PyMOL>load ./selSi.pdb,obj ObjectMolReadPDBStr: read MODEL 1 ObjectMolReadPDBStr: read MODEL 2 ObjectMolReadPDBStr: read MODEL 3 ObjectMolReadPDBStr: read MODEL 4 ObjectMolReadPDBStr: read MODEL 5 ObjectMolReadPDBStr: read MODEL 6 ObjectMolReadPDBStr: read MODEL 7 ObjectMolReadPDBStr: read MODEL 8 ObjectMolReadPDBStr: read MODEL 9 ObjectMolReadPDBStr: read MODEL 10 ObjectMolReadPDBStr: read MODEL 11 ObjectMolReadPDBStr: read MODEL 12 ObjectMolReadPDBStr: read MODEL 13 ObjectMolReadPDBStr: read MODEL 14 ObjectMolReadPDBStr: read MODEL 15 ObjectMolReadPDBStr: read MODEL 16 ObjectMolReadPDBStr: read MODEL 17 ObjectMolReadPDBStr: read MODEL 18 ObjectMolReadPDBStr: read MODEL 19 ObjectMolReadPDBStr: read MODEL 20 CmdLoad: "./selSi.pdb" loaded as "obj". PyMOL>hide everything, all PyMOL>dss PyMOL>show cartoon, all PyMOL>set bg_rgb, [1,1,1] Setting: bg_rgb set to [ 1.00000, 1.00000, 1.00000 ]. PyMOL>color red, ss h Executive: Colored 106 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 2436 atoms. PyMOL>set cartoon_highlight_color,yellow Setting: cartoon_highlight_color set to yellow. PyMOL>orient PyMOL>set ray_trace_mode, 3 Setting: ray_trace_mode set to 3. PyMOL>set antialias, 2 Setting: antialias set to 2. PyMOL>ray 600,600 Ray: render time: 1.82 sec. = 1976.8 frames/hour (1.82 sec. accum.). PyMOL>png molecule.png ScenePNG: wrote 600x600 pixel image to file "molecule.png". PyMOL>set stereo,1 Setting: stereo set to on. PyMOL>set all_states,1 Setting: all_states set to on. PyMOL>stereo walleye Setting: stereo_mode set to 3. PyMOL>select bb,n. c+ca+n Selector: selection "bb" defined with 480 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 480 atoms. PyMOL>set line_width,0.5 Setting: line_width set to 0.50000. PyMOL>set bg_rgb, [1,1,1] Setting: bg_rgb set to [ 1.00000, 1.00000, 1.00000 ]. PyMOL>zoom complete=1 PyMOL>set ray_trace_mode, 0 Setting: ray_trace_mode set to 0. PyMOL>ray 1200,600 Ray: render time: 6.82 sec. = 527.7 frames/hour (8.64 sec. accum.). PyMOL>png stereo.png ScenePNG: wrote 1200x600 pixel image to file "stereo.png". PyMOL>run /data/PSVS/PSVS-v1.4-dev/strcalc//average3d.py PyMOL>from average3d import avgStates Traceback (most recent call last): File "/farm/software/pymol-1.1r1-x64/modules/pymol/parser.py", line 455, in parse exec(layer.com2+"\n",self.pymol_names,self.pymol_names) File "", line 1, in ? ImportError: No module named average3d PyMOL>set all_states,1 Setting: all_states set to on. PyMOL>set stereo,0 Setting: stereo set to off. PyMOL>hide everything, all PyMOL>avgStates('obj','name CA',1,0,'yesfit_ALL','yes',1,0,0) -------------------------------------------------------------------------------- Averaging 20 states [1, 20] of object "obj and name CA" (20 total states) to get new single-state object "yesfit_ALL"... -------------------------------------------------------------------------------- -> proceeding WITH FITTING to reference state... intrafit_rmsds = [-1.0, 3.952409029006958, 5.0270004272460938, 6.4785289764404297, 5.799191951751709, 4.2880759239196777, 3.7578842639923096, 4.2062902450561523, 4.0942988395690918, 4.4420690536499023, 4.6859250068664551, 5.5010910034179688, 5.7698349952697754, 3.8576366901397705, 5.6480851173400879, 4.675168514251709, 4.3877649307250977, 5.847679615020752, 6.5527949333190918, 5.5245990753173828] -> atom index_map = [None, 2, 21, 31, 50, 67, 78, 100, 121, 132, 146, 160, 177, 193, 208, 219, 238, 257, 267, 282, 301, 320, 336, 352, 371, 386, 408, 425, 447, 457, 471, 485, 497, 516, 527, 546, 563, 573, 592, 599, 613, 624, 640, 654, 671, 690, 709, 724, 748, 770, 786, 800, 811, 826, 837, 861, 878, 888, 904, 914, 929, 946, 966, 976, 998, 1008, 1027, 1037, 1054, 1065, 1081, 1103, 1114, 1128, 1147, 1162, 1179, 1196, 1213, 1230, 1247, 1265, 1284, 1294, 1313, 1330, 1341, 1363, 1384, 1395, 1409, 1423, 1440, 1456, 1471, 1482, 1501, 1520, 1530, 1545, 1564, 1583, 1599, 1615, 1634, 1649, 1671, 1688, 1710, 1720, 1734, 1748, 1760, 1779, 1790, 1809, 1826, 1836, 1855, 1862, 1876, 1887, 1903, 1917, 1934, 1953, 1972, 1987, 2011, 2033, 2049, 2063, 2074, 2089, 2100, 2124, 2141, 2151, 2167, 2177, 2192, 2209, 2229, 2239, 2261, 2271, 2290, 2300, 2317, 2328, 2344, 2366, 2377, 2391, 2410, 2425, 2442, 2459, 2476, 2493, 2510] "obj and name CA" index = 1 rmsd = 12.030 "obj and name CA" index = 2 rmsd = 10.727 "obj and name CA" index = 3 rmsd = 9.520 "obj and name CA" index = 4 rmsd = 7.807 "obj and name CA" index = 5 rmsd = 5.820 "obj and name CA" index = 6 rmsd = 4.243 "obj and name CA" index = 7 rmsd = 2.850 "obj and name CA" index = 8 rmsd = 2.664 "obj and name CA" index = 9 rmsd = 2.551 "obj and name CA" index = 10 rmsd = 2.254 "obj and name CA" index = 11 rmsd = 1.760 "obj and name CA" index = 12 rmsd = 1.323 "obj and name CA" index = 13 rmsd = 1.206 "obj and name CA" index = 14 rmsd = 1.083 "obj and name CA" index = 15 rmsd = 0.880 "obj and name CA" index = 16 rmsd = 0.914 "obj and name CA" index = 17 rmsd = 0.961 "obj and name CA" index = 18 rmsd = 0.834 "obj and name CA" index = 19 rmsd = 0.745 "obj and name CA" index = 20 rmsd = 1.000 "obj and name CA" index = 21 rmsd = 1.041 "obj and name CA" index = 22 rmsd = 0.830 "obj and name CA" index = 23 rmsd = 0.961 "obj and name CA" index = 24 rmsd = 1.161 "obj and name CA" index = 25 rmsd = 1.043 "obj and name CA" index = 26 rmsd = 1.079 "obj and name CA" index = 27 rmsd = 1.271 "obj and name CA" index = 28 rmsd = 1.208 "obj and name CA" index = 29 rmsd = 1.412 "obj and name CA" index = 30 rmsd = 1.328 "obj and name CA" index = 31 rmsd = 1.299 "obj and name CA" index = 32 rmsd = 1.193 "obj and name CA" index = 33 rmsd = 0.988 "obj and name CA" index = 34 rmsd = 1.019 "obj and name CA" index = 35 rmsd = 1.093 "obj and name CA" index = 36 rmsd = 0.861 "obj and name CA" index = 37 rmsd = 0.930 "obj and name CA" index = 38 rmsd = 1.055 "obj and name CA" index = 39 rmsd = 0.975 "obj and name CA" index = 40 rmsd = 0.898 "obj and name CA" index = 41 rmsd = 0.956 "obj and name CA" index = 42 rmsd = 1.155 "obj and name CA" index = 43 rmsd = 1.109 "obj and name CA" index = 44 rmsd = 1.155 "obj and name CA" index = 45 rmsd = 1.327 "obj and name CA" index = 46 rmsd = 1.487 "obj and name CA" index = 47 rmsd = 1.585 "obj and name CA" index = 48 rmsd = 1.549 "obj and name CA" index = 49 rmsd = 1.374 "obj and name CA" index = 50 rmsd = 1.492 "obj and name CA" index = 51 rmsd = 1.483 "obj and name CA" index = 52 rmsd = 1.746 "obj and name CA" index = 53 rmsd = 1.451 "obj and name CA" index = 54 rmsd = 1.249 "obj and name CA" index = 55 rmsd = 1.167 "obj and name CA" index = 56 rmsd = 1.181 "obj and name CA" index = 57 rmsd = 1.259 "obj and name CA" index = 58 rmsd = 1.131 "obj and name CA" index = 59 rmsd = 0.908 "obj and name CA" index = 60 rmsd = 0.867 "obj and name CA" index = 61 rmsd = 0.891 "obj and name CA" index = 62 rmsd = 0.983 "obj and name CA" index = 63 rmsd = 0.999 "obj and name CA" index = 64 rmsd = 1.069 "obj and name CA" index = 65 rmsd = 1.195 "obj and name CA" index = 66 rmsd = 1.416 "obj and name CA" index = 67 rmsd = 1.403 "obj and name CA" index = 68 rmsd = 1.292 "obj and name CA" index = 69 rmsd = 1.270 "obj and name CA" index = 70 rmsd = 1.584 "obj and name CA" index = 71 rmsd = 1.664 "obj and name CA" index = 72 rmsd = 1.642 "obj and name CA" index = 73 rmsd = 1.792 "obj and name CA" index = 74 rmsd = 2.504 "obj and name CA" index = 75 rmsd = 4.116 "obj and name CA" index = 76 rmsd = 4.887 "obj and name CA" index = 77 rmsd = 6.641 "obj and name CA" index = 78 rmsd = 7.746 "obj and name CA" index = 79 rmsd = 9.371 "obj and name CA" index = 80 rmsd = 11.433 "obj and name CA" index = 81 rmsd = 12.030 "obj and name CA" index = 82 rmsd = 10.727 "obj and name CA" index = 83 rmsd = 9.520 "obj and name CA" index = 84 rmsd = 7.807 "obj and name CA" index = 85 rmsd = 5.820 "obj and name CA" index = 86 rmsd = 4.243 "obj and name CA" index = 87 rmsd = 2.850 "obj and name CA" index = 88 rmsd = 2.664 "obj and name CA" index = 89 rmsd = 2.551 "obj and name CA" index = 90 rmsd = 2.254 "obj and name CA" index = 91 rmsd = 1.760 "obj and name CA" index = 92 rmsd = 1.323 "obj and name CA" index = 93 rmsd = 1.206 "obj and name CA" index = 94 rmsd = 1.084 "obj and name CA" index = 95 rmsd = 0.880 "obj and name CA" index = 96 rmsd = 0.914 "obj and name CA" index = 97 rmsd = 0.961 "obj and name CA" index = 98 rmsd = 0.834 "obj and name CA" index = 99 rmsd = 0.745 "obj and name CA" index = 100 rmsd = 1.001 "obj and name CA" index = 101 rmsd = 1.041 "obj and name CA" index = 102 rmsd = 0.830 "obj and name CA" index = 103 rmsd = 0.961 "obj and name CA" index = 104 rmsd = 1.161 "obj and name CA" index = 105 rmsd = 1.043 "obj and name CA" index = 106 rmsd = 1.079 "obj and name CA" index = 107 rmsd = 1.271 "obj and name CA" index = 108 rmsd = 1.208 "obj and name CA" index = 109 rmsd = 1.412 "obj and name CA" index = 110 rmsd = 1.328 "obj and name CA" index = 111 rmsd = 1.299 "obj and name CA" index = 112 rmsd = 1.193 "obj and name CA" index = 113 rmsd = 0.987 "obj and name CA" index = 114 rmsd = 1.019 "obj and name CA" index = 115 rmsd = 1.092 "obj and name CA" index = 116 rmsd = 0.861 "obj and name CA" index = 117 rmsd = 0.930 "obj and name CA" index = 118 rmsd = 1.055 "obj and name CA" index = 119 rmsd = 0.975 "obj and name CA" index = 120 rmsd = 0.898 "obj and name CA" index = 121 rmsd = 0.955 "obj and name CA" index = 122 rmsd = 1.155 "obj and name CA" index = 123 rmsd = 1.109 "obj and name CA" index = 124 rmsd = 1.155 "obj and name CA" index = 125 rmsd = 1.326 "obj and name CA" index = 126 rmsd = 1.487 "obj and name CA" index = 127 rmsd = 1.585 "obj and name CA" index = 128 rmsd = 1.549 "obj and name CA" index = 129 rmsd = 1.374 "obj and name CA" index = 130 rmsd = 1.492 "obj and name CA" index = 131 rmsd = 1.483 "obj and name CA" index = 132 rmsd = 1.746 "obj and name CA" index = 133 rmsd = 1.451 "obj and name CA" index = 134 rmsd = 1.249 "obj and name CA" index = 135 rmsd = 1.167 "obj and name CA" index = 136 rmsd = 1.181 "obj and name CA" index = 137 rmsd = 1.259 "obj and name CA" index = 138 rmsd = 1.131 "obj and name CA" index = 139 rmsd = 0.907 "obj and name CA" index = 140 rmsd = 0.867 "obj and name CA" index = 141 rmsd = 0.890 "obj and name CA" index = 142 rmsd = 0.983 "obj and name CA" index = 143 rmsd = 0.999 "obj and name CA" index = 144 rmsd = 1.069 "obj and name CA" index = 145 rmsd = 1.195 "obj and name CA" index = 146 rmsd = 1.416 "obj and name CA" index = 147 rmsd = 1.403 "obj and name CA" index = 148 rmsd = 1.292 "obj and name CA" index = 149 rmsd = 1.270 "obj and name CA" index = 150 rmsd = 1.584 "obj and name CA" index = 151 rmsd = 1.664 "obj and name CA" index = 152 rmsd = 1.642 "obj and name CA" index = 153 rmsd = 1.792 "obj and name CA" index = 154 rmsd = 2.503 "obj and name CA" index = 155 rmsd = 4.116 "obj and name CA" index = 156 rmsd = 4.887 "obj and name CA" index = 157 rmsd = 6.641 "obj and name CA" index = 158 rmsd = 7.746 "obj and name CA" index = 159 rmsd = 9.371 "obj and name CA" index = 160 rmsd = 11.432 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 318 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 4910 atoms. PyMOL>set cartoon_highlight_color,yellow Setting: cartoon_highlight_color set to yellow. PyMOL>set bg_rgb, [1,1,1] Setting: bg_rgb set to [ 1.00000, 1.00000, 1.00000 ]. PyMOL>set ray_trace_mode, 3 Setting: ray_trace_mode set to 3. PyMOL>ray 600,600 Ray: render time: 1.88 sec. = 1910.2 frames/hour (10.53 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit