binding_pocket_predictions/predict_apol1/visualizations/apol1.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/apol1.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/apol1.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 [2046,2048,2049,122,1050,1052,2631,1055,2013,2042,2044,2045,2022,2024,2047,2651,86,81,87,88,90,92,2074,2075,2652,2653,2628,2632,2643,2646,2650,2629,2675,2055,2676,1084,2630,1088,1161,675,676,677,645,85,2076,2094,2095,606,607,611,613,637,602,604,2012,2014,2015,1019,1020,1053,963,1021,60,64,65,2683,69,71,2705,2706,2702,2704,2647,2672,2659,2673,2660,51,30,2707,2708,141,118,120,121,145,147,149,151,117,123,124,127,1046,1047,1048,1056,158,159,160,1092,3044,91,2947,126,128,1094,1095,1096,2984,1098,2982,2983,1133,1049,150,152,1025,938,936,937,987,1016] 
set surface_color,  pcol1, surf_pocket1 
set_color pcol2 = [0.490,0.278,0.702]
select surf_pocket2, protein and id [1281,1810,1812,1811,1255,1257,1242,1245,2750,2779,2751,2752,2867,2869,1814,1279,1280,2835,2837,2838,2836,2868,1305,1868,2690,1867,2725,1839,1841,1831,1833,1838,1215,1219,2718,2716] 
set surface_color,  pcol2, surf_pocket2 
set_color pcol3 = [0.902,0.361,0.682]
select surf_pocket3, protein and id [1023,146,173,993,207,1024,1025,1034,994,1047,1056,1059,1062,3045,158,160,144,154,157,145] 
set surface_color,  pcol3, surf_pocket3 
set_color pcol4 = [0.702,0.408,0.278]
select surf_pocket4, protein and id [114,880,110,140,121,137,901,638,938,658,669] 
set surface_color,  pcol4, surf_pocket4 
   
        
        deselect
        
        orient