Datasets:
File size: 4,714 Bytes
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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/dpp9.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/dpp9.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 [1025,1957,1910,1052,1053,1014,1956,1958,1018,1017,1504,1506,1508,985,987,989,990,1026,988,1022,1925,1916,1918,1919,1924,2257,2258,1931,1927,2429,2430,2431,978,2420,2422,2415,2426,2412,1906,1911,1516,2011,2019,1623,1904,1912,1512,1878,1876,1885,1893,1895,1643,1647,1806,1624,1642,1635,991,1807,1831,1833,1843,1844,1870,1875,1848,1837,1825]
set surface_color, pcol1, surf_pocket1
set_color pcol2 = [0.278,0.310,0.702]
select surf_pocket2, protein and id [5858,6102,6488,6749,1965,1966,1975,1073,1074,1077,6746,6744,5856,5224,5191,5193,5859,5860,5862,1963,1994,5217,1072,5206,5212,1976,6129,6133,6131,6099,6049,5866]
set surface_color, pcol2, surf_pocket2
set_color pcol3 = [0.498,0.361,0.902]
select surf_pocket3, protein and id [4033,5213,5479,5481,5482,5489,4030,5229,385,5302,5254,5255,5256,4547,5268,5270,5275,4586,5487,3991,4001,4003,4007,4043,4237,4238,4425,4412,4414,4423,4524,4527,4528,4529,388,4409,4407,4406,4408,4027,4028,4017,4018,4008,4013,4016,4020,3997,4023,3599,3992]
set surface_color, pcol3, surf_pocket3
set_color pcol4 = [0.525,0.278,0.702]
select surf_pocket4, protein and id [5189,5310,5185,5241,5318,5320,5174,5307,5313,6744,6751,5171,5173,5844,5845,5846,5847,5849,5831,5834,6834,6837,6868,5335,5337,6845,6832,6756,6759,6761,6763,5842,5350,5372]
set surface_color, pcol4, surf_pocket4
set_color pcol5 = [0.851,0.361,0.902]
select surf_pocket5, protein and id [4378,4380,4381,4626,4627,4629,4418,4364,4369,4375,4609,4608,4756,4752,4593,4809,4400,4402,4403,4539,4541,4572]
set surface_color, pcol5, surf_pocket5
set_color pcol6 = [0.702,0.278,0.600]
select surf_pocket6, protein and id [2462,6523,6525,6527,6528,2303,6500,6502,6503,6521,2298,2300,2305,6087,6089,6090,6524,6526]
set surface_color, pcol6, surf_pocket6
set_color pcol7 = [0.902,0.361,0.596]
select surf_pocket7, protein and id [3466,3478,4096,4098,3468,3469,3470,3471,3473,4299,4301,4120,4121,4122,4094,3546,3548,3696,3534,3681,3682]
set surface_color, pcol7, surf_pocket7
set_color pcol8 = [0.702,0.278,0.325]
select surf_pocket8, protein and id [2841,2843,2928,2042,2044,2047,2055,1530,2846,2850,2926,2059,1552]
set surface_color, pcol8, surf_pocket8
set_color pcol9 = [0.902,0.478,0.361]
select surf_pocket9, protein and id [349,374,616,372,371,357,4815,4818,4794,4798,4799,619,831,4789,4801,4805,832]
set surface_color, pcol9, surf_pocket9
set_color pcol10 = [0.702,0.510,0.278]
select surf_pocket10, protein and id [2764,3036,3303,3018,3035,3862,3828,3833,3830,2754,3823,3821,3019,2781,2782,2783,2759,2774,2775,3846,3858,3855,3866]
set surface_color, pcol10, surf_pocket10
set_color pcol11 = [0.902,0.831,0.361]
select surf_pocket11, protein and id [3599,5506,3992,3398,5544,3991,5479,5482]
set surface_color, pcol11, surf_pocket11
deselect
orient
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