Datasets:
File size: 4,447 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/lrp2.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/lrp2.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 [6457,6500,6501,6471,6497,6475,6121,6125,6458,5748,5390,5757,5753,5755,5392,5750,5754,5776,5398,5067,5772,5774,5778,5038,6509,6447,6449,6450,6451,5394,5399,5026,5031,5033,6452,5035,5039,5063]
set surface_color, pcol1, surf_pocket1
set_color pcol2 = [0.278,0.310,0.702]
select surf_pocket2, protein and id [3955,3960,3962,3261,3609,3255,4464,4117,4121,4455,4126,4515,4518,3269,3271,4125,3273,4511,3604,3974,3976,3968,3972,3645,3978,3646,3267,3622,4526,4512,3964,3618,3614,3616,3259,3263,4019]
set surface_color, pcol2, surf_pocket2
set_color pcol3 = [0.498,0.361,0.902]
select surf_pocket3, protein and id [2486,2488,2528,2535,2538,2541,2478,2542,2490,2025,2031,2036,2011,2481,2483,2491,2519,2474,2472,2581,2040,2042,2044,2049,2560,2559,2456,2441,2580,2004,2010,2534,2530,2533]
set surface_color, pcol3, surf_pocket3
set_color pcol4 = [0.525,0.278,0.702]
select surf_pocket4, protein and id [3364,3362,3503,3179,3194,3185,3191,3195,3193,3403,3216,3402,3380,3434,3436,3438,3502]
set surface_color, pcol4, surf_pocket4
set_color pcol5 = [0.851,0.361,0.902]
select surf_pocket5, protein and id [4190,4071,4073,4192,4347,4191,4348,4116,4119,4188,4173,4172,4287,4281,4094,4096,4038,4045,4048,4049,4050,4051,4322,4052,4032,4294,4292,4295]
set surface_color, pcol5, surf_pocket5
set_color pcol6 = [0.702,0.278,0.600]
select surf_pocket6, protein and id [4117,4455,4110,4111,4113,4118,4448,4451,3953,3955,3962,3255,3948,3951,3604,3603,4100,4102]
set surface_color, pcol6, surf_pocket6
set_color pcol7 = [0.902,0.361,0.596]
select surf_pocket7, protein and id [5126,5131,5128,5132,4945,4942,4947,4950,4951,4982,4981,5005,5029,5122,5025,5028,5104,5105,5106]
set surface_color, pcol7, surf_pocket7
set_color pcol8 = [0.702,0.278,0.325]
select surf_pocket8, protein and id [5373,5732,5731,6102,5707,5711,5713,5717,6084,6085,6221,5504,5710,5714,5709,5712,5716,5508,5507]
set surface_color, pcol8, surf_pocket8
set_color pcol9 = [0.902,0.478,0.361]
select surf_pocket9, protein and id [7209,7210,7054,7089,7248,7240,7239,7252,7336,7321,7095,7208,7086,7093]
set surface_color, pcol9, surf_pocket9
set_color pcol10 = [0.702,0.510,0.278]
select surf_pocket10, protein and id [6257,6362,6439,6442,6174,6448,6256,6176,6177,6179,6363]
set surface_color, pcol10, surf_pocket10
set_color pcol11 = [0.902,0.831,0.361]
select surf_pocket11, protein and id [4504,4130,4135,4145,4514,4149,2828,2720,2855,2856,2858,4141,2830,2718,2719,4299]
set surface_color, pcol11, surf_pocket11
deselect
orient
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