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 49 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 1854 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: 0.80 sec. = 4519.7 frames/hour (0.80 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: 3.28 sec. = 1097.2 frames/hour (4.08 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, 13.756289482116699, 12.724454879760742, 13.822002410888672, 8.4989852905273438, 7.5608296394348145, 10.331971168518066, 15.839217185974121, 12.750574111938477, 10.390044212341309, 8.6955795288085938, 12.483251571655273, 11.277190208435059, 15.512168884277344, 6.6777949333190918, 11.916017532348633, 18.159200668334961, 12.86213493347168, 8.7093162536621094, 19.778457641601562] -> 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 = 26.476 "obj and name CA" index = 2 rmsd = 25.667 "obj and name CA" index = 3 rmsd = 25.044 "obj and name CA" index = 4 rmsd = 23.925 "obj and name CA" index = 5 rmsd = 23.216 "obj and name CA" index = 6 rmsd = 22.247 "obj and name CA" index = 7 rmsd = 20.875 "obj and name CA" index = 8 rmsd = 20.795 "obj and name CA" index = 9 rmsd = 19.510 "obj and name CA" index = 10 rmsd = 18.713 "obj and name CA" index = 11 rmsd = 17.469 "obj and name CA" index = 12 rmsd = 17.000 "obj and name CA" index = 13 rmsd = 15.958 "obj and name CA" index = 14 rmsd = 14.627 "obj and name CA" index = 15 rmsd = 13.446 "obj and name CA" index = 16 rmsd = 12.799 "obj and name CA" index = 17 rmsd = 11.695 "obj and name CA" index = 18 rmsd = 10.955 "obj and name CA" index = 19 rmsd = 9.858 "obj and name CA" index = 20 rmsd = 8.853 "obj and name CA" index = 21 rmsd = 8.249 "obj and name CA" index = 22 rmsd = 8.197 "obj and name CA" index = 23 rmsd = 7.140 "obj and name CA" index = 24 rmsd = 5.871 "obj and name CA" index = 25 rmsd = 5.784 "obj and name CA" index = 26 rmsd = 6.445 "obj and name CA" index = 27 rmsd = 5.691 "obj and name CA" index = 28 rmsd = 6.695 "obj and name CA" index = 29 rmsd = 7.675 "obj and name CA" index = 30 rmsd = 7.159 "obj and name CA" index = 31 rmsd = 5.244 "obj and name CA" index = 32 rmsd = 5.798 "obj and name CA" index = 33 rmsd = 6.778 "obj and name CA" index = 34 rmsd = 5.642 "obj and name CA" index = 35 rmsd = 4.477 "obj and name CA" index = 36 rmsd = 6.060 "obj and name CA" index = 37 rmsd = 6.578 "obj and name CA" index = 38 rmsd = 5.106 "obj and name CA" index = 39 rmsd = 5.016 "obj and name CA" index = 40 rmsd = 6.832 "obj and name CA" index = 41 rmsd = 7.000 "obj and name CA" index = 42 rmsd = 6.081 "obj and name CA" index = 43 rmsd = 7.401 "obj and name CA" index = 44 rmsd = 7.194 "obj and name CA" index = 45 rmsd = 8.666 "obj and name CA" index = 46 rmsd = 9.358 "obj and name CA" index = 47 rmsd = 8.408 "obj and name CA" index = 48 rmsd = 7.187 "obj and name CA" index = 49 rmsd = 6.026 "obj and name CA" index = 50 rmsd = 6.255 "obj and name CA" index = 51 rmsd = 6.045 "obj and name CA" index = 52 rmsd = 6.440 "obj and name CA" index = 53 rmsd = 5.633 "obj and name CA" index = 54 rmsd = 4.461 "obj and name CA" index = 55 rmsd = 5.361 "obj and name CA" index = 56 rmsd = 5.988 "obj and name CA" index = 57 rmsd = 4.876 "obj and name CA" index = 58 rmsd = 4.768 "obj and name CA" index = 59 rmsd = 6.592 "obj and name CA" index = 60 rmsd = 7.022 "obj and name CA" index = 61 rmsd = 6.188 "obj and name CA" index = 62 rmsd = 7.777 "obj and name CA" index = 63 rmsd = 6.897 "obj and name CA" index = 64 rmsd = 8.282 "obj and name CA" index = 65 rmsd = 8.198 "obj and name CA" index = 66 rmsd = 8.594 "obj and name CA" index = 67 rmsd = 6.981 "obj and name CA" index = 68 rmsd = 5.938 "obj and name CA" index = 69 rmsd = 7.000 "obj and name CA" index = 70 rmsd = 6.999 "obj and name CA" index = 71 rmsd = 5.105 "obj and name CA" index = 72 rmsd = 5.477 "obj and name CA" index = 73 rmsd = 7.396 "obj and name CA" index = 74 rmsd = 6.874 "obj and name CA" index = 75 rmsd = 5.496 "obj and name CA" index = 76 rmsd = 6.929 "obj and name CA" index = 77 rmsd = 8.626 "obj and name CA" index = 78 rmsd = 9.846 "obj and name CA" index = 79 rmsd = 9.469 "obj and name CA" index = 80 rmsd = 9.253 "obj and name CA" index = 81 rmsd = 7.962 "obj and name CA" index = 82 rmsd = 7.087 "obj and name CA" index = 83 rmsd = 6.066 "obj and name CA" index = 84 rmsd = 6.564 "obj and name CA" index = 85 rmsd = 5.987 "obj and name CA" index = 86 rmsd = 6.288 "obj and name CA" index = 87 rmsd = 5.519 "obj and name CA" index = 88 rmsd = 3.810 "obj and name CA" index = 89 rmsd = 3.829 "obj and name CA" index = 90 rmsd = 3.927 "obj and name CA" index = 91 rmsd = 2.874 "obj and name CA" index = 92 rmsd = 2.033 "obj and name CA" index = 93 rmsd = 2.712 "obj and name CA" index = 94 rmsd = 3.332 "obj and name CA" index = 95 rmsd = 3.239 "obj and name CA" index = 96 rmsd = 3.898 "obj and name CA" index = 97 rmsd = 4.628 "obj and name CA" index = 98 rmsd = 5.325 "obj and name CA" index = 99 rmsd = 5.948 "obj and name CA" index = 100 rmsd = 6.573 "obj and name CA" index = 101 rmsd = 7.333 "obj and name CA" index = 102 rmsd = 7.005 "obj and name CA" index = 103 rmsd = 7.823 "obj and name CA" index = 104 rmsd = 7.855 "obj and name CA" index = 105 rmsd = 9.556 "obj and name CA" index = 106 rmsd = 9.955 "obj and name CA" index = 107 rmsd = 10.033 "obj and name CA" index = 108 rmsd = 8.418 "obj and name CA" index = 109 rmsd = 8.983 "obj and name CA" index = 110 rmsd = 9.953 "obj and name CA" index = 111 rmsd = 8.462 "obj and name CA" index = 112 rmsd = 6.949 "obj and name CA" index = 113 rmsd = 8.490 "obj and name CA" index = 114 rmsd = 9.674 "obj and name CA" index = 115 rmsd = 11.503 "obj and name CA" index = 116 rmsd = 12.639 "obj and name CA" index = 117 rmsd = 13.557 "obj and name CA" index = 118 rmsd = 15.474 "obj and name CA" index = 119 rmsd = 16.704 "obj and name CA" index = 120 rmsd = 18.298 "obj and name CA" index = 121 rmsd = 20.057 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 147 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 3771 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: 1.55 sec. = 2319.2 frames/hour (5.63 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit