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/tbc1d1.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/tbc1d1.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 [7704,7706,3971,3914,3915,3916,3917,3942,3943,3945,3946,3947,3949,3950,7694,7700,7690,7691,7684,7686,7512,7616,7618,7652,7452,7474,7448,7479,7481,8495,8497,8499,8530,7485,7487,8520,8523,7473,7510,7519,8531,8533,3938,3937,3940,7674,7675,7677,7646,7648,7650,7682,7639,7641,7645] | |
| set surface_color, pcol1, surf_pocket1 | |
| set_color pcol2 = [0.278,0.310,0.702] | |
| select surf_pocket2, protein and id [4034,4035,4066,4036,3980,7415,7417,7451,7100,4067,7419,7418,7398,7401,7087,7091,7092,7095,7096,7443,7775,7734,7735,7737,7400,4002,3978,4005,4006,4012,7378] | |
| set surface_color, pcol2, surf_pocket2 | |
| set_color pcol3 = [0.498,0.361,0.902] | |
| select surf_pocket3, protein and id [2166,2309,2167,2129,2153,2165,1422,1424,2232,2131,2240,2271,2284,2236,1420,2241,2308,1419,2287,2288,2289,2290,2291,2154] | |
| set surface_color, pcol3, surf_pocket3 | |
| set_color pcol4 = [0.525,0.278,0.702] | |
| select surf_pocket4, protein and id [1571,1608,1609,1432,2631,2632,2802,2804,2803,1430,1594,2604,2607,2255,2256,2257,2282,1428,1431,2283,2239,1632] | |
| set surface_color, pcol4, surf_pocket4 | |
| set_color pcol5 = [0.851,0.361,0.902] | |
| select surf_pocket5, protein and id [7338,7336,7362,7434,7468,8470,8469,8471,7343,7973,8001,7975,7497,8432,7965,7991,7967,7963,7964,7968,7459,7498,7764,7766] | |
| set surface_color, pcol5, surf_pocket5 | |
| set_color pcol6 = [0.702,0.278,0.600] | |
| select surf_pocket6, protein and id [259,275,261,3073,3703,3704,3705,3089,3036,3701,3702,3042,3048,3097,3049,258,262] | |
| set surface_color, pcol6, surf_pocket6 | |
| set_color pcol7 = [0.902,0.361,0.596] | |
| select surf_pocket7, protein and id [6444,6443,6477,6508,6509,6472,6446,7277,7251,7260,7280,7282,6470,7323,7247,7248,6603,7249,6604,7324] | |
| set surface_color, pcol7, surf_pocket7 | |
| set_color pcol8 = [0.702,0.278,0.325] | |
| select surf_pocket8, protein and id [311,310,312,3499,3498,3536,323,324,327,328,871,872,3500,346] | |
| set surface_color, pcol8, surf_pocket8 | |
| set_color pcol9 = [0.902,0.478,0.361] | |
| select surf_pocket9, protein and id [3295,3298,3391,3393,3269,3271,3553,3519,3416,3418,3387,3419,3551,3382,3359] | |
| set surface_color, pcol9, surf_pocket9 | |
| set_color pcol10 = [0.702,0.510,0.278] | |
| select surf_pocket10, protein and id [2738,2740,2741,2193,2194,2195,2692,1461,2758,2759,2187,2196,2192,2200,2172,2185,1443,1444,1447] | |
| set surface_color, pcol10, surf_pocket10 | |
| set_color pcol11 = [0.902,0.831,0.361] | |
| select surf_pocket11, protein and id [2937,2939,2940,2941,2943,2944,2543,2535,2544,2554,2557,2558,2559,2550,2552,2912,2533,2539,2541] | |
| set surface_color, pcol11, surf_pocket11 | |
| deselect | |
| orient | |