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 64 atoms. PyMOL>color cyan,ss s Executive: Colored 25 atoms. PyMOL>color gray,ss ""+l Executive: Colored 2795 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: 1.36 sec. = 2656.3 frames/hour (1.36 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: 4.53 sec. = 795.6 frames/hour (5.88 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, 5.889214038848877, 5.1893911361694336, 4.8067865371704102, 4.2078003883361816, 5.0995655059814453, 3.287264347076416, 4.8819670677185059, 6.1273984909057617, 4.0047359466552734, 6.7655606269836426, 7.5832095146179199, 7.064551830291748, 6.4812092781066895, 7.1320943832397461, 6.1430907249450684, 5.2261877059936523, 5.2391667366027832, 5.0427422523498535, 4.2942090034484863] -> 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 = 6.489 "obj and name CA" index = 2 rmsd = 5.115 "obj and name CA" index = 3 rmsd = 3.790 "obj and name CA" index = 4 rmsd = 3.338 "obj and name CA" index = 5 rmsd = 3.041 "obj and name CA" index = 6 rmsd = 2.801 "obj and name CA" index = 7 rmsd = 2.549 "obj and name CA" index = 8 rmsd = 2.278 "obj and name CA" index = 9 rmsd = 2.008 "obj and name CA" index = 10 rmsd = 1.849 "obj and name CA" index = 11 rmsd = 1.883 "obj and name CA" index = 12 rmsd = 1.721 "obj and name CA" index = 13 rmsd = 1.444 "obj and name CA" index = 14 rmsd = 1.536 "obj and name CA" index = 15 rmsd = 1.429 "obj and name CA" index = 16 rmsd = 1.433 "obj and name CA" index = 17 rmsd = 1.732 "obj and name CA" index = 18 rmsd = 1.844 "obj and name CA" index = 19 rmsd = 1.822 "obj and name CA" index = 20 rmsd = 2.005 "obj and name CA" index = 21 rmsd = 1.843 "obj and name CA" index = 22 rmsd = 1.941 "obj and name CA" index = 23 rmsd = 2.387 "obj and name CA" index = 24 rmsd = 2.476 "obj and name CA" index = 25 rmsd = 2.508 "obj and name CA" index = 26 rmsd = 2.605 "obj and name CA" index = 27 rmsd = 2.212 "obj and name CA" index = 28 rmsd = 1.868 "obj and name CA" index = 29 rmsd = 1.935 "obj and name CA" index = 30 rmsd = 1.914 "obj and name CA" index = 31 rmsd = 1.619 "obj and name CA" index = 32 rmsd = 1.474 "obj and name CA" index = 33 rmsd = 1.601 "obj and name CA" index = 34 rmsd = 1.544 "obj and name CA" index = 35 rmsd = 1.278 "obj and name CA" index = 36 rmsd = 1.313 "obj and name CA" index = 37 rmsd = 1.550 "obj and name CA" index = 38 rmsd = 1.354 "obj and name CA" index = 39 rmsd = 1.208 "obj and name CA" index = 40 rmsd = 1.575 "obj and name CA" index = 41 rmsd = 1.731 "obj and name CA" index = 42 rmsd = 1.656 "obj and name CA" index = 43 rmsd = 1.799 "obj and name CA" index = 44 rmsd = 2.134 "obj and name CA" index = 45 rmsd = 2.214 "obj and name CA" index = 46 rmsd = 2.207 "obj and name CA" index = 47 rmsd = 2.427 "obj and name CA" index = 48 rmsd = 2.752 "obj and name CA" index = 49 rmsd = 2.749 "obj and name CA" index = 50 rmsd = 2.803 "obj and name CA" index = 51 rmsd = 2.499 "obj and name CA" index = 52 rmsd = 2.062 "obj and name CA" index = 53 rmsd = 2.045 "obj and name CA" index = 54 rmsd = 1.465 "obj and name CA" index = 55 rmsd = 1.352 "obj and name CA" index = 56 rmsd = 1.126 "obj and name CA" index = 57 rmsd = 1.190 "obj and name CA" index = 58 rmsd = 1.217 "obj and name CA" index = 59 rmsd = 1.506 "obj and name CA" index = 60 rmsd = 1.936 "obj and name CA" index = 61 rmsd = 1.861 "obj and name CA" index = 62 rmsd = 1.461 "obj and name CA" index = 63 rmsd = 1.462 "obj and name CA" index = 64 rmsd = 1.170 "obj and name CA" index = 65 rmsd = 0.925 "obj and name CA" index = 66 rmsd = 0.994 "obj and name CA" index = 67 rmsd = 1.192 "obj and name CA" index = 68 rmsd = 1.365 "obj and name CA" index = 69 rmsd = 1.500 "obj and name CA" index = 70 rmsd = 2.059 "obj and name CA" index = 71 rmsd = 2.510 "obj and name CA" index = 72 rmsd = 2.972 "obj and name CA" index = 73 rmsd = 3.279 "obj and name CA" index = 74 rmsd = 3.762 "obj and name CA" index = 75 rmsd = 3.811 "obj and name CA" index = 76 rmsd = 3.252 "obj and name CA" index = 77 rmsd = 2.886 "obj and name CA" index = 78 rmsd = 2.499 "obj and name CA" index = 79 rmsd = 2.071 "obj and name CA" index = 80 rmsd = 1.730 "obj and name CA" index = 81 rmsd = 1.440 "obj and name CA" index = 82 rmsd = 1.039 "obj and name CA" index = 83 