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/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 | |