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 56 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 1844 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: 0.93 sec. = 3851.8 frames/hour (0.93 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 363 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 363 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: 2.75 sec. = 1310.0 frames/hour (3.68 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, 5.8741879463195801, 8.030003547668457, 11.989006042480469, 8.2134866714477539, 13.950081825256348, 13.543034553527832, 11.809516906738281, 16.649776458740234, 7.2220263481140137, 10.532387733459473, 10.630309104919434, 8.1714620590209961, 8.4089632034301758, 10.167178153991699, 10.578509330749512, 5.9018106460571289, 16.668874740600586] -> atom index_map = [None, 2, 21, 28, 45, 62, 79, 96, 113, 130, 141, 158, 175, 185, 202, 222, 236, 250, 264, 284, 291, 298, 309, 328, 340, 354, 378, 388, 407, 421, 437, 452, 467, 491, 501, 523, 540, 552, 569, 586, 606, 623, 634, 653, 675, 689, 708, 719, 726, 746, 765, 779, 786, 798, 815, 825, 849, 863, 883, 903, 923, 940, 951, 958, 977, 991, 1008, 1022, 1038, 1057, 1067, 1084, 1103, 1127, 1137, 1156, 1166, 1178, 1195, 1209, 1223, 1235, 1242, 1266, 1283, 1295, 1312, 1328, 1343, 1363, 1374, 1393, 1403, 1420, 1442, 1461, 1480, 1502, 1521, 1543, 1562, 1579, 1586, 1607, 1624, 1643, 1657, 1668, 1678, 1697, 1711, 1725, 1741, 1758, 1780, 1797, 1814, 1828, 1844, 1854, 1873, 1884] "obj and name CA" index = 1 rmsd = 26.721 "obj and name CA" index = 2 rmsd = 25.963 "obj and name CA" index = 3 rmsd = 24.538 "obj and name CA" index = 4 rmsd = 22.837 "obj and name CA" index = 5 rmsd = 22.043 "obj and name CA" index = 6 rmsd = 20.079 "obj and name CA" index = 7 rmsd = 19.555 "obj and name CA" index = 8 rmsd = 18.421 "obj and name CA" index = 9 rmsd = 17.827 "obj and name CA" index = 10 rmsd = 17.711 "obj and name CA" index = 11 rmsd = 17.167 "obj and name CA" index = 12 rmsd = 16.750 "obj and name CA" index = 13 rmsd = 16.307 "obj and name CA" index = 14 rmsd = 14.240 "obj and name CA" index = 15 rmsd = 13.277 "obj and name CA" index = 16 rmsd = 11.475 "obj and name CA" index = 17 rmsd = 9.466 "obj and name CA" index = 18 rmsd = 8.521 "obj and name CA" index = 19 rmsd = 7.340 "obj and name CA" index = 20 rmsd = 6.451 "obj and name CA" index = 21 rmsd = 6.151 "obj and name CA" index = 22 rmsd = 6.775 "obj and name CA" index = 23 rmsd = 6.580 "obj and name CA" index = 24 rmsd = 5.395 "obj and name CA" index = 25 rmsd = 5.163 "obj and name CA" index = 26 rmsd = 6.234 "obj and name CA" index = 27 rmsd = 6.218 "obj and name CA" index = 28 rmsd = 7.448 "obj and name CA" index = 29 rmsd = 8.462 "obj and name CA" index = 30 rmsd = 7.972 "obj and name CA" index = 31 rmsd = 6.427 "obj and name CA" index = 32 rmsd = 6.855 "obj and name CA" index = 33 rmsd = 7.620 "obj and name CA" index = 34 rmsd = 6.481 "obj and name CA" index = 35 rmsd = 5.365 "obj and name CA" index = 36 rmsd = 6.439 "obj and name CA" index = 37 rmsd = 6.633 "obj and name CA" index = 38 rmsd = 5.283 "obj and name CA" index = 39 rmsd = 5.128 "obj and name CA" index = 40 rmsd = 6.289 "obj and name CA" index = 41 rmsd = 5.967 "obj and name CA" index = 42 rmsd = 5.094 "obj and name CA" index = 43 rmsd = 6.098 "obj and name CA" index = 44 rmsd = 5.902 "obj and name CA" index = 45 rmsd = 6.613 "obj and name CA" index = 46 rmsd = 7.598 "obj and name CA" index = 47 rmsd = 7.139 "obj and name CA" index = 48 rmsd = 5.868 "obj and name CA" index = 49 rmsd = 4.753 "obj and name CA" index = 50 rmsd = 4.285 "obj and name CA" index = 51 rmsd = 3.788 "obj and name CA" index = 52 rmsd = 4.116 "obj and name CA" index = 53 rmsd = 3.877 "obj and name CA" index = 54 rmsd = 3.023 "obj and name CA" index = 55 rmsd = 3.325 "obj and name CA" index = 56 rmsd = 3.907 "obj and name CA" index = 57 rmsd = 3.300 "obj and name CA" index = 58 rmsd = 2.771 "obj and name CA" index = 59 rmsd = 3.912 "obj and name CA" index = 60 rmsd = 4.328 "obj and name CA" index = 61 rmsd = 3.850 "obj and name CA" index = 62 rmsd = 4.823 "obj and name CA" index = 63 rmsd = 4.308 "obj and name CA" index = 64 rmsd = 5.234 "obj and name CA" index = 65 rmsd = 5.002 "obj and name CA" index = 66 rmsd = 4.955 "obj and name CA" index = 67 rmsd = 3.840 "obj and name CA" index = 68 rmsd = 3.024 "obj and name CA" index = 69 rmsd = 3.308 "obj and name CA" index = 70 rmsd = 3.088 "obj and name CA" index = 71 rmsd = 2.083 "obj and name CA" index = 72 rmsd = 2.140 "obj and name CA" index = 73 rmsd = 3.060 "obj and name CA" index = 74 rmsd = 2.996 "obj and name CA" index = 75 rmsd = 2.886 "obj and name CA" index = 76 rmsd = 3.427 "obj and name CA" index = 77 rmsd = 4.568 "obj and name CA" index = 78 rmsd = 5.296 "obj and name CA" index = 79 rmsd = 4.473 "obj and name CA" index = 80 rmsd = 4.822 "obj and name CA" index = 81 rmsd = 4.060 "obj and name CA" index = 82 rmsd = 3.983 "obj and name CA" index = 83 rmsd = 3.634 "obj and name CA" index = 84 rmsd = 4.825 "obj and name CA" index = 85 rmsd = 5.283 "obj and name CA" index = 86 rmsd = 5.485 "obj and name CA" index = 87 rmsd = 4.123 "obj and name CA" index = 88 rmsd = 3.582 "obj and name CA" index = 89 rmsd = 4.448 "obj and name CA" index = 90 rmsd = 3.860 "obj and name CA" index = 91 rmsd = 2.516 "obj and name CA" index = 92 rmsd = 3.117 "obj and name CA" index = 93 rmsd = 3.500 "obj and name CA" index = 94 rmsd = 2.527 "obj and name CA" index = 95 rmsd = 2.415 "obj and name CA" index = 96 rmsd = 3.300 "obj and name CA" index = 97 rmsd = 3.343 "obj and name CA" index = 98 rmsd = 3.158 "obj and name CA" index = 99 rmsd = 3.908 "obj and name CA" index = 100 rmsd = 4.385 "obj and name CA" index = 101 rmsd = 4.478 "obj and name CA" index = 102 rmsd = 4.000 "obj and name CA" index = 103 rmsd = 3.958 "obj and name CA" index = 104 rmsd = 4.071 "obj and name CA" index = 105 rmsd = 4.472 "obj and name CA" index = 106 rmsd = 4.567 "obj and name CA" index = 107 rmsd = 4.998 "obj and name CA" index = 108 rmsd = 4.677 "obj and name CA" index = 109 rmsd = 5.730 "obj and name CA" index = 110 rmsd = 6.882 "obj and name CA" index = 111 rmsd = 6.845 "obj and name CA" index = 112 rmsd = 5.492 "obj and name CA" index = 113 rmsd = 5.946 "obj and name CA" index = 114 rmsd = 7.575 "obj and name CA" index = 115 rmsd = 9.121 "obj and name CA" index = 116 rmsd = 10.046 "obj and name CA" index = 117 rmsd = 11.065 "obj and name CA" index = 118 rmsd = 12.864 "obj and name CA" index = 119 rmsd = 14.311 "obj and name CA" index = 120 rmsd = 16.062 "obj and name CA" index = 121 rmsd = 17.829 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 168 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 3747 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: 1.69 sec. = 2134.2 frames/hour (5.37 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit