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/pcsk9.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/pcsk9.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 [4467,4476,4462,4463,4824,4826,4809,4813,4821,4812,4829,4249,4247,4808,4804,4806,3776,3786,4260,4261,3775,4262,3763,3787,3704,4875,4878,4279,4283,4830,4838,3695,3697,3700] | |
| set surface_color, pcol1, surf_pocket1 | |
| set_color pcol2 = [0.278,0.298,0.702] | |
| select surf_pocket2, protein and id [4317,4319,4318,4344,4345,4348,3769,3905,3745,3747,3749,3757,3911,4286,4366,4370,4839,4346,4347,4353,4365,4276,4278,4280,4281,4282,4285,4836,4838,4300,4301,4299,4496] | |
| set surface_color, pcol2, surf_pocket2 | |
| set_color pcol3 = [0.533,0.361,0.902] | |
| select surf_pocket3, protein and id [531,532,554,556,558,560,545,1184,1185,1186,1182,2008,1179,1181,1183,1191,2454,2452,2690] | |
| set surface_color, pcol3, surf_pocket3 | |
| set_color pcol4 = [0.565,0.278,0.702] | |
| select surf_pocket4, protein and id [630,943,2302,939,2323,2325,636,654,1119,656,1110,2322,2350,2347,2349,2343,937,932,950] | |
| set surface_color, pcol4, surf_pocket4 | |
| set_color pcol5 = [0.902,0.361,0.878] | |
| select surf_pocket5, protein and id [4776,4777,4761,4918,3164,3450,3458,3452,4753,4754,4756,3163] | |
| set surface_color, pcol5, surf_pocket5 | |
| set_color pcol6 = [0.702,0.278,0.533] | |
| select surf_pocket6, protein and id [884,973,2049,1651,1656,1659,1660,1662,989,598,885,987,1650,1156,579,2035,577,595,576] | |
| set surface_color, pcol6, surf_pocket6 | |
| set_color pcol7 = [0.902,0.361,0.490] | |
| select surf_pocket7, protein and id [1422,1412,1916,1917,1918,1919,3031,3033,1361,1428,3001,3004,3005,3009,1903,1907,1360,3003,1425,1905,1923,1920,1921] | |
| set surface_color, pcol7, surf_pocket7 | |
| set_color pcol8 = [0.702,0.329,0.278] | |
| select surf_pocket8, protein and id [2013,2014,1190,1206,1205,2006,2008,2002,1486,1776,1777,1779,1789,1792,1794,1795,1798] | |
| set surface_color, pcol8, surf_pocket8 | |
| set_color pcol9 = [0.902,0.620,0.361] | |
| select surf_pocket9, protein and id [4462,4463,4248,4250,4808,4806,5089,4616,5075,4615,4448,4465] | |
| set surface_color, pcol9, surf_pocket9 | |
| set_color pcol10 = [0.702,0.631,0.278] | |
| select surf_pocket10, protein and id [1261,2822,1251,1253,1279,1265,1277,2969,1890,1893,1894] | |
| set surface_color, pcol10, surf_pocket10 | |
| deselect | |
| orient | |