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 90 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 2047 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: 1.90 sec. = 1899.5 frames/hour (1.90 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 387 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 387 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: 5.68 sec. = 634.2 frames/hour (7.57 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, 4.4631781578063965, 3.2118422985076904, 3.6000113487243652, 3.6869742870330811, 3.9805822372436523, 2.8985612392425537, 4.1354641914367676, 3.5953483581542969, 3.3364639282226562, 3.6547338962554932, 2.7850942611694336, 2.8179185390472412, 2.4691781997680664, 2.9718852043151855, 2.9090769290924072, 3.5119333267211914, 3.6189620494842529, 3.5300784111022949, 3.5236871242523193] -> atom index_map = [None, 2, 21, 32, 51, 62, 76, 87, 97, 112, 128, 149, 170, 185, 200, 210, 225, 240, 260, 279, 290, 312, 319, 331, 350, 366, 383, 393, 404, 419, 441, 462, 483, 505, 515, 525, 540, 555, 565, 584, 606, 625, 644, 660, 679, 694, 708, 722, 741, 763, 778, 797, 811, 825, 839, 855, 877, 891, 913, 920, 944, 968, 990, 1001, 1016, 1030, 1049, 1069, 1091, 1101, 1112, 1134, 1153, 1172, 1196, 1207, 1221, 1235, 1249, 1264, 1283, 1297, 1316, 1335, 1359, 1381, 1392, 1402, 1426, 1440, 1459, 1476, 1492, 1507, 1514, 1534, 1551, 1566, 1585, 1596, 1615, 1629, 1644, 1666, 1681, 1697, 1719, 1741, 1760, 1782, 1797, 1809, 1825, 1849, 1871, 1890, 1906, 1925, 1945, 1955, 1971, 1985, 1996, 2015, 2030, 2047, 2064, 2081, 2098, 2115] "obj and name CA" index = 1 rmsd = 8.285 "obj and name CA" index = 2 rmsd = 6.238 "obj and name CA" index = 3 rmsd = 3.398 "obj and name CA" index = 4 rmsd = 1.273 "obj and name CA" index = 5 rmsd = 0.867 "obj and name CA" index = 6 rmsd = 0.793 "obj and name CA" index = 7 rmsd = 0.677 "obj and name CA" index = 8 rmsd = 0.640 "obj and name CA" index = 9 rmsd = 0.660 "obj and name CA" index = 10 rmsd = 0.556 "obj and name CA" index = 11 rmsd = 0.554 "obj and name CA" index = 12 rmsd = 0.731 "obj and name CA" index = 13 rmsd = 0.715 "obj and name CA" index = 14 rmsd = 0.646 "obj and name CA" index = 15 rmsd = 0.800 "obj and name CA" index = 16 rmsd = 0.936 "obj and name CA" index = 17 rmsd = 0.888 "obj and name CA" index = 18 rmsd = 0.910 "obj and name CA" index = 19 rmsd = 1.131 "obj and name CA" index = 20 rmsd = 1.159 "obj and name CA" index = 21 rmsd = 1.050 "obj and name CA" index = 22 rmsd = 0.916 "obj and name CA" index = 23 rmsd = 0.810 "obj and name CA" index = 24 rmsd = 0.823 "obj and name CA" index = 25 rmsd = 0.734 "obj and name CA" index = 26 rmsd = 0.680 "obj and name CA" index = 27 rmsd = 0.670 "obj and name CA" index = 28 rmsd = 0.660 "obj and name CA" index = 29 rmsd = 0.606 "obj and name CA" index = 30 rmsd = 0.771 "obj and name CA" index = 31 rmsd = 0.594 "obj and name CA" index = 32 rmsd = 0.472 "obj and name CA" index = 33 rmsd = 0.427 "obj and name CA" index = 34 rmsd = 0.423 "obj and name CA" index = 35 rmsd = 0.489 "obj and name CA" index = 36 rmsd = 0.474 "obj and name CA" index = 37 rmsd = 0.500 "obj and name CA" index = 38 rmsd = 0.524 "obj and name CA" index = 39 rmsd = 0.572 "obj and name CA" index = 40 rmsd = 0.672 "obj and name CA" index = 41 rmsd = 0.749 "obj and name CA" index = 42 rmsd = 0.821 "obj and name CA" index = 43 rmsd = 0.864 "obj and name CA" index = 44 rmsd = 0.911 "obj and name CA" index = 45 rmsd = 1.030 "obj and name CA" index = 46 rmsd = 1.258 "obj and name CA" index = 47 rmsd = 0.933 "obj and name CA" index = 48 rmsd = 1.030 "obj and name CA" index = 49 rmsd = 0.988 "obj and name CA" index = 50 rmsd = 0.762 "obj and name CA" index = 51 rmsd = 0.825 "obj and name CA" index = 52 rmsd = 1.013 "obj and name CA" index = 53 rmsd = 0.959 "obj and name CA" index = 54 rmsd = 0.975 "obj and name CA" index = 55 rmsd = 1.251 "obj and name CA" index = 56 rmsd = 1.457 "obj and name CA" index = 57 rmsd = 1.524 "obj and name CA" index = 58 rmsd = 2.078 "obj and name CA" index = 59 rmsd = 1.405 "obj and name CA" index = 60 rmsd = 0.863 "obj and name CA" index = 61 rmsd = 1.217 "obj and name CA" index = 62 rmsd = 0.978 "obj and name CA" index = 63 rmsd = 1.125 "obj and name CA" index = 64 rmsd = 0.935 "obj and name CA" index = 65 rmsd = 0.629 "obj and name CA" index = 66 rmsd = 0.861 "obj and name CA" index = 67 rmsd = 0.977 "obj and name CA" index = 68 rmsd = 0.806 "obj and name CA" index = 69 rmsd = 0.845 "obj and name CA" index = 70 rmsd = 1.002 "obj and name CA" index = 71 rmsd = 1.004 "obj and name CA" index = 72 rmsd = 0.975 "obj and name CA" index = 73 rmsd = 1.033 "obj and name CA" index = 74 rmsd = 1.434 "obj and name CA" index = 75 rmsd = 1.352 "obj and name CA" index = 76 rmsd = 1.015 "obj and name CA" index = 77 rmsd = 0.820 "obj and name CA" index = 78 rmsd = 0.842 "obj and name CA" index = 79 rmsd = 0.759 "obj and name CA" index = 80 rmsd = 0.725 "obj and name CA" index = 81 rmsd = 0.793 "obj and name CA" index = 82 rmsd = 0.680 "obj and name CA" index = 83 rmsd = 0.622 "obj and name CA" index = 84 rmsd = 0.745 "obj and name CA" index = 85 rmsd = 0.665 "obj and name CA" index = 86 rmsd = 0.655 "obj and name CA" index = 87 rmsd = 0.856 "obj and name CA" index = 88 rmsd = 0.786 "obj and name CA" index = 89 rmsd = 1.128 "obj and name CA" index = 90 rmsd = 1.474 "obj and name CA" index = 91 rmsd = 1.405 "obj and name CA" index = 92 rmsd = 1.558 "obj and name CA" index = 93 rmsd = 2.240 "obj and name CA" index = 94 rmsd = 3.562 "obj and name CA" index = 95 rmsd = 3.978 "obj and name CA" index = 96 rmsd = 3.159 "obj and name CA" index = 97 rmsd = 2.718 "obj and name CA" index = 98 rmsd = 1.491 "obj and name CA" index = 99 rmsd = 1.169 "obj and name CA" index = 100 rmsd = 1.065 "obj and name CA" index = 101 rmsd = 0.850 "obj and name CA" index = 102 rmsd = 0.943 "obj and name CA" index = 103 rmsd = 0.833 "obj and name CA" index = 104 rmsd = 0.613 "obj and name CA" index = 105 rmsd = 0.704 "obj and name CA" index = 106 rmsd = 0.683 "obj and name CA" index = 107 rmsd = 0.651 "obj and name CA" index = 108 rmsd = 0.692 "obj and name CA" index = 109 rmsd = 0.774 "obj and name CA" index = 110 rmsd = 0.707 "obj and name CA" index = 111 rmsd = 0.524 "obj and name CA" index = 112 rmsd = 0.614 "obj and name CA" index = 113 rmsd = 0.725 "obj and name CA" index = 114 rmsd = 0.608 "obj and name CA" index = 115 rmsd = 0.611 "obj and name CA" index = 116 rmsd = 0.744 "obj and name CA" index = 117 rmsd = 0.743 "obj and name CA" index = 118 rmsd = 0.681 "obj and name CA" index = 119 rmsd = 0.796 "obj and name CA" index = 120 rmsd = 0.893 "obj and name CA" index = 121 rmsd = 0.912 "obj and name CA" index = 122 rmsd = 0.919 "obj and name CA" index = 123 rmsd = 1.030 "obj and name CA" index = 124 rmsd = 2.800 "obj and name CA" index = 125 rmsd = 4.674 "obj and name CA" index = 126 rmsd = 5.530 "obj and name CA" index = 127 rmsd = 5.988 "obj and name CA" index = 128 rmsd = 7.110 "obj and name CA" index = 129 rmsd = 9.113 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 270 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 4127 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: 2.15 sec. = 1678.3 frames/hour (9.72 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit