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 63 atoms. PyMOL>color cyan,ss s Executive: Colored 16 atoms. PyMOL>color gray,ss ""+l Executive: Colored 2808 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: 1.45 sec. = 2486.4 frames/hour (1.45 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 525 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 525 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: 5.00 sec. = 720.2 frames/hour (6.45 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, 4.6177473068237305, 5.6505961418151855, 6.603309154510498, 5.0083174705505371, 4.402287483215332, 5.846489429473877, 4.9733796119689941, 8.4192409515380859, 7.5399274826049805, 6.7594318389892578, 7.4005331993103027, 6.7805485725402832, 5.5017437934875488, 4.824915885925293, 7.6415729522705078, 2.8111081123352051, 5.9706320762634277, 2.8140404224395752, 4.2798995971679688] -> atom index_map = [None, 2, 21, 31, 43, 58, 68, 82, 106, 130, 146, 162, 173, 188, 207, 221, 237, 256, 278, 292, 306, 316, 323, 337, 361, 373, 397, 412, 431, 455, 471, 488, 512, 531, 553, 568, 583, 604, 621, 632, 651, 670, 694, 715, 731, 746, 760, 774, 796, 810, 820, 832, 846, 858, 882, 902, 926, 945, 960, 971, 985, 1007, 1022, 1029, 1043, 1067, 1091, 1111, 1118, 1140, 1151, 1175, 1196, 1215, 1232, 1244, 1263, 1282, 1304, 1325, 1340, 1360, 1372, 1391, 1406, 1426, 1438, 1457, 1471, 1490, 1504, 1525, 1539, 1553, 1567, 1577, 1591, 1606, 1625, 1635, 1651, 1665, 1680, 1699, 1711, 1718, 1740, 1754, 1764, 1786, 1803, 1824, 1848, 1855, 1862, 1884, 1903, 1914, 1933, 1947, 1959, 1976, 1996, 2018, 2032, 2051, 2075, 2085, 2109, 2123, 2139, 2153, 2175, 2195, 2202, 2221, 2231, 2248, 2267, 2284, 2294, 2313, 2320, 2339, 2346, 2360, 2384, 2403, 2413, 2429, 2444, 2463, 2477, 2489, 2508, 2527, 2544, 2566, 2573, 2589, 2608, 2625, 2642, 2664, 2679, 2701, 2712, 2726, 2743, 2762, 2777, 2794, 2811, 2828, 2845, 2862] "obj and name CA" index = 1 rmsd = 6.941 "obj and name CA" index = 2 rmsd = 5.355 "obj and name CA" index = 3 rmsd = 3.856 "obj and name CA" index = 4 rmsd = 3.274 "obj and name CA" index = 5 rmsd = 3.079 "obj and name CA" index = 6 rmsd = 2.957 "obj and name CA" index = 7 rmsd = 2.721 "obj and name CA" index = 8 rmsd = 2.227 "obj and name CA" index = 9 rmsd = 2.126 "obj and name CA" index = 10 rmsd = 2.077 "obj and name CA" index = 11 rmsd = 1.941 "obj and name CA" index = 12 rmsd = 1.750 "obj and name CA" index = 13 rmsd = 1.394 "obj and name CA" index = 14 rmsd = 1.585 "obj and name CA" index = 15 rmsd = 1.492 "obj and name CA" index = 16 rmsd = 1.451 "obj and name CA" index = 17 rmsd = 1.827 "obj and name CA" index = 18 rmsd = 1.877 "obj and name CA" index = 19 rmsd = 1.821 "obj and name CA" index = 20 rmsd = 1.897 "obj and name CA" index = 21 rmsd = 1.718 "obj and name CA" index = 22 rmsd = 1.645 "obj and name CA" index = 23 rmsd = 2.169 "obj and name CA" index = 24 rmsd = 2.198 "obj and name CA" index = 25 rmsd = 2.248 "obj and name CA" index = 26 rmsd = 2.426 "obj and name CA" index = 27 rmsd = 2.035 "obj and name CA" index = 28 rmsd = 1.604 "obj and name CA" index = 29 rmsd = 1.634 "obj and name CA" index = 30 rmsd = 1.656 "obj and name CA" index = 31 rmsd = 1.416 "obj and name CA" index = 32 rmsd = 1.200 "obj and name CA" index = 33 rmsd = 1.453 "obj and name CA" index = 34 rmsd = 1.424 "obj and name CA" index = 35 rmsd = 1.170 "obj and name CA" index = 36 rmsd = 1.325 "obj and name CA" index = 37 rmsd = 1.640 "obj and name CA" index = 38 rmsd = 1.526 "obj and name CA" index = 39 rmsd = 1.453 "obj and name CA" index = 40 rmsd = 2.058 "obj and name CA" index = 41 rmsd = 2.311 "obj and name CA" index = 42 rmsd = 1.895 "obj and name CA" index = 43 rmsd = 2.048 "obj and name CA" index = 44 rmsd = 2.664 "obj and name CA" index = 45 rmsd = 2.664 "obj and name CA" index = 46 rmsd = 2.512 "obj and name CA" index = 47 rmsd = 3.022 "obj and name CA" index = 48 rmsd = 3.171 "obj and name CA" index = 49 rmsd = 2.950 "obj and name CA" index = 50 rmsd = 3.191 "obj and name CA" index = 51 rmsd = 2.948 "obj and name CA" index = 52 rmsd = 2.513 "obj and name CA" index = 53 rmsd = 2.464 "obj and name CA" index = 54 rmsd = 1.917 "obj and name CA" index = 55 rmsd = 1.877 "obj and name CA" index = 56 rmsd = 1.466 "obj and name CA" index = 57 rmsd = 1.389 "obj and name CA" index = 58 rmsd = 1.184 "obj and name CA" index = 59 rmsd = 1.386 "obj and name CA" index = 60 rmsd = 1.581 "obj and name CA" index = 61 rmsd = 1.518 "obj and name CA" index = 62 rmsd = 1.216 "obj and name CA" index = 63 rmsd = 1.220 "obj and name CA" index = 64 rmsd = 1.119 "obj and name CA" index = 65 rmsd = 0.936 "obj and name CA" index = 66 rmsd = 1.190 "obj and name CA" index = 67 rmsd = 1.597 "obj and name CA" index = 68 rmsd = 1.728 "obj and name CA" index = 69 rmsd = 1.867 "obj and name CA" index = 70 rmsd = 2.334 "obj and name CA" index = 71 rmsd = 2.607 "obj and name CA" index = 72 rmsd = 2.780 "obj and name CA" index = 73 rmsd = 2.979 "obj and name CA" index = 74 rmsd = 3.416 "obj and name CA" index = 75 rmsd = 3.426 "obj and name CA" index = 76 rmsd = 2.913 "obj and name CA" index = 77 rmsd = 2.721 "obj and name CA" index = 78 rmsd = 2.446 "obj and name CA" index = 79 rmsd = 2.193 "obj and name CA" index = 80 rmsd = 1.947 "obj and name CA" index = 81 rmsd = 1.746 "obj and name CA" index = 82 rmsd = 1.376 "obj and name CA" index = 83 rmsd = 1.149 "obj and name CA" index = 84 rmsd = 1.080 "obj and name CA" index = 85 rmsd = 1.151 "obj and name CA" index = 86 rmsd = 1.096 "obj and name CA" index = 87 rmsd = 1.397 "obj and name CA" index = 88 rmsd = 2.018 "obj and name CA" index = 89 rmsd = 2.069 "obj and name CA" index = 90 rmsd = 1.543 "obj and name CA" index = 91 rmsd = 1.702 "obj and name CA" index = 92 rmsd = 1.924 "obj and name CA" index = 93 rmsd = 1.679 "obj and name CA" index = 94 rmsd = 1.192 "obj and name CA" index = 95 rmsd = 1.115 "obj and name CA" index = 96 rmsd = 1.351 "obj and name CA" index = 97 rmsd = 1.016 "obj and name CA" index = 98 rmsd = 1.253 "obj and name CA" index = 99 rmsd = 1.547 "obj and name CA" index = 100 rmsd = 2.043 "obj and name CA" index = 101 rmsd = 2.137 "obj and name CA" index = 102 rmsd = 2.051 "obj and name CA" index = 103 rmsd = 2.375 "obj and name CA" index = 104 rmsd = 3.049 "obj and name CA" index = 105 rmsd = 3.045 "obj and name CA" index = 106 rmsd = 2.704 "obj and name CA" index = 107 rmsd = 3.044 "obj and name CA" index = 108 rmsd = 3.062 "obj and name CA" index = 109 rmsd = 2.170 "obj and name CA" index = 110 rmsd = 2.470 "obj and name CA" index = 111 rmsd = 2.999 "obj and name CA" index = 112 rmsd = 2.809 "obj and name CA" index = 113 rmsd = 2.382 "obj and name CA" index = 114 rmsd = 1.704 "obj and name CA" index = 115 rmsd = 1.521 "obj and name CA" index = 116 rmsd = 1.552 "obj and name CA" index = 117 rmsd = 1.404 "obj and name CA" index = 118 rmsd = 1.895 "obj and name CA" index = 119 rmsd = 2.166 "obj and name CA" index = 120 rmsd = 2.394 "obj and name CA" index = 121 rmsd = 1.923 "obj and name CA" index = 122 rmsd = 2.080 "obj and name CA" index = 123 rmsd = 2.219 "obj and name CA" index = 124 rmsd = 2.004 "obj and name CA" index = 125 rmsd = 1.589 "obj and name CA" index = 126 rmsd = 2.062 "obj and name CA" index = 127 rmsd = 2.456 "obj and name CA" index = 128 rmsd = 2.040 "obj and name CA" index = 129 rmsd = 1.798 "obj and name CA" index = 130 rmsd = 1.965 "obj and name CA" index = 131 rmsd = 1.740 "obj and name CA" index = 132 rmsd = 1.300 "obj and name CA" index = 133 rmsd = 1.172 "obj and name CA" index = 134 rmsd = 1.110 "obj and name CA" index = 135 rmsd = 1.084 "obj and name CA" index = 136 rmsd = 1.011 "obj and name CA" index = 137 rmsd = 1.008 "obj and name CA" index = 138 rmsd = 1.144 "obj and name CA" index = 139 rmsd = 1.389 "obj and name CA" index = 140 rmsd = 1.397 "obj and name CA" index = 141 rmsd = 1.104 "obj and name CA" index = 142 rmsd = 1.033 "obj and name CA" index = 143 rmsd = 1.453 "obj and name CA" index = 144 rmsd = 1.499 "obj and name CA" index = 145 rmsd = 1.237 "obj and name CA" index = 146 rmsd = 1.558 "obj and name CA" index = 147 rmsd = 1.911 "obj and name CA" index = 148 rmsd = 1.907 "obj and name CA" index = 149 rmsd = 2.000 "obj and name CA" index = 150 rmsd = 2.010 "obj and name CA" index = 151 rmsd = 2.254 "obj and name CA" index = 152 rmsd = 2.524 "obj and name CA" index = 153 rmsd = 2.711 "obj and name CA" index = 154 rmsd = 2.764 "obj and name CA" index = 155 rmsd = 3.096 "obj and name CA" index = 156 rmsd = 3.535 "obj and name CA" index = 157 rmsd = 3.654 "obj and name CA" index = 158 rmsd = 3.396 "obj and name CA" index = 159 rmsd = 3.103 "obj and name CA" index = 160 rmsd = 3.862 "obj and name CA" index = 161 rmsd = 4.441 "obj and name CA" index = 162 rmsd = 4.852 "obj and name CA" index = 163 rmsd = 4.425 "obj and name CA" index = 164 rmsd = 4.836 "obj and name CA" index = 165 rmsd = 4.998 "obj and name CA" index = 166 rmsd = 5.553 "obj and name CA" index = 167 rmsd = 5.962 "obj and name CA" index = 168 rmsd = 6.645 "obj and name CA" index = 169 rmsd = 8.554 "obj and name CA" index = 170 rmsd = 10.565 "obj and name CA" index = 171 rmsd = 12.734 "obj and name CA" index = 172 rmsd = 14.779 "obj and name CA" index = 173 rmsd = 16.750 "obj and name CA" index = 174 rmsd = 18.188 "obj and name CA" index = 175 rmsd = 19.984 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 189 atoms. PyMOL>color cyan,ss s Executive: Colored 48 atoms. PyMOL>color gray,ss ""+l Executive: Colored 5703 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: 1.63 sec. = 2206.2 frames/hour (8.08 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit