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/gpr75.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/gpr75.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 [2882,2496,2875,2883,2885,612,614,616,651,1113,1705,1108,1109,1110,1106,2873,2878,2880,2881,3710,3712,3715,2919,2932,2935,2936,2929,2917,623,3722,3723,3724,3725,3727,622,624,3707,594,597,609,596,1140,1139,546,548,3696,541,543,544,564,505,650,469,470,468,465,493,495,506,502,504,542,492,494,3708,3717,3740,3745,3747,3749,3751,3753,3750,1761,1147,3720,3691,3692,2909,2912,2464,2466,2467,2473,1731,2443,2445,1760] | |
| set surface_color, pcol1, surf_pocket1 | |
| set_color pcol2 = [0.302,0.278,0.702] | |
| select surf_pocket2, protein and id [1275,1252,606,641,600,601,602,1251,1214,1245,1211,604,1070,1098,1128,1132,1125,1099,1102,1183,1184,607,1181,1093,1094,1096] | |
| set surface_color, pcol2, surf_pocket2 | |
| set_color pcol3 = [0.631,0.361,0.902] | |
| select surf_pocket3, protein and id [2517,2850,2876,2495,2524,2875,2883,2885,2888,1058,1708,2821,2823,1059] | |
| set surface_color, pcol3, surf_pocket3 | |
| set_color pcol4 = [0.678,0.278,0.702] | |
| select surf_pocket4, protein and id [1591,1594,2770,2574,2600,981,1488,1477,2768,1005] | |
| set surface_color, pcol4, surf_pocket4 | |
| set_color pcol5 = [0.902,0.361,0.682] | |
| select surf_pocket5, protein and id [2814,2815,2842,2866,2867,2868,409,375,376,406,2832,2833,2834] | |
| set surface_color, pcol5, surf_pocket5 | |
| set_color pcol6 = [0.702,0.278,0.341] | |
| select surf_pocket6, protein and id [1623,1629,1633,1657,2576,2577,1625,1658,2548,2550,2553,2579,1655,2559] | |
| set surface_color, pcol6, surf_pocket6 | |
| set_color pcol7 = [0.902,0.522,0.361] | |
| select surf_pocket7, protein and id [305,307,309,310,2743,283,329,331,820,821,2740] | |
| set surface_color, pcol7, surf_pocket7 | |
| set_color pcol8 = [0.702,0.596,0.278] | |
| select surf_pocket8, protein and id [1394,953,1417,1418,918,919,921,915,917,891,892,893,1436,1440,1425,1427,1428,1430,1432,894] | |
| set surface_color, pcol8, surf_pocket8 | |
| deselect | |
| orient | |