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 32 atoms. PyMOL>color cyan,ss s Executive: Colored 24 atoms. PyMOL>color gray,ss ""+l Executive: Colored 2308 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: 1.46 sec. = 2471.8 frames/hour (1.46 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 474 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 474 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: 5.87 sec. = 613.2 frames/hour (7.33 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, 5.3200783729553223, 5.2283844947814941, 6.9168715476989746, 9.2363777160644531, 7.6109318733215332, 6.4261245727539062, 5.5218195915222168, 5.7070307731628418, 7.4808382987976074, 7.4129157066345215, 6.3474230766296387, 8.8037805557250977, 7.397712230682373, 10.49708080291748, 5.5136814117431641, 7.6788358688354492, 5.2295312881469727, 7.5325512886047363, 11.023752212524414] -> atom index_map = [None, 2, 21, 43, 62, 79, 93, 105, 119, 129, 143, 153, 172, 186, 200, 216, 230, 240, 261, 268, 280, 287, 308, 327, 342, 358, 372, 389, 405, 429, 449, 460, 477, 487, 506, 516, 536, 546, 560, 575, 582, 596, 612, 622, 633, 657, 671, 687, 704, 728, 742, 752, 764, 783, 797, 807, 818, 837, 856, 873, 890, 900, 910, 917, 936, 946, 961, 977, 993, 1017, 1029, 1043, 1062, 1072, 1092, 1111, 1123, 1138, 1152, 1167, 1177, 1184, 1194, 1201, 1211, 1235, 1249, 1259, 1273, 1283, 1297, 1312, 1328, 1347, 1366, 1382, 1389, 1403, 1410, 1434, 1458, 1475, 1492, 1511, 1530, 1537, 1551, 1566, 1583, 1599, 1623, 1637, 1656, 1675, 1685, 1702, 1709, 1725, 1732, 1748, 1763, 1773, 1790, 1802, 1816, 1833, 1843, 1853, 1863, 1887, 1901, 1922, 1936, 1955, 1974, 1991, 2001, 2016, 2023, 2047, 2071, 2087, 2103, 2119, 2129, 2148, 2167, 2181, 2193, 2200, 2212, 2223, 2242, 2257, 2274, 2291, 2308, 2325, 2342] "obj and name CA" index = 1 rmsd = 15.081 "obj and name CA" index = 2 rmsd = 14.171 "obj and name CA" index = 3 rmsd = 13.129 "obj and name CA" index = 4 rmsd = 13.278 "obj and name CA" index = 5 rmsd = 11.641 "obj and name CA" index = 6 rmsd = 9.138 "obj and name CA" index = 7 rmsd = 8.056 "obj and name CA" index = 8 rmsd = 6.552 "obj and name CA" index = 9 rmsd = 5.064 "obj and name CA" index = 10 rmsd = 3.330 "obj and name CA" index = 11 rmsd = 2.386 "obj and name CA" index = 12 rmsd = 1.999 "obj and name CA" index = 13 rmsd = 1.902 "obj and name CA" index = 14 rmsd = 1.752 "obj and name CA" index = 15 rmsd = 2.086 "obj and name CA" index = 16 rmsd = 2.018 "obj and name CA" index = 17 rmsd = 1.980 "obj and name CA" index = 18 rmsd = 2.550 "obj and name CA" index = 19 rmsd = 2.484 "obj and name CA" index = 20 rmsd = 2.519 "obj and name CA" index = 21 rmsd = 2.173 "obj and name CA" index = 22 rmsd = 1.895 "obj and name CA" index = 23 rmsd = 1.964 "obj and name CA" index = 24 rmsd = 1.909 "obj and name CA" index = 25 rmsd = 2.189 "obj and name CA" index = 26 rmsd = 2.616 "obj and name CA" index = 27 rmsd = 2.537 "obj and