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 8 atoms. PyMOL>color cyan,ss s Executive: Colored 53 atoms. PyMOL>color gray,ss ""+l Executive: Colored 2197 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: 1.81 sec. = 1988.5 frames/hour (1.81 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: 7.27 sec. = 495.1 frames/hour (9.08 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, 1.1747113466262817, 1.1743154525756836, 1.3851410150527954, 1.071219801902771, 1.62291419506073, 1.1538492441177368, 1.3356624841690063, 1.6797819137573242, 1.3396996259689331, 1.4678691625595093, 1.2205765247344971, 1.1427915096282959, 1.3886783123016357, 1.3120197057723999, 1.1371501684188843, 1.1982791423797607, 1.1165552139282227, 1.2394783496856689, 1.5081188678741455] -> 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 = 3.317 "obj and name CA" index = 2 rmsd = 1.718 "obj and name CA" index = 3 rmsd = 1.047 "obj and name CA" index = 4 rmsd = 0.591 "obj and name CA" index = 5 rmsd = 0.395 "obj and name CA" index = 6 rmsd = 0.295 "obj and name CA" index = 7 rmsd = 0.322 "obj and name CA" index = 8 rmsd = 0.479 "obj and name CA" index = 9 rmsd = 0.565 "obj and name CA" index = 10 rmsd = 0.700 "obj and name CA" index = 11 rmsd = 0.567 "obj and name CA" index = 12 rmsd = 0.582 "obj and name CA" index = 13 rmsd = 0.378 "obj and name CA" index = 14 rmsd = 0.401 "obj and name CA" index = 15 rmsd = 0.359 "obj and name CA" index = 16 rmsd = 0.432 "obj and name CA" index = 17 rmsd = 0.434 "obj and name CA" index = 18 rmsd = 0.503 "obj and name CA" index = 19 rmsd = 0.496 "obj and name CA" index = 20 rmsd = 0.393 "obj and name CA" index = 21 rmsd = 0.689 "obj and name CA" index = 22 rmsd = 0.707 "obj and name CA" index = 23 rmsd = 0.809 "obj and name CA" index = 24 rmsd = 0.839 "obj and name CA" index = 25 rmsd = 0.592 "obj and name CA" index = 26 rmsd = 0.552 "obj and name CA" index = 27 rmsd = 0.477 "obj and name CA" index = 28 rmsd = 0.466 "obj and name CA" index = 29 rmsd = 0.623 "obj and name CA" index = 30 rmsd = 0.539 "obj and name CA" index = 31 rmsd = 0.550 "obj and name CA" index = 32 rmsd = 0.833 "obj and name CA" index = 33 rmsd = 1.513 "obj and name CA" index = 34 rmsd = 1.098 "obj and name CA" index = 35 rmsd = 1.199 "obj and name CA" index = 36 rmsd = 1.076 "obj and name CA" index = 37 rmsd = 0.992 "obj and name CA" index = 38 rmsd = 0.510 "obj and name CA" index = 39 rmsd = 0.310 "obj and name CA" index = 40 rmsd = 0.292 "obj and name CA" index = 41 rmsd = 0.388 "obj and name CA" index = 42 rmsd = 0.643 "obj and name CA" index = 43 rmsd = 0.560 "obj and name CA" index = 44 rmsd = 0.736 "obj and name CA" index = 45 rmsd = 0.515 "obj and name CA" index = 46 rmsd = 0.477 "obj and name CA" index = 47 rmsd = 0.425 "obj and name CA" index = 48 rmsd = 0.362 "obj and name CA" index = 49 rmsd = 0.329 "obj and name CA" index = 50 rmsd = 0.315 "obj and name CA" index = 51 rmsd = 0.300 "obj and name CA" index = 52 rmsd = 0.341 "obj and name CA" index = 53 rmsd = 0.357 "obj and name CA" index = 54 rmsd = 0.541 "obj and name CA" index = 55 rmsd = 0.423 "obj and name CA" index = 56 rmsd = 0.378 "obj and name CA" index = 57 rmsd = 0.304 "obj and name CA" index = 58 rmsd = 0.317 "obj and name CA" index = 59 rmsd = 0.258 "obj and name CA" index = 60 rmsd = 0.296 "obj and name CA" index = 61 rmsd = 0.272 "obj and name CA" index = 62 rmsd = 0.272 "obj and name CA" index = 63 rmsd = 0.344 "obj and name CA" index = 64 rmsd = 0.382 "obj and name CA" index = 65 rmsd = 0.347 "obj and name CA" index = 66 rmsd = 0.335 "obj and name CA" index = 67 rmsd = 0.540 "obj and name CA" index = 68 rmsd = 0.676 "obj and name CA" index = 69 rmsd = 0.560 "obj and name CA" index = 70 rmsd = 0.446 "obj and name CA" index = 71 rmsd = 0.385 "obj and name CA" index = 72 rmsd = 0.305 "obj and name CA" index = 73 rmsd = 0.334 "obj and name CA" index = 74 rmsd = 0.319 "obj and name CA" index = 75 rmsd = 0.330 "obj and name CA" index = 76 rmsd = 0.306 "obj and name CA" index = 77 rmsd = 0.359 "obj and name CA" index = 78 rmsd = 0.467 "obj and name CA" index = 79 rmsd = 0.622 "obj and name CA" index = 80 rmsd = 0.596 "obj and name CA" index = 81 rmsd = 0.614 "obj and name CA" index = 82 rmsd = 0.625 "obj and name CA" index = 83 rmsd = 0.649 "obj and name CA" index = 84 rmsd = 0.674 "obj and name CA" index = 85 rmsd = 0.541 "obj and name CA" index = 86 rmsd = 0.452 "obj and name CA" index = 87 rmsd = 0.423 "obj and name CA" index = 88 rmsd = 0.395 "obj and name CA" index = 89 rmsd = 0.457 "obj and name CA" index = 90 rmsd = 0.524 "obj and name CA" index = 91 rmsd = 0.618 "obj and name CA" index = 92 rmsd = 0.558 "obj and name CA" index = 93 rmsd = 0.640 "obj and name CA" index = 94 rmsd = 0.888 "obj and name CA" index = 95 rmsd = 1.543 "obj and name CA" index = 96 rmsd = 1.242 "obj and name CA" index = 97 rmsd = 1.556 "obj and name CA" index = 98 rmsd = 2.030 "obj and name CA" index = 99 rmsd = 1.395 "obj and name CA" index = 100 rmsd = 1.173 "obj and name CA" index = 101 rmsd = 0.838 "obj and name CA" index = 102 rmsd = 0.486 "obj and name CA" index = 103 rmsd = 0.505 "obj and name CA" index = 104 rmsd = 0.442 "obj and name CA" index = 105 rmsd = 0.418 "obj and name CA" index = 106 rmsd = 0.452 "obj and name CA" index = 107 rmsd = 0.626 "obj and name CA" index = 108 rmsd = 0.596 "obj and name CA" index = 109 rmsd = 0.453 "obj and name CA" index = 110 rmsd = 0.373 "obj and name CA" index = 111 rmsd = 0.377 "obj and name CA" index = 112 rmsd = 0.347 "obj and name CA" index = 113 rmsd = 0.303 "obj and name CA" index = 114 rmsd = 0.266 "obj and name CA" index = 115 rmsd = 0.316 "obj and name CA" index = 116 rmsd = 0.283 "obj and name CA" index = 117 rmsd = 0.351 "obj and name CA" index = 118 rmsd = 0.318 "obj and name CA" index = 119 rmsd = 0.436 "obj and name CA" index = 120 rmsd = 0.581 "obj and name CA" index = 121 rmsd = 0.491 "obj and name CA" index = 122 rmsd = 0.600 "obj and name CA" index = 123 rmsd = 0.597 "obj and name CA" index = 124 rmsd = 0.598 "obj and name CA" index = 125 rmsd = 0.449 "obj and name CA" index = 126 rmsd = 0.378 "obj and name CA" index = 127 rmsd = 0.329 "obj and name CA" index = 128 rmsd = 0.352 "obj and name CA" index = 129 rmsd = 0.403 "obj and name CA" index = 130 rmsd = 0.328 "obj and name CA" index = 131 rmsd = 0.290 "obj and name CA" index = 132 rmsd = 0.361 "obj and name CA" index = 133 rmsd = 0.295 "obj and name CA" index = 134 rmsd = 0.355 "obj and name CA" index = 135 rmsd = 0.349 "obj and name CA" index = 136 rmsd = 0.457 "obj and name CA" index = 137 rmsd = 0.420 "obj and name CA" index = 138 rmsd = 0.469 "obj and name CA" index = 139 rmsd = 0.548 "obj and name CA" index = 140 rmsd = 1.359 "obj and name CA" index = 141 rmsd = 2.487 "obj and name CA" index = 142 rmsd = 4.522 "obj and name CA" index = 143 rmsd = 5.659 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 159 atoms. PyMOL>color gray,ss ""+l Executive: Colored 4469 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: 2.44 sec. = 1473.7 frames/hour (11.53 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit