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 2311 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: 1.52 sec. = 2363.8 frames/hour (1.52 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: 6.32 sec. = 569.3 frames/hour (7.85 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, 6.3683919906616211, 6.3566861152648926, 8.3795070648193359, 5.908073902130127, 9.6143550872802734, 5.1672530174255371, 4.4573788642883301, 9.0407428741455078, 8.0565824508666992, 11.296079635620117, 7.1277861595153809, 7.9552974700927734, 5.1353073120117188, 7.6988325119018555, 7.7806034088134766, 8.9483652114868164, 7.6652379035949707, 8.5289907455444336, 8.8159933090209961] -> 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 = 18.542 "obj and name CA" index = 2 rmsd = 17.562 "obj and name CA" index = 3 rmsd = 16.032 "obj and name CA" index = 4 rmsd = 15.668 "obj and name CA" index = 5 rmsd = 13.783 "obj and name CA" index = 6 rmsd = 11.042 "obj and name CA" index = 7 rmsd = 8.834 "obj and name CA" index = 8 rmsd = 6.621 "obj and name CA" index = 9 rmsd = 5.257 "obj and name CA" index = 10 rmsd = 3.468 "obj and name CA" index = 11 rmsd = 2.614 "obj and name CA" index = 12 rmsd = 2.216 "obj and name CA" index = 13 rmsd = 2.055 "obj and name CA" index = 14 rmsd = 2.003 "obj and name CA" index = 15 rmsd = 2.518 "obj and name CA" index = 16 rmsd = 2.444 "obj and name CA" index = 17 rmsd = 2.345 "obj and name CA" index = 18 rmsd = 3.186 "obj and name CA" index = 19 rmsd = 3.059 "obj and name CA" index = 20 rmsd = 3.015 "obj and name CA" index = 21 rmsd = 2.503 "obj and name CA" index = 22 rmsd = 2.172 "obj and name CA" index = 23 rmsd = 2.296 "obj and name CA" index = 24 rmsd = 2.154 "obj and name CA" index = 25 rmsd = 2.643 "obj and name CA" index = 26 rmsd = 3.173 "obj and name CA" index = 27 rmsd = 2.927 "obj and name CA" index = 28 rmsd = 2.751 "obj and name CA" index = 29 rmsd = 2.586 "obj and name CA" index = 30 rmsd = 2.850 "obj and name CA" index = 31 rmsd = 2.634 "obj and name CA" index = 32 rmsd = 2.269 "obj and name CA" index = 33 rmsd = 2.072 "obj and name CA" index = 34 rmsd = 1.883 "obj and name CA" index = 35 rmsd = 1.842 "obj and name CA" index = 36 rmsd = 1.784 "obj and name CA" index = 37 rmsd = 1.974 "obj and name CA" index = 38 rmsd = 2.633 "obj and name CA" index = 39 rmsd = 2.777 "obj and name CA" index = 40 rmsd = 2.857 "obj and name CA" index = 41 rmsd = 2.438 "obj and name CA" index = 42 rmsd = 2.579 "obj and name CA" index = 43 rmsd = 2.633 "obj and name CA" index = 44 rmsd = 2.539 "obj and name CA" index = 45 rmsd = 3.036 "obj and name CA" index = 46 rmsd = 2.616 "obj and name CA" index = 47 rmsd = 3.025 "obj and name CA" index = 48 rmsd = 2.621 "obj and name CA" index = 49 rmsd = 2.248 "obj and name CA" index = 50 rmsd = 2.920 "obj and name CA" index = 51 rmsd = 3.115 "obj and name CA" index = 52 rmsd = 2.492 "obj and name CA" index = 53 rmsd = 2.789 "obj and name CA" index = 54 rmsd = 2.547 "obj and name CA" index = 55 rmsd = 2.783 "obj and name CA" index = 56 rmsd = 2.578 "obj and name CA" index = 57 rmsd = 2.169 "obj and name CA" index = 58 rmsd = 2.350 "obj and name CA" index = 59 rmsd = 2.568 "obj and name CA" index = 60 rmsd = 2.232 "obj and name CA" index = 61 rmsd = 2.196 "obj and name CA" index = 62 rmsd = 2.577 "obj and name CA" index = 63 rmsd = 2.784 "obj and name CA" index = 64 rmsd = 3.329 "obj and name CA" index = 65 rmsd = 3.745 "obj and name CA" index = 66 rmsd = 4.778 "obj and name CA" index = 67 rmsd = 6.063 "obj and name CA" index = 68 rmsd = 7.574 "obj and name CA" index = 69 rmsd = 8.477 "obj and name CA" index = 70 rmsd = 9.326 "obj and name CA" index = 71 rmsd = 10.725 "obj and name CA" index = 72 rmsd = 10.249 "obj and name CA" index = 73 rmsd = 10.074 "obj and name CA" index = 74 rmsd = 