set surface_color,  pcol2, surf_pocket2 
set_color pcol3 = [0.902,0.361,0.682]
select surf_pocket3, protein and id [639,1784,596,598,841,611,1772,1775,603,1802,1805,2443,2444,839,840,837,638,2398,1774,2472] 
set surface_color,  pcol3, surf_pocket3 
set_color pcol4 = [0.702,0.408,0.278]
select surf_pocket4, protein and id [2023,2202,2206,2207,2204,2025,2001,2296,2298,2201,2203,2299,2165,2301,2303,2199,2178,2200,2180,2017,2300] 
set surface_color,  pcol4, surf_pocket4 
   
        
        deselect
        
        orient