name CA" index = 28 rmsd = 2.424 "obj and name CA" index = 29 rmsd = 2.355 "obj and name CA" index = 30 rmsd = 2.547 "obj and name CA" index = 31 rmsd = 2.483 "obj and name CA" index = 32 rmsd = 2.138 "obj and name CA" index = 33 rmsd = 2.020 "obj and name CA" index = 34 rmsd = 1.879 "obj and name CA" index = 35 rmsd = 1.834 "obj and name CA" index = 36 rmsd = 1.780 "obj and name CA" index = 37 rmsd = 1.952 "obj and name CA" index = 38 rmsd = 2.429 "obj and name CA" index = 39 rmsd = 2.531 "obj and name CA" index = 40 rmsd = 2.891 "obj and name CA" index = 41 rmsd = 2.501 "obj and name CA" index = 42 rmsd = 2.711 "obj and name CA" index = 43 rmsd = 2.624 "obj and name CA" index = 44 rmsd = 2.487 "obj and name CA" index = 45 rmsd = 2.936 "obj and name CA" index = 46 rmsd = 2.675 "obj and name CA" index = 47 rmsd = 2.862 "obj and name CA" index = 48 rmsd = 2.716 "obj and name CA" index = 49 rmsd = 2.320 "obj and name CA" index = 50 rmsd = 2.796 "obj and name CA" index = 51 rmsd = 3.054 "obj and name CA" index = 52 rmsd = 2.556 "obj and name CA" index = 53 rmsd = 2.918 "obj and name CA" index = 54 rmsd = 2.691 "obj and name CA" index = 55 rmsd = 2.830 "obj and name CA" index = 56 rmsd = 2.587 "obj and name CA" index = 57 rmsd = 2.228 "obj and name CA" index = 58 rmsd = 2.325 "obj and name CA" index = 59 rmsd = 2.485 "obj and name CA" index = 60 rmsd = 2.145 "obj and name CA" index = 61 rmsd = 2.010 "obj and name CA" index = 62 rmsd = 2.379 "obj and name CA" index = 63 rmsd = 2.403 "obj and name CA" index = 64 rmsd = 3.127 "obj and name CA" index = 65 rmsd = 3.836 "obj and name CA" index = 66 rmsd = 4.935 "obj and name CA" index = 67 rmsd = 6.115 "obj and name CA" index = 68 rmsd = 7.839 "obj and name CA" index = 69 rmsd = 8.449 "obj and name CA" index = 70 rmsd = 9.089 "obj and name CA" index = 71 rmsd = 10.289 "obj and name CA" index = 72 rmsd = 10.399 "obj and name CA" index = 73 rmsd = 10.242 "obj and name CA" index = 74 rmsd = 10.952 "obj and name CA" index = 75 rmsd = 10.617 "obj and name CA" index = 76 rmsd = 9.346 "obj and name CA" index = 77 rmsd = 8.743 "obj and name CA" index = 78 rmsd = 8.069 "obj and name CA" index = 79 rmsd = 8.210 "obj and name CA" index = 80 rmsd = 8.379 "obj and name CA" index = 81 rmsd = 8.015 "obj and name CA" index = 82 rmsd = 6.971 "obj and name CA" index = 83 rmsd = 6.518 "obj and name CA" index = 84 rmsd = 4.704 "obj and name CA" index = 85 rmsd = 4.111 "obj and name CA" index = 86 rmsd = 4.049 "obj and name CA" index = 87 rmsd = 3.252 "obj and name CA" index = 88 rmsd = 2.325 "obj and name CA" index = 89 rmsd = 1.978 "obj and name CA" index = 90 rmsd = 2.019 "obj and name CA" index = 91 rmsd = 1.773 "obj and name CA" index = 92 rmsd = 1.559 "obj and name CA" index = 93 rmsd = 1.462 "obj and name CA" index = 94 rmsd = 1.532 "obj and name CA" index = 95 rmsd = 1.509 "obj and name CA" index = 96 rmsd = 1.937 "obj and name CA" index = 97 rmsd = 2.121 "obj and name CA" index = 98 rmsd = 2.351 "obj and name CA" index = 99 rmsd = 2.897 "obj and name CA" index = 100 rmsd = 2.633 "obj and name CA" index = 101 rmsd = 2.616 "obj and name CA" index = 102 rmsd = 2.678 "obj and name CA" index = 103 rmsd = 2.549 "obj and name CA" index = 104 rmsd = 2.980 "obj and name CA" index = 105 rmsd = 3.145 "obj and name CA" index = 106 rmsd = 3.384 "obj and name CA" index = 107 rmsd = 2.858 "obj and name CA" index = 108 rmsd = 2.455 "obj and name CA" index = 109 rmsd = 2.907 "obj and name CA" index = 110 rmsd = 2.773 "obj and name CA" index = 111 rmsd = 2.309 "obj and name CA" index = 112 rmsd = 2.545 "obj and name CA" index = 113 rmsd = 2.772 "obj and name CA" index = 114 rmsd = 2.649 "obj and name CA" index = 115 rmsd = 2.619 "obj and name CA" index = 116 rmsd = 2.197 "obj and name CA" index = 117 rmsd = 2.204 "obj and name CA" index = 118 rmsd = 1.984 "obj and name CA" index = 119 rmsd = 1.966 "obj and name CA" index = 120 rmsd = 1.981 "obj and name CA" index = 121 rmsd = 1.988 "obj and name CA" index = 122 rmsd = 1.924 "obj and name CA" index = 123 rmsd = 1.571 "obj and name CA" index = 124 rmsd = 1.665 "obj and name CA" index = 125 rmsd = 1.815 "obj and name CA" index = 126 rmsd = 1.448 "obj and name CA" index = 127 rmsd = 1.413 "obj and name CA" index = 128 rmsd = 1.759 "obj and name CA" index = 129 rmsd = 1.755 "obj and name CA" index = 130 rmsd = 1.439 "obj and name CA" index = 131 rmsd = 1.730 "obj and name CA" index = 132 rmsd = 2.090 "obj and name CA" index = 133 rmsd = 1.932 "obj and name CA" index = 134 rmsd = 1.848 "obj and name CA" index = 135 rmsd = 2.393 "obj and name CA" index = 136 rmsd = 2.506 "obj and name CA" index = 137 rmsd = 2.363 "obj and name CA" index = 138 rmsd = 2.263 "obj and name CA" index = 139 rmsd = 1.951 "obj and name CA" index = 140 rmsd = 1.652 "obj and name CA" index = 141 rmsd = 1.506 "obj and name CA" index = 142 rmsd = 1.364 "obj and name CA" index = 143 rmsd = 1.523 "obj and name CA" index = 144 rmsd = 1.466 "obj and name CA" index = 145 rmsd = 1.761 "obj and name CA" index = 146 rmsd = 1.942 "obj and name CA" index = 147 rmsd = 2.418 "obj and name CA" index = 148 rmsd = 2.787 "obj and name CA" index = 149 rmsd = 3.913 "obj and name CA" index = 150 rmsd = 4.257 "obj and name CA" index = 151 rmsd = 6.013 "obj and name CA" index = 152 rmsd = 7.264 "obj and name CA" index = 153 rmsd = 8.192 "obj and name CA" index = 154 rmsd = 10.241 "obj and name CA" index = 155 rmsd = 11.894 "obj and name CA" index = 156 rmsd = 12.500 "obj and name CA" index = 157 rmsd = 13.991 "obj and name CA" index = 158 rmsd = 14.809 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 96 atoms. PyMOL>color cyan,ss s Executive: Colored 72 atoms. PyMOL>color gray,ss ""+l Executive: Colored 4712 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: 2.26 sec. = 1592.5 frames/hour (9.59 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit