Datasets:
| 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/gys1.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/gys1.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 [357,325,327,328,329,324,326,2651,2652,2653,2055,2227,1625,1629,1626,336,331,4134,285,321,338,1441,4107,4110,4121,2711,4097,4098,4125,4128,4130,4132,4143,2643,2644,2646,1671,1674,2656,1446,1635,1444,1443,1457,1168,1467,4105,4106,4087,4092,4083,2710,4103] | |
| set surface_color, pcol1, surf_pocket1 | |
| set_color pcol2 = [0.278,0.310,0.702] | |
| select surf_pocket2, protein and id [2198,2199,4895,4897,2197,5086,5080,5082,5083,5079,5081,2219,4868,4871,2204,4866,4293,4320,4321,4322,4329,4331,4332,4289,2062,2065,2070,2203,2205,2206,2193,2200,2188,4283,4286,4120,4264,134,136,138,5104,5105,5098,5099,5100,5594,5054,140,5570,4834,4855,4856,4859,4854,108,110,4836,109,102] | |
| set surface_color, pcol2, surf_pocket2 | |
| set_color pcol3 = [0.498,0.361,0.902] | |
| select surf_pocket3, protein and id [4636,4679,4681,4637,4638,4639,4642,2567,2594,4670,4673,4709,2365,2368,2397,2395,2396,2373,2340,2342,2338,2370,2372,2584] | |
| set surface_color, pcol3, surf_pocket3 | |
| set_color pcol4 = [0.525,0.278,0.702] | |
| select surf_pocket4, protein and id [478,479,480,671,664,661,663,199,223,675,1314,1315,1343,1376,1374,211,1377,1341,1344,1357,205,206,212,502,503] | |
| set surface_color, pcol4, surf_pocket4 | |
| set_color pcol5 = [0.851,0.361,0.902] | |
| select surf_pocket5, protein and id [3948,3950,3951,3952,3953,3954,3956,4164,2642,2943,4143,4163,2643,2644,2646,2645,2945,3867,3871,3862,3864,3859] | |
| set surface_color, pcol5, surf_pocket5 | |
| set_color pcol6 = [0.702,0.278,0.600] | |
| select surf_pocket6, protein and id [1230,1262,1264,1266,1268,1269,1267,1271,1272,1265,1013,1015,969,1002,1232,1543,1038] | |
| set surface_color, pcol6, surf_pocket6 | |
| set_color pcol7 = [0.902,0.361,0.596] | |
| select surf_pocket7, protein and id [5055,140,141,158,5619,5620,5594,5587,5588,5589,5590,5591,133,134,135,136,137,138,119,156,157,111,114,115,124,129] | |
| set surface_color, pcol7, surf_pocket7 | |
| set_color pcol8 = [0.702,0.278,0.325] | |
| select surf_pocket8, protein and id [5053,5055,141,5017,177,178,4892,4921,4917,5036,5029,5021,5027,5032,4893,4895,4897] | |
| set surface_color, pcol8, surf_pocket8 | |
| set_color pcol9 = [0.902,0.478,0.361] | |
| select surf_pocket9, protein and id [3566,3668,3667,3018,3563,3562,3550,3552,3556,3580,3625,3701,3624,3698,3696,3567,3561,3739,3741] | |
| set surface_color, pcol9, surf_pocket9 | |
| set_color pcol10 = [0.702,0.510,0.278] | |
| select surf_pocket10, protein and id [4076,4078,1727,1728,1759,1719,4075,4488,4489,2728,2692,2694,1699,1711,1712,4436,4072,4074,4442,2693,2735,2727,4073,4483,4485,4469,4478,4482] | |
| set surface_color, pcol10, surf_pocket10 | |
| set_color pcol11 = [0.902,0.831,0.361] | |
| select surf_pocket11, protein and id [4853,4887,4892,4891,135,136,137,4921,4922,141,4890,4852,4893,5029] | |
| set surface_color, pcol11, surf_pocket11 | |
| deselect | |
| orient | |