10.568 "obj and name CA" index = 75 rmsd = 10.540 "obj and name CA" index = 76 rmsd = 9.705 "obj and name CA" index = 77 rmsd = 9.230 "obj and name CA" index = 78 rmsd = 8.641 "obj and name CA" index = 79 rmsd = 8.640 "obj and name CA" index = 80 rmsd = 8.506 "obj and name CA" index = 81 rmsd = 8.198 "obj and name CA" index = 82 rmsd = 7.307 "obj and name CA" index = 83 rmsd = 7.041 "obj and name CA" index = 84 rmsd = 5.194 "obj and name CA" index = 85 rmsd = 5.010 "obj and name CA" index = 86 rmsd = 4.684 "obj and name CA" index = 87 rmsd = 3.387 "obj and name CA" index = 88 rmsd = 2.376 "obj and name CA" index = 89 rmsd = 1.844 "obj and name CA" index = 90 rmsd = 1.585 "obj and name CA" index = 91 rmsd = 1.272 "obj and name CA" index = 92 rmsd = 1.339 "obj and name CA" index = 93 rmsd = 1.190 "obj and name CA" index = 94 rmsd = 1.308 "obj and name CA" index = 95 rmsd = 1.376 "obj and name CA" index = 96 rmsd = 1.922 "obj and name CA" index = 97 rmsd = 2.122 "obj and name CA" index = 98 rmsd = 2.522 "obj and name CA" index = 99 rmsd = 3.143 "obj and name CA" index = 100 rmsd = 2.763 "obj and name CA" index = 101 rmsd = 2.595 "obj and name CA" index = 102 rmsd = 2.448 "obj and name CA" index = 103 rmsd = 2.380 "obj and name CA" index = 104 rmsd = 2.921 "obj and name CA" index = 105 rmsd = 3.100 "obj and name CA" index = 106 rmsd = 3.303 "obj and name CA" index = 107 rmsd = 2.745 "obj and name CA" index = 108 rmsd = 2.403 "obj and name CA" index = 109 rmsd = 2.869 "obj and name CA" index = 110 rmsd = 2.816 "obj and name CA" index = 111 rmsd = 2.396 "obj and name CA" index = 112 rmsd = 2.566 "obj and name CA" index = 113 rmsd = 2.958 "obj and name CA" index = 114 rmsd = 2.810 "obj and name CA" index = 115 rmsd = 2.647 "obj and name CA" index = 116 rmsd = 2.094 "obj and name CA" index = 117 rmsd = 1.839 "obj and name CA" index = 118 rmsd = 1.655 "obj and name CA" index = 119 rmsd = 1.557 "obj and name CA" index = 120 rmsd = 1.624 "obj and name CA" index = 121 rmsd = 1.649 "obj and name CA" index = 122 rmsd = 1.747 "obj and name CA" index = 123 rmsd = 1.524 "obj and name CA" index = 124 rmsd = 1.681 "obj and name CA" index = 125 rmsd = 1.592 "obj and name CA" index = 126 rmsd = 1.234 "obj and name CA" index = 127 rmsd = 1.382 "obj and name CA" index = 128 rmsd = 1.720 "obj and name CA" index = 129 rmsd = 1.505 "obj and name CA" index = 130 rmsd = 1.305 "obj and name CA" index = 131 rmsd = 1.746 "obj and name CA" index = 132 rmsd = 1.881 "obj and name CA" index = 133 rmsd = 1.660 "obj and name CA" index = 134 rmsd = 1.780 "obj and name CA" index = 135 rmsd = 2.184 "obj and name CA" index = 136 rmsd = 2.106 "obj and name CA" index = 137 rmsd = 2.050 "obj and name CA" index = 138 rmsd = 2.013 "obj and name CA" index = 139 rmsd = 1.717 "obj and name CA" index = 140 rmsd = 1.496 "obj and name CA" index = 141 rmsd = 1.528 "obj and name CA" index = 142 rmsd = 1.318 "obj and name CA" index = 143 rmsd = 1.535 "obj and name CA" index = 144 rmsd = 1.585 "obj and name CA" index = 145 rmsd = 1.838 "obj and name CA" index = 146 rmsd = 2.144 "obj and name CA" index = 147 rmsd = 3.018 "obj and name CA" index = 148 rmsd = 3.472 "obj and name CA" index = 149 rmsd = 3.996 "obj and name CA" index = 150 rmsd = 4.246 "obj and name CA" index = 151 rmsd = 5.683 "obj and name CA" index = 152 rmsd = 6.824 "obj and name CA" index = 153 rmsd = 7.806 "obj and name CA" index = 154 rmsd = 9.923 "obj and name CA" index = 155 rmsd = 11.652 "obj and name CA" index = 156 rmsd = 12.128 "obj and name CA" index = 157 rmsd = 13.238 "obj and name CA" index = 158 rmsd = 14.104 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 4715 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: 2.06 sec. = 1750.5 frames/hour (9.90 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit