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/scn10a.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/scn10a.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 [11157,11159,7056,7058,7059,11187,11189,6305,6723,6725,11158,11160,6330,6332,6333,6691,11124,11095,6692,7023,7024,11190,6749,11197,11199,11207,10234,10235,10236,11231,6278,6280,7048,6281,6279,6303,6307,6309,6230,11198,11200,6237,6211,11167,11169,11171,6253,6179,6212] | |
| set surface_color, pcol1, surf_pocket1 | |
| set_color pcol2 = [0.278,0.408,0.702] | |
| select surf_pocket2, protein and id [2842,6998,7000,7001,6750,6756,6758,6761,6762,6763,6972,6974,6975,2027,2051,2057,3167,3169,2836,6982,2806,2808,2809,2059,11215,11179,10838,11188,13613,10832,10836,3106,3144,3145,3152,3153,2840,2841,2847,2848,2854,2859,10833,10848,2083,3114,3116,2852,13612,13236,13244,10826,10847,2774,2776,7006,6997,6999,7003,7025,7023,6977,6980,2000,2028,3168,7009,6981,3177,7026,7028,7031,7032,7022,7052,11186,11223,11224,11181,13679,11250,13652,13680,11212,11216,13643,11249,7067] | |
| set surface_color, pcol2, surf_pocket2 | |
| set_color pcol3 = [0.361,0.475,0.902] | |
| select surf_pocket3, protein and id [13620,10799,10800,13552,10764,10762,10763,11240,11208,11210,11212,13621,10247,10252,10249,10253,10766,11209,11215,11177,11179,10820,10821,10827,10190,10220,13586,13588,13550,10210,11242] | |
| set surface_color, pcol3, surf_pocket3 | |
| set_color pcol4 = [0.278,0.329,0.702] | |
| select surf_pocket4, protein and id [3054,3018,12900,13174,13204,3087,13672,3084,3085,3086,3088,3089,3117,3118,12866,13230,12791,3063,3053,3055,13206,3017,3082,3079,3077,12808,12840,12841,12842,12870,12874,12876,12815,12812,12813,12819] | |
| set surface_color, pcol4, surf_pocket4 | |
| set_color pcol5 = [0.361,0.373,0.902] | |
| select surf_pocket5, protein and id [6211,11167,11169,11171,6018,6052,6054,6023,6185,6187,6156,6081,6155,6179,6208,6212,6078,6079,6070,6080,6082,6083,5835,6186,11170,6025,10230,10232,10269,10236,10238,10239,6042,10268,11168,11166,10278,10279,10280,11132,10302,6015,10301,11133,11097,10227] | |
| set surface_color, pcol5, surf_pocket5 | |
| set_color pcol6 = [0.310,0.278,0.702] | |
| select surf_pocket6, protein and id [12578,3062,3028,3030,3034,3036,12575,12599,12602,2127,2156,2128,3093,3096,3097,12761,3094,2094,2076,2104,2106,2108,12633,12634,12661,12737,2068,2096,2097,12702,12736,3125] | |
| set surface_color, pcol6, surf_pocket6 | |
| set_color pcol7 = [0.451,0.361,0.902] | |
| select surf_pocket7, protein and id [10882,13274,13275,13277,13053,13215,13216,13251,13253,13287,2886,2888,2928,2929,2891,2893,2895,2896,13051,13052,13054,13055,13056,13058,13094,6767,2866,6770,6771,10848,6772,10849,10870,10872,10846,6800,6801,6802,6737,6803,10874] | |
| set surface_color, pcol7, surf_pocket7 | |
| set_color pcol8 = [0.392,0.278,0.702] | |
| select surf_pocket8, protein and id [6114,5673,5674,5300,3917,5254,5301,5302,5258,5255,6113,7213,7212,3924,5785,5786,5705,5706,6112,5638,5322,5324,5325,5292,5294,5295,5296,5298,5332,6109,5799,5800,5805,5840,6091,6088,6087,6089,6090,5784,5816,5817] | |
| set surface_color, pcol8, surf_pocket8 | |
| set_color pcol9 = [0.553,0.361,0.902] | |
| select surf_pocket9, protein and id [14402,14371,14403,13856,13858,13859,13860,14364,14365,14367,14369,14370,13803,13815,14434,14469,14496,14497,14526,14461,14463,14377,14373,14341,14342,14527,14468,11544,11546,11548,14345,13897,13899,13853,13855,13830,13857] | |
| set surface_color, pcol9, surf_pocket9 | |
| set_color pcol10 = [0.471,0.278,0.702] | |
| select surf_pocket10, protein and id [1905,1554,1556,1557,1860,1861,1862,1541,1543,1571,1094,1869,1841,1539,1502,1407,1408,1377,1121,1123,1124,1488,1493,840,1436,1437,1440,1489,1490,1491,857,1098,1043,1044,1088,1090,494,835,1096,487,836,831,833] | |
| set surface_color, pcol10, surf_pocket10 | |
| set_color pcol11 = [0.655,0.361,0.902] | |
| select surf_pocket11, protein and id [12873,12875,12881,12908,12876,12877,12910,12904,12906,12911,13147,13145,9241,13143,12850,9196,9220,9221,9216,9217,10040,10041,10062,9199,12884,10004,9978] | |
| set surface_color, pcol11, surf_pocket11 | |
| set_color pcol12 = [0.549,0.278,0.702] | |
| select surf_pocket12, protein and id [6986,6990,6989,6957,6959,6325,6358,6360,6361,6362,6381,6382,1772,6411,6925,6928,6933,6324,6326,1781,1783,1809,1779,6348,6350,1770,1832,1833,1807] | |
| set surface_color, pcol12, surf_pocket12 | |
| set_color pcol13 = [0.757,0.361,0.902] | |
| select surf_pocket13, protein and id [6204,7117,7119,6168,6170,6173,6146,6178,7148,6147,11285,10183,11260,11261,11231,10206,10178,10151,10172] | |
| set surface_color, pcol13, surf_pocket13 | |
| set_color pcol14 = [0.627,0.278,0.702] | |
| select surf_pocket14, protein and id [12857,12858,10115,10012,10093,10094,12919,9989,12918,9988,9963,9669,9665,9696,12891,13594,13595,13596,12929,12892] | |
| set surface_color, pcol14, surf_pocket14 | |
| set_color pcol15 = [0.859,0.361,0.902] | |
| select surf_pocket15, protein and id [3228,3263,7100,7103,6245,3221,3256,3257,3259,7070,7072,7071,7073,7077,6254,7074,7078,3250,3224,3252,1935,3253,3254,3226,1918,6274,6246,1920,6273,7040,7039,7041,7042,7038,1914,1919,1888,1944,3281,3283,3284,1909,1911] | |
| set surface_color, pcol15, surf_pocket15 | |
| set_color pcol16 = [0.702,0.278,0.690] | |
| select surf_pocket16, protein and id [12251,12254,12280,12281,12184,12210,11608,12185,11711,12263,12668,12264,11784,12122,12152,12153,11741,11730,11732,11733,12638,12639,11816,11839,12640,12641,12642,12645,11804,11807,12672,11781,11783,11785,11736,11740,11814,11815] | |
| set surface_color, pcol16, surf_pocket16 | |
| set_color pcol17 = [0.902,0.361,0.839] | |
| select surf_pocket17, protein and id [9939,9963,12955,12956,12954,9931,9930,12928,13532,12953,12949,12951,12952,13502,13526,13528,12980,13503,13504,13557,13523,13560,13596,12929,12931] | |
| set surface_color, pcol17, surf_pocket17 | |
| set_color pcol18 = [0.702,0.278,0.612] | |
| select surf_pocket18, protein and id [13753,13755,13756,13776,13752,13722,13825,13828,13830,13831,13833,12775,12741,12743,12744,12746,12745,12720,12721,13841,13839,13840,12716,11493,11523,13779,13780,13781,13750,13725,13832,11491,12773,12777,13777,13820,13822,13775,13782,13783] | |
| set surface_color, pcol18, surf_pocket18 | |
| set_color pcol19 = [0.902,0.361,0.733] | |
| select surf_pocket19, protein and id [1162,1183,1181,1824,1825,1846,1848,6316,6339,6342,6341,6343,6308,6309,6310,6337,6340] | |
| set surface_color, pcol19, surf_pocket19 | |
| set_color pcol20 = [0.702,0.278,0.533] | |
| select surf_pocket20, protein and id [1563,1564,1829,1832,1833,1593,1856,6317,1940,1943,1926,1927,1952,6296,7017,6324,6326,6986,6990,6989,6361] | |
| set surface_color, pcol20, surf_pocket20 | |
| set_color pcol21 = [0.902,0.361,0.631] | |
| select surf_pocket21, protein and id [6341,6343,1210,6310,1190,1185,6664,6650,6652,6654,6662,11124,11095,6690,6692,6689,6691] | |
| set surface_color, pcol21, surf_pocket21 | |
| set_color pcol22 = [0.702,0.278,0.451] | |
| select surf_pocket22, protein and id [10027,10030,9541,9705,9126,9129,9131,9124,9130,10019,10018,9662,9659,9070,9071,9579,9540,9577,9118,9120,9649,9675] | |
| set surface_color, pcol22, surf_pocket22 | |
| set_color pcol23 = [0.902,0.361,0.529] | |
| select surf_pocket23, protein and id [13787,3189,13735,13736,2021,3188,2010,2014,1989,12718,12720,12719,12695,12717,12722,12727,12728,12723,12729,13754,13755,13756,13763,3211,13762] | |
| set surface_color, pcol23, surf_pocket23 | |
| set_color pcol24 = [0.702,0.278,0.373] | |
| select surf_pocket24, protein and id [1416,1633,1382,1384,1385,1610,1612,1613,1357,1664,1356,1387,1355,1641,1662] | |
| set surface_color, pcol24, surf_pocket24 | |
| set_color pcol25 = [0.902,0.361,0.427] | |
| select surf_pocket25, protein and id [11269,13626,13628,11409,13658,13659,11295,11297,11301,13684,11266,11267,11268,11330,10106,10130,10105,10107,10109,10114] | |
| set surface_color, pcol25, surf_pocket25 | |
| set_color pcol26 = [0.702,0.278,0.294] | |
| select surf_pocket26, protein and id [14345,11561,11563,11565,11566,13896,13899,14335,11575,14002,14000,14001,11574,14344,14330,11567,14562,14564,14331,14003,14343] | |
| set surface_color, pcol26, surf_pocket26 | |
| set_color pcol27 = [0.902,0.392,0.361] | |
| select surf_pocket27, protein and id [8778,8779,8980,8984,8985,8781,8784,8794,8945,8949,8977,8979,8947,8951,8982,8978,8981,8959,8908] | |
| set surface_color, pcol27, surf_pocket27 | |
| set_color pcol28 = [0.702,0.345,0.278] | |
| select surf_pocket28, protein and id [2432,2433,2475,2466,2960,2489,2491,2492,2484,2486,2434,13074,13081,2923,2925,2964,2935,2895,2937,2924,2929] | |
| set surface_color, pcol28, surf_pocket28 | |
| set_color pcol29 = [0.902,0.498,0.361] | |
| select surf_pocket29, protein and id [6616,6643,6617,6632,6635,6674,11032,6568,11023,6570,6572,6574] | |
| set surface_color, pcol29, surf_pocket29 | |
| set_color pcol30 = [0.702,0.427,0.278] | |
| select surf_pocket30, protein and id [5368,5579,5581,5569,5317,5347,5604,5605,5606,5607] | |
| set surface_color, pcol30, surf_pocket30 | |
| set_color pcol31 = [0.902,0.600,0.361] | |
| select surf_pocket31, protein and id [13707,7066,11249,11277,7067,13679,11250,13680,3177,7095] | |
| set surface_color, pcol31, surf_pocket31 | |
| set_color pcol32 = [0.702,0.506,0.278] | |
| select surf_pocket32, protein and id [9122,9119,9121,9497,9495,9064,9143,9144,9146,9148,9156,9469,9468] | |
| set surface_color, pcol32, surf_pocket32 | |
| set_color pcol33 = [0.902,0.702,0.361] | |
| select surf_pocket33, protein and id [9714,9715,9716,9554,9633,9634,9635,9555,9590,9592,9632] | |
| set surface_color, pcol33, surf_pocket33 | |
| set_color pcol34 = [0.702,0.584,0.278] | |
| select surf_pocket34, protein and id [8829,8875,8876,8877,8893,8794,8792,8793,8795,8796,8797,8823] | |
| set surface_color, pcol34, surf_pocket34 | |
| set_color pcol35 = [0.902,0.804,0.361] | |
| select surf_pocket35, protein and id [14563,14565,14591,14592,14013,14014,14003,14628,14606,14589,14607,14001,14636] | |
| set surface_color, pcol35, surf_pocket35 | |
| set_color pcol36 = [0.702,0.663,0.278] | |
| select surf_pocket36, protein and id [1450,1454,1451,1453,1455,1612,1613,899,1641] | |
| set surface_color, pcol36, surf_pocket36 | |
| set_color pcol37 = [0.894,0.902,0.361] | |
| select surf_pocket37, protein and id [8973,8970,8972,8948,8951,8952,8969,9005,9008,8981,8971,8786] | |
| set surface_color, pcol37, surf_pocket37 | |
| set_color pcol38 = [0.655,0.702,0.278] | |
| select surf_pocket38, protein and id [7110,7120,11200,11226,11228,7087,11195] | |
| set surface_color, pcol38, surf_pocket38 | |
| deselect | |
| orient | |