binding_pocket_predictions/predict_cfhr5/visualizations/cfhr5.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/cfhr5.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/cfhr5.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 [441,3895,447,476,3891,530,532,534,3921,436,240,242,243,244,245,246,247,3850,3937,3939,3942,267,3946,3941,264,262,3848,437,440,490,522,525,528,513,239,241,250,252,256,434,464,698,699,3902,825,484,489,3878,3864,3862,3888,3889,3916,3899] 
set surface_color,  pcol1, surf_pocket1 
set_color pcol2 = [0.365,0.278,0.702]
select surf_pocket2, protein and id [1868,1863,1865,1870,1874,1867,1854,2293,2291,2446,1884,1890,2459,2461,2460,1911,1916,1918,1921,1924,1903,1873,1925,2288,2286,2289] 
set surface_color,  pcol2, surf_pocket2 
set_color pcol3 = [0.792,0.361,0.902]
select surf_pocket3, protein and id [1125,1127,1128,1167,1168,1164,1153,1159,1170,1126,1513,1515,1522,1523,1506,940,1121,1123,1124,1532,1526,1529] 
set surface_color,  pcol3, surf_pocket3 
set_color pcol4 = [0.702,0.278,0.533]
select surf_pocket4, protein and id [275,3837,3839,414,263,265,544,547,548,261,410,264,3841,3842,3845,3955,3836,3959,3970,3971,3972,3953,3958,3834,267,3945,3946,3947] 
set surface_color,  pcol4, surf_pocket4 
set_color pcol5 = [0.902,0.361,0.361]
select surf_pocket5, protein and id [1054,1057,1060,1046,1061,701,705,706,710,1063,696,469,471,688,691,711] 
set surface_color,  pcol5, surf_pocket5 
set_color pcol6 = [0.702,0.533,0.278]
select surf_pocket6, protein and id [1439,1441,1442,1444,1445,1991,3189,3192,2029,2033,2016,2018,2028,3205,1989,1992,1990,2009] 
set surface_color,  pcol6, surf_pocket6 
   
        
        deselect
        
        orient