Datasets:
File size: 4,593 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/map3k15.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/map3k15.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 [3699,3726,3728,3727,3701,3070,2776,3759,3459,3068,3069,3072,2721,3064,3066,3067,2745,3687,3690,3691,2190,2194,2477,2478,2479,2480,2481,2482,2442,2444,2719,2754,2772,2749,2751,3703,3422,3424,3425,3426,3457,3450,3452,3416,3418,3432,3428,2720,3732,3735,3730,3682,3090,3488,3451,3453,2453,2454]
set surface_color, pcol1, surf_pocket1
set_color pcol2 = [0.278,0.310,0.702]
select surf_pocket2, protein and id [4654,4656,5486,4651,4653,4711,4650,4694,4707,4710,4708,5453,5450,5451,4532,4533,4970,4584,5424,5426,4635,4636,5428,5430,4632,4634,5456,4571,4556,4549,4551,4631,4633,4566,5460,5462,5463,5464,5465,6277,6276,5494,6285,6288,6274,6278,6302,6303,6305,6281,6283,6284]
set surface_color, pcol2, surf_pocket2
set_color pcol3 = [0.498,0.361,0.902]
select surf_pocket3, protein and id [5157,5160,5317,5215,5754,5757,5760,6150,6151,5161,5733,6230,6125,6232,6234,6236,6233,5762,5735,5721,5739,5753,5503,5504,5715,5716,5473,6241,6248,5216,5163,5164,5166,5175,5176,6239,5213,5158,5162,5333]
set surface_color, pcol3, surf_pocket3
set_color pcol4 = [0.525,0.278,0.702]
select surf_pocket4, protein and id [3530,3528,3529,3531,3532,3946,3524,3506,3789,3832,3849,3508,3509,3787,3791,3794,3917,3918,3798,3800]
set surface_color, pcol4, surf_pocket4
set_color pcol5 = [0.851,0.361,0.902]
select surf_pocket5, protein and id [4654,4656,5486,4651,4653,4650,5452,5453,5450,5451,4969,4532,4533,5484,4970,4549,4551,5462]
set surface_color, pcol5, surf_pocket5
set_color pcol6 = [0.702,0.278,0.600]
select surf_pocket6, protein and id [4699,4688,4689,4695,4701,4703,4427,4150,4168,4169,4162,4430,4431,4432,4713,4718,4720,4437,4472,4144,4161]
set surface_color, pcol6, surf_pocket6
set_color pcol7 = [0.902,0.361,0.596]
select surf_pocket7, protein and id [3187,3183,3185,3264,3265,3266,3298,3299,3300,3518,3519,3521,3513,3494,3493,3288,3291]
set surface_color, pcol7, surf_pocket7
set_color pcol8 = [0.702,0.278,0.325]
select surf_pocket8, protein and id [3710,4035,4767,3624,3621,3627,3998,4000,4001,4002,4009,3662,3620]
set surface_color, pcol8, surf_pocket8
set_color pcol9 = [0.902,0.478,0.361]
select surf_pocket9, protein and id [3934,3938,3572,3904,3978,3600,4197,4219,4220,3976,3571,3578,3551,3569]
set surface_color, pcol9, surf_pocket9
set_color pcol10 = [0.702,0.510,0.278]
select surf_pocket10, protein and id [5454,5455,5626,5481,5452,5453,5450,5451,5486,4970,4574,5456,4573,4976,4549,4978,5482]
set surface_color, pcol10, surf_pocket10
set_color pcol11 = [0.902,0.831,0.361]
select surf_pocket11, protein and id [1391,1392,1537,1568,1574,1570,1548,1531,1342]
set surface_color, pcol11, surf_pocket11
deselect
orient
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