rmsd = 0.829 "obj and name CA" index = 84 rmsd = 0.820 "obj and name CA" index = 85 rmsd = 1.090 "obj and name CA" index = 86 rmsd = 1.203 "obj and name CA" index = 87 rmsd = 1.457 "obj and name CA" index = 88 rmsd = 1.939 "obj and name CA" index = 89 rmsd = 2.026 "obj and name CA" index = 90 rmsd = 1.493 "obj and name CA" index = 91 rmsd = 1.527 "obj and name CA" index = 92 rmsd = 1.820 "obj and name CA" index = 93 rmsd = 1.632 "obj and name CA" index = 94 rmsd = 1.192 "obj and name CA" index = 95 rmsd = 1.051 "obj and name CA" index = 96 rmsd = 1.119 "obj and name CA" index = 97 rmsd = 0.748 "obj and name CA" index = 98 rmsd = 0.914 "obj and name CA" index = 99 rmsd = 1.226 "obj and name CA" index = 100 rmsd = 1.570 "obj and name CA" index = 101 rmsd = 1.833 "obj and name CA" index = 102 rmsd = 1.696 "obj and name CA" index = 103 rmsd = 1.720 "obj and name CA" index = 104 rmsd = 2.235 "obj and name CA" index = 105 rmsd = 2.319 "obj and name CA" index = 106 rmsd = 2.412 "obj and name CA" index = 107 rmsd = 2.650 "obj and name CA" index = 108 rmsd = 3.035 "obj and name CA" index = 109 rmsd = 2.186 "obj and name CA" index = 110 rmsd = 2.530 "obj and name CA" index = 111 rmsd = 2.963 "obj and name CA" index = 112 rmsd = 2.759 "obj and name CA" index = 113 rmsd = 1.928 "obj and name CA" index = 114 rmsd = 1.297 "obj and name CA" index = 115 rmsd = 1.291 "obj and name CA" index = 116 rmsd = 1.666 "obj and name CA" index = 117 rmsd = 1.612 "obj and name CA" index = 118 rmsd = 2.074 "obj and name CA" index = 119 rmsd = 2.412 "obj and name CA" index = 120 rmsd = 2.454 "obj and name CA" index = 121 rmsd = 1.927 "obj and name CA" index = 122 rmsd = 1.938 "obj and name CA" index = 123 rmsd = 2.244 "obj and name CA" index = 124 rmsd = 2.017 "obj and name CA" index = 125 rmsd = 1.554 "obj and name CA" index = 126 rmsd = 1.922 "obj and name CA" index = 127 rmsd = 2.249 "obj and name CA" index = 128 rmsd = 1.829 "obj and name CA" index = 129 rmsd = 1.566 "obj and name CA" index = 130 rmsd = 1.540 "obj and name CA" index = 131 rmsd = 1.436 "obj and name CA" index = 132 rmsd = 1.197 "obj and name CA" index = 133 rmsd = 1.181 "obj and name CA" index = 134 rmsd = 1.101 "obj and name CA" index = 135 rmsd = 1.132 "obj and name CA" index = 136 rmsd = 1.052 "obj and name CA" index = 137 rmsd = 0.941 "obj and name CA" index = 138 rmsd = 1.138 "obj and name CA" index = 139 rmsd = 1.355 "obj and name CA" index = 140 rmsd = 1.295 "obj and name CA" index = 141 rmsd = 1.140 "obj and name CA" index = 142 rmsd = 1.164 "obj and name CA" index = 143 rmsd = 1.682 "obj and name CA" index = 144 rmsd = 1.941 "obj and name CA" index = 145 rmsd = 1.645 "obj and name CA" index = 146 rmsd = 1.834 "obj and name CA" index = 147 rmsd = 2.405 "obj and name CA" index = 148 rmsd = 2.414 "obj and name CA" index = 149 rmsd = 2.198 "obj and name CA" index = 150 rmsd = 2.225 "obj and name CA" index = 151 rmsd = 2.696 "obj and name CA" index = 152 rmsd = 2.647 "obj and name CA" index = 153 rmsd = 2.496 "obj and name CA" index = 154 rmsd = 2.752 "obj and name CA" index = 155 rmsd = 3.011 "obj and name CA" index = 156 rmsd = 2.966 "obj and name CA" index = 157 rmsd = 3.075 "obj and name CA" index = 158 rmsd = 2.768 "obj and name CA" index = 159 rmsd = 2.665 "obj and name CA" index = 160 rmsd = 3.302 "obj and name CA" index = 161 rmsd = 4.197 "obj and name CA" index = 162 rmsd = 4.512 "obj and name CA" index = 163 rmsd = 4.351 "obj and name CA" index = 164 rmsd = 5.019 "obj and name CA" index = 165 rmsd = 5.413 "obj and name CA" index = 166 rmsd = 5.815 "obj and name CA" index = 167 rmsd = 6.157 "obj and name CA" index = 168 rmsd = 6.970 "obj and name CA" index = 169 rmsd = 8.435 "obj and name CA" index = 170 rmsd = 10.470 "obj and name CA" index = 171 rmsd = 12.393 "obj and name CA" index = 172 rmsd = 14.565 "obj and name CA" index = 173 rmsd = 16.178 "obj and name CA" index = 174 rmsd = 17.877 "obj and name CA" index = 175 rmsd = 20.186 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 192 atoms. PyMOL>color cyan,ss s Executive: Colored 75 atoms. PyMOL>color gray,ss ""+l Executive: Colored 5670 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: 1.53 sec. = 2356.8 frames/hour (7.41 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit