mirror of
https://github.com/rdk/p2rank.git
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75 lines
2.2 KiB
Promela
75 lines
2.2 KiB
Promela
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from pymol import cmd,stored
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set depth_cue, 1
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set fog_start, 0.4
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set_color b_col, [36,36,85]
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set_color t_col, [10,10,10]
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set bg_rgb_bottom, b_col
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set bg_rgb_top, t_col
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set bg_gradient
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set spec_power = 200
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set spec_refl = 0
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load "data/1fbl.pdb", protein
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create ligands, protein and organic
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select xlig, protein and organic
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delete xlig
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hide everything, all
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color white, elem c
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color bluewhite, protein
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#show_as cartoon, protein
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show surface, protein
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#set transparency, 0.15
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show sticks, ligands
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set stick_color, magenta
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# SAS points
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load "data/1fbl.pdb_points.pdb.gz", points
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hide nonbonded, points
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show nb_spheres, points
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set sphere_scale, 0.2, points
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cmd.spectrum("b", "green_red", selection="points", minimum=0, maximum=0.7)
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stored.list=[]
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cmd.iterate("(resn STP)","stored.list.append(resi)") # read info about residues STP
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lastSTP=stored.list[-1] # get the index of the last residue
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hide lines, resn STP
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cmd.select("rest", "resn STP and resi 0")
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for my_index in range(1,int(lastSTP)+1): cmd.select("pocket"+str(my_index), "resn STP and resi "+str(my_index))
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for my_index in range(1,int(lastSTP)+1): cmd.show("spheres","pocket"+str(my_index))
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for my_index in range(1,int(lastSTP)+1): cmd.set("sphere_scale","0.4","pocket"+str(my_index))
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for my_index in range(1,int(lastSTP)+1): cmd.set("sphere_transparency","0.1","pocket"+str(my_index))
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set_color pcol1 = [0.361,0.576,0.902]
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select surf_pocket1, protein and id [991,992,993,994,1033,1035,1036,1026,664,670,676,971,679,958,959,960,961,962,963,938,942,972,934,929,943,989,1016,32,692,700,33,1118,1119,658,659,1122,1124,651,1112,1106]
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set surface_color, pcol1, surf_pocket1
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set_color pcol2 = [0.490,0.278,0.702]
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select surf_pocket2, protein and id [2109,2144,2091,2092,1991,2150,2151,2161,2163,2444,1891,2426,2439,1910,2064,1909,1890,1926]
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set surface_color, pcol2, surf_pocket2
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set_color pcol3 = [0.902,0.361,0.682]
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select surf_pocket3, protein and id [760,761,730,728,746,173,514,515,171,172,501,472,499,532,560]
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set surface_color, pcol3, surf_pocket3
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set_color pcol4 = [0.702,0.408,0.278]
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select surf_pocket4, protein and id [1488,1497,1513,1619,1620,1769,1490,1756,1757,1489,1766,1917,1499,2030,2031,2034,2035]
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set surface_color, pcol4, surf_pocket4
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deselect
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orient
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