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/dnmt3a.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/dnmt3a.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 [6962,6964,6965,6966,6967,6968,6971,5484,5486,5467,5472,5474,5475,5477,5479,5481,5132,5140,5144,5169,6496,6501,6502,5488,5494,4948,4947,4950,5464,5465,4986,4956,4957,4959,4964,5133,6973,5880,6153,6156,6960,6477,6479,6492,6494,5894,5514,5516,6495,5531,6985,6987,6991,6986,6988,6990] | |
| set surface_color, pcol1, surf_pocket1 | |
| set_color pcol2 = [0.302,0.278,0.702] | |
| select surf_pocket2, protein and id [2534,2537,2526,2267,2263,2265,2301,2295,2296,2297,2300,2752,2750,2539,2524,2766,2767,2763,2240,2266,2260,2262,2493,2495,2496,2293,2294,2298,2291,2556,2751] | |
| set surface_color, pcol2, surf_pocket2 | |
| set_color pcol3 = [0.631,0.361,0.902] | |
| select surf_pocket3, protein and id [4498,4488,4489,4494,4858,4625,7104,4272,4273,4627,4259,4829,4840,4842,4844,4846,4859,4836] | |
| set surface_color, pcol3, surf_pocket3 | |
| set_color pcol4 = [0.678,0.278,0.702] | |
| select surf_pocket4, protein and id [4691,4692,4693,4700,4701,4703,4746,4665,4804,4805,6222,6210,6225,6215,6221,6197,4788,6202,4789,4719,6240,6049,6228,6231,6032,6027] | |
| set surface_color, pcol4, surf_pocket4 | |
| set_color pcol5 = [0.902,0.361,0.682] | |
| select surf_pocket5, protein and id [6021,4784,4786,4790,4793,5845,5849,5851,4794,4817,6204,4796,5750,5753,5823,5749,6009,6016,6017] | |
| set surface_color, pcol5, surf_pocket5 | |
| set_color pcol6 = [0.702,0.278,0.341] | |
| select surf_pocket6, protein and id [4379,4397,4399,4455,4428,4429,4481,4539,4541,4358,4378,4463] | |
| set surface_color, pcol6, surf_pocket6 | |
| set_color pcol7 = [0.902,0.522,0.361] | |
| select surf_pocket7, protein and id [4911,4914,5435,5805,5802,4893,4883,4885,4886,5434,5436,4838,5816,7123,4880,7109,7125,4864,4837] | |
| set surface_color, pcol7, surf_pocket7 | |
| set_color pcol8 = [0.702,0.596,0.278] | |
| select surf_pocket8, protein and id [7136,7137,4246,7143,4265,4256,4258,4260,4254,4105,4108,4106,4234,4095,4096,4089,4093,4094] | |
| set surface_color, pcol8, surf_pocket8 | |
| deselect | |
| orient | |