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 PyMOL>color cyan,ss s Executive: Colored 76 atoms. PyMOL>color gray,ss ""+l Executive: Colored 2212 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: 1.47 sec. = 2456.1 frames/hour (1.47 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 426 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 426 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: 6.11 sec. = 589.4 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, 3.2882926464080811, 3.2878878116607666, 4.7695260047912598, 3.3687787055969238, 3.7998738288879395, 3.4997475147247314, 3.7595486640930176, 2.9851274490356445, 3.1653823852539062, 4.3620109558105469, 2.7228245735168457, 3.7740259170532227, 4.3628664016723633, 3.8249514102935791, 3.6975476741790771, 3.1351747512817383, 3.0819587707519531, 3.0823748111724854, 3.1551709175109863] -> atom index_map = [None, 2, 21, 33, 47, 71, 88, 108, 127, 138, 157, 171, 178, 194, 205, 227, 243, 260, 271, 291, 303, 317, 339, 354, 373, 392, 411, 426, 440, 459, 476, 483, 499, 518, 529, 548, 570, 577, 592, 614, 633, 640, 659, 681, 698, 717, 729, 748, 770, 780, 787, 804, 820, 835, 851, 866, 873, 892, 911, 923, 933, 952, 968, 989, 1003, 1022, 1037, 1054, 1071, 1088, 1105, 1122, 1140, 1159, 1171, 1185, 1209, 1226, 1246, 1265, 1276, 1295, 1309, 1316, 1332, 1343, 1365, 1381, 1398, 1409, 1429, 1441, 1455, 1477, 1492, 1511, 1530, 1549, 1564, 1578, 1597, 1614, 1621, 1637, 1656, 1667, 1686, 1708, 1715, 1730, 1752, 1771, 1778, 1797, 1819, 1836, 1855, 1867, 1886, 1908, 1918, 1925, 1942, 1958, 1973, 1989, 2004, 2011, 2030, 2049, 2061, 2071, 2090, 2106, 2127, 2141, 2160, 2175, 2192, 2209, 2226, 2243, 2260] "obj and name CA" index = 1 rmsd = 4.080 "obj and name CA" index = 2 rmsd = 2.302 "obj and name CA" index = 3 rmsd = 1.242 "obj and name CA" index = 4 rmsd = 1.028 "obj and name CA" index = 5 rmsd = 0.784 "obj and name CA" index = 6 rmsd = 0.664 "obj and name CA" index = 7 rmsd = 0.582 "obj and name CA" index = 8 rmsd = 0.563 "obj and name CA" index = 9 rmsd = 0.550 "obj and name CA" index = 10 rmsd = 0.623 "obj and name CA" index = 11 rmsd = 0.704 "obj and name CA" index = 12 rmsd = 0.669 "obj and name CA" index = 13 rmsd = 0.795 "obj and name CA" index = 14 rmsd = 0.862 "obj and name CA" index = 15 rmsd = 0.813 "obj and name CA" index = 16 rmsd = 0.872 "obj and name CA" index = 17 rmsd = 0.871 "obj and name CA" index = 18 rmsd = 0.873 "obj and name CA" index = 19 rmsd = 0.945 "obj and name CA" index = 20 rmsd = 0.963 "obj and name CA" index = 21 rmsd = 0.868 "obj and name CA" index = 22 rmsd = 0.795 "obj and name CA" index = 23 rmsd = 0.741 "obj and name CA" index = 24 rmsd = 0.707 "obj and name CA" index = 25 rmsd = 0.677 "obj and name CA" index = 26 rmsd = 0.736 "obj and name CA" index = 27 rmsd = 0.699 "obj and name CA" index = 28 rmsd = 0.925 "obj and name CA" index = 29 rmsd = 1.533 "obj and name CA" index = 30 rmsd = 0.827 "obj and name CA" index = 31 rmsd = 0.779 "obj and name CA" index = 32 rmsd = 0.661 "obj and name CA" index = 33 rmsd = 0.669 "obj and name CA" index = 34 rmsd = 0.716 "obj and name CA" index = 35 rmsd = 0.771 "obj and name CA" index = 36 rmsd = 0.822 "obj and name CA" index = 37 rmsd = 0.911 "obj and name CA" index = 38 rmsd = 0.923 "obj and name CA" index = 39 rmsd = 0.814 "obj and name CA" index = 40 rmsd = 0.891 "obj and name CA" index = 41 rmsd = 1.512 "obj and name CA" index = 42 rmsd = 2.317 "obj and name CA" index = 43 rmsd = 3.031 "obj and name CA" index = 44 rmsd = 3.190 "obj and name CA" index = 45 rmsd = 2.475 "obj and name CA" index = 46 rmsd = 1.543 "obj and name CA" index = 47 rmsd = 1.884 "obj and name CA" index = 48 rmsd = 1.529 "obj and name CA" index = 49 rmsd = 0.784 "obj and name CA" index = 50 rmsd = 0.666 "obj and name CA" index = 51 rmsd = 0.605 "obj and name CA" index = 52 rmsd = 0.645 "obj and name CA" index = 53 rmsd = 0.714 "obj and name CA" index = 54 rmsd = 0.785 "obj and name CA" index = 55 rmsd = 0.846 "obj and name CA" index = 56 rmsd = 0.900 "obj and name CA" index = 57 rmsd = 0.896 "obj and name CA" index = 58 rmsd = 0.997 "obj and name CA" index = 59 rmsd = 0.898 "obj and name CA" index = 60 rmsd = 0.768 "obj and name CA" index = 61 rmsd = 0.704 "obj and name CA" index = 62 rmsd = 0.652 "obj and name CA" index = 63 rmsd = 1.160 "obj and name CA" index = 64 rmsd = 2.139 "obj and name CA" index = 65 rmsd = 3.636 "obj and name CA" index = 66 rmsd = 4.661 "obj and name CA" index = 67 rmsd = 6.484 "obj and name CA" index = 68 rmsd = 8.509 "obj and name CA" index = 69 rmsd = 10.115 "obj and name CA" index = 70 rmsd = 11.411 "obj and name CA" index = 71 rmsd = 12.510 "obj and name CA" index = 72 rmsd = 4.080 "obj and name CA" index = 73 rmsd = 2.302 "obj and name CA" index = 74 rmsd = 1.242 "obj and name CA" index = 75 rmsd = 1.028 "obj and name CA" index = 76 rmsd = 0.783 "obj and name CA" index = 77 rmsd = 0.664 "obj and name CA" index = 78 rmsd = 0.582 "obj and name CA" index = 79 rmsd = 0.563 "obj and name CA" index = 80 rmsd = 0.550 "obj and name CA" index = 81 rmsd = 0.623 "obj and name CA" index = 82 rmsd = 0.704 "obj and name CA" index = 83 rmsd = 0.669 "obj and name CA" index = 84 rmsd = 0.795 "obj and name CA" index = 85 rmsd = 0.862 "obj and name CA" index = 86 rmsd = 0.813 "obj and name CA" index = 87 rmsd = 