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 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 8 atoms. PyMOL>color cyan,ss s Executive: Colored 60 atoms. PyMOL>color gray,ss ""+l Executive: Colored 2183 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: 1.72 sec. = 2089.1 frames/hour (1.72 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 429 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 429 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: 7.09 sec. = 507.5 frames/hour (8.82 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 18 states [1, 18] of object "obj and name CA" (18 total states) to get new single-state object "yesfit_ALL"... -------------------------------------------------------------------------------- -> proceeding WITH FITTING to reference state... intrafit_rmsds = [-1.0, 1.3454916477203369, 1.400577187538147, 1.0391824245452881, 1.5592254400253296, 1.603551983833313, 1.2646102905273438, 1.4235388040542603, 1.4857003688812256, 1.2419313192367554, 1.1067672967910767, 1.6127016544342041, 1.4687361717224121, 1.5256814956665039, 1.5468112230300903, 1.1346409320831299, 1.395452618598938, 1.7655235528945923] -> atom index_map = [None, 2, 21, 45, 67, 86, 98, 117, 128, 147, 158, 169, 184, 191, 202, 217, 233, 252, 271, 281, 295, 306, 317, 329, 344, 366, 383, 397, 411, 426, 440, 459, 478, 490, 497, 511, 525, 540, 554, 574, 598, 612, 626, 640, 647, 664, 684, 698, 715, 730, 750, 769, 788, 799, 819, 836, 858, 875, 891, 915, 934, 949, 973, 992, 1008, 1027, 1044, 1055, 1076, 1096, 1112, 1129, 1143, 1162, 1184, 1203, 1218, 1240, 1251, 1265, 1276, 1298, 1313, 1327, 1343, 1355, 1375, 1390, 1407, 1431, 1450, 1465, 1487, 1499, 1518, 1534, 1551, 1565, 1580, 1587, 1604, 1623, 1640, 1654, 1669, 1684, 1703, 1719, 1729, 1746, 1753, 1764, 1774, 1788, 1809, 1828, 1852, 1872, 1891, 1910, 1926, 1937, 1947, 1967, 1979, 1996, 2016, 2026, 2037, 2053, 2070, 2081, 2097, 2108, 2118, 2133, 2140, 2154, 2170, 2186, 2197, 2211, 2230, 2241] "obj and name CA" index = 1 rmsd = 3.016 "obj and name CA" index = 2 rmsd = 1.757 "obj and name CA" index = 3 rmsd = 1.097 "obj and name CA" index = 4 rmsd = 0.598 "obj and name CA" index = 5 rmsd = 0.443 "obj and name CA" index = 6 rmsd = 0.304 "obj and name CA" index = 7 rmsd = 0.310 "obj and name CA" index = 8 rmsd = 0.485 "obj and name CA" index = 9 rmsd = 0.573 "obj and name CA" index = 10 rmsd = 0.730 "obj and name CA" index = 11 rmsd = 0.574 "obj and name CA" index = 12 rmsd = 0.569 "obj and name CA" index = 13 rmsd = 0.383 "obj and name CA" index = 14 rmsd = 0.376 "obj and name CA" index = 15 rmsd = 0.361 "obj and name CA" index = 16 rmsd = 0.412 "obj and name CA" index = 17 rmsd = 0.431 "obj and name CA" index = 18 rmsd = 0.502 "obj and name CA" index = 19 rmsd = 0.553 "obj and name CA" index = 20 rmsd = 0.473 "obj and name CA" index = 21 rmsd = 0.720 "obj and name CA" index = 22 rmsd = 0.800 "obj and name CA" index = 23 rmsd = 0.771 "obj and name CA" index = 24 rmsd = 0.884 "obj and name CA" index = 25 rmsd = 0.797 "obj and name CA" index = 26 rmsd = 0.586 "obj and name CA" index = 27 rmsd = 0.519 "obj and name CA" index = 28 rmsd = 0.609 "obj and name CA" index = 29 rmsd = 0.724 "obj and name CA" index = 30 rmsd = 0.572 "obj and name CA" index = 31 rmsd = 0.549 "obj and name CA" index = 32 rmsd = 0.723 "obj and name CA" index = 33 rmsd = 1.552 "obj and name CA" index = 34 rmsd = 1.265 "obj and name CA" index = 35 rmsd = 1.428 "obj and name CA" index = 36 rmsd = 1.312 "obj and name CA" index = 37 rmsd = 1.219 "obj and name CA" index = 38 rmsd = 0.668 "obj and name CA" index = 39 rmsd = 0.368 "obj and name CA" index = 40 rmsd = 0.369 "obj and name CA" index = 41 rmsd = 0.538 "obj and name CA" index = 42 rmsd = 0.954 "obj and name CA" index = 43 rmsd = 0.893 "obj and name CA" index = 44 rmsd = 0.795 "obj and name CA" index = 45 rmsd = 0.567 "obj and name CA" index = 46 rmsd = 0.531 "obj and name CA" index = 47 rmsd = 0.569 "obj and name CA" index = 48 rmsd = 0.418 "obj and name CA" index = 49 rmsd = 0.327 "obj and name CA" index = 50 rmsd = 0.306 "obj and name CA" index = 51 rmsd = 0.295 "obj and name CA" index = 52 rmsd = 0.308 "obj and name CA" index = 53 rmsd = 0.299 "obj and name CA" index = 54 rmsd = 0.355 "obj and name CA" index = 55 rmsd = 0.435 "obj and name CA" index = 56 rmsd = 0.358 "obj and name CA" index = 57 rmsd = 0.278 "obj and name CA" index = 58 rmsd = 0.280 "obj and name CA" index = 59 rmsd = 0.243 "obj and name CA" index = 60 rmsd = 0.289 "obj and name CA" index = 61 rmsd = 0.311 "obj and name CA" index = 62 rmsd = 0.304 "obj and name CA" index = 63 rmsd = 0.375 "obj and name CA" index = 64 rmsd = 0.409 "obj and name CA" index = 65 rmsd = 0.367 "obj and name CA" index = 66 rmsd = 0.360 "obj and name CA" index = 67 rmsd = 0.569 "obj and name CA" index = 68 rmsd = 0.588 "obj and name CA" index = 69 rmsd = 0.546 "obj and name CA" index = 70 rmsd = 0.560 "obj and name CA" index = 71 rmsd = 0.390 "obj and name CA" index = 72 rmsd = 0.328 "obj and name CA" index = 73 rmsd = 0.360 "obj and name CA" index = 74 rmsd = 0.300 "obj and name CA" index = 75 rmsd = 0.352 "obj and name CA" index = 76 rmsd = 0.309 "obj and name CA" index = 77 rmsd = 0.318 "obj and name CA" index = 78 rmsd = 0.364 "obj and name CA" index = 79 rmsd = 0.536 "obj and name CA" index = 80 rmsd = 0.567 "obj and name CA" index = 81 rmsd = 0.601 "obj and name CA" index = 82 rmsd = 0.599 "obj and name CA" index = 83 rmsd = 0.662 "obj and name CA" index = 84 rmsd = 0.724 "obj and name CA" index = 85 rmsd = 0.566 "obj and name CA" index = 86 rmsd = 0.472 "obj and name CA" index = 87 rmsd = 0.449 "obj and name CA" index = 88 rmsd = 0.393 "obj and name CA" index = 89 rmsd = 0.474 "obj and name CA" index = 90 rmsd = 0.488 "obj and name CA" index = 91 rmsd = 0.590 "obj and name CA" index = 92 rmsd = 0.517 "obj and name CA" index = 93 rmsd = 0.814 "obj and name CA" index = 94 rmsd = 0.864 "obj and name CA" index = 95 rmsd = 1.440 "obj and name CA" index = 96 rmsd = 1.295 "obj and name CA" index = 97 rmsd = 1.739 "obj and name CA" index = 98 rmsd = 2.353 "obj and name CA" index = 99 rmsd = 1.724 "obj and name CA" index = 100 rmsd = 1.317 "obj and name CA" index = 101 rmsd = 0.900 "obj and name CA" index = 102 rmsd = 0.558 "obj and name CA" index = 103 rmsd = 0.617 "obj and name CA" index = 104 rmsd = 0.469 "obj and name CA" index = 105 rmsd = 0.434 "obj and name CA" index = 106 rmsd = 0.450 "obj and name CA" index = 107 rmsd = 0.634 "obj and name CA" index = 108 rmsd = 0.509 "obj and name CA" index = 109 rmsd = 0.379 "obj and name CA" index = 110 rmsd = 0.361 "obj and name CA" index = 111 rmsd = 0.315 "obj and name CA" index = 112 rmsd = 0.297 "obj and name CA" index = 113 rmsd = 0.303 "obj and name CA" index = 114 rmsd = 0.278 "obj and name CA" index = 115 rmsd = 0.364 "obj and name CA" index = 116 rmsd = 0.309 "obj and name CA" index = 117 rmsd = 0.380 "obj and name CA" index = 118 rmsd = 0.363 "obj and name CA" index = 119 rmsd = 0.426 "obj and name CA" index = 120 rmsd = 0.707 "obj and name CA" index = 121 rmsd = 0.616 "obj and name CA" index = 122 rmsd = 0.673 "obj and name CA" index = 123 rmsd = 0.655 "obj and name CA" index = 124 rmsd = 0.776 "obj and name CA" index = 125 rmsd = 0.590 "obj and name CA" index = 126 rmsd = 0.480 "obj and name CA" index = 127 rmsd = 0.406 "obj and name CA" index = 128 rmsd = 0.386 "obj and name CA" index = 129 rmsd = 0.406 "obj and name CA" index = 130 rmsd = 0.363 "obj and name CA" index = 131 rmsd = 0.329 "obj and name CA" index = 132 rmsd = 0.350 "obj and name CA" index = 133 rmsd = 0.278 "obj and name CA" index = 134 rmsd = 0.287 "obj and name CA" index = 135 rmsd = 0.309 "obj and name CA" index = 136 rmsd = 0.397 "obj and name CA" index = 137 rmsd = 0.376 "obj and name CA" index = 138 rmsd = 0.375 "obj and name CA" index = 139 rmsd = 0.468 "obj and name CA" index = 140 rmsd = 1.262 "obj and name CA" index = 141 rmsd = 2.386 "obj and name CA" index = 142 rmsd = 4.095 "obj and name CA" index = 143 rmsd = 5.046 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 24 atoms. PyMOL>color cyan,ss s Executive: Colored 180 atoms. PyMOL>color gray,ss ""+l Executive: Colored 4441 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: 2.38 sec. = 1514.9 frames/hour (11.19 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit