binding_pocket_predictions/predict_card6/visualizations/card6.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/card6.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/card6.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 [6376,6316,6326,6327,6342,6344,6367,6368,6369,6370,6371,6373,4316,4572,6381,6382,6383,4556,4557,4558,4560,6379,6420,4372,4370,4345,4346,4347,4383,4306,4308,4310,4312,6291,6292,6289,6315] 
set surface_color,  pcol1, surf_pocket1 
set_color pcol2 = [0.329,0.278,0.702]
select surf_pocket2, protein and id [5277,5279,5281,5316,3120,3336,5252,5253,5283,5280,5282,5284,3086,3093,3096,3121,3066,3069,2408,3083,2407,3072,3337,3284,2379,2382,3305] 
set surface_color,  pcol2, surf_pocket2 
set_color pcol3 = [0.698,0.361,0.902]
select surf_pocket3, protein and id [4063,3210,3861,3209,3778,4045,4050,4061,4066,3214,3779,4146,4147,4149,3816,3208,3207,3782,4065,4166,4168,4176,4070,4172,4173] 
set surface_color,  pcol3, surf_pocket3 
set_color pcol4 = [0.702,0.278,0.639]
select surf_pocket4, protein and id [3697,3705,3709,3896,3897,3898,3899,3656,3684,3882,3883,3722,3724,3877,3710,3713,3717,3718,3719,3652,4257,4258,3967,3968,3971,4259,4256,4242,4252,4260,3014] 
set surface_color,  pcol4, surf_pocket4 
set_color pcol5 = [0.902,0.361,0.545]
select surf_pocket5, protein and id [3737,3763,3766,3741,3743,4890,4892,4947,4946,3765,3731,3732,3735,4949,4950,4953,3696,3704] 
set surface_color,  pcol5, surf_pocket5 
set_color pcol6 = [0.702,0.353,0.278]
select surf_pocket6, protein and id [3669,3672,89,4496,87,88,4468,4506,4507,4477,4478,4481,4498,4497] 
set surface_color,  pcol6, surf_pocket6 
set_color pcol7 = [0.902,0.729,0.361]
select surf_pocket7, protein and id [4434,4533,4545] 
set surface_color,  pcol7, surf_pocket7 
   
        
        deselect
        
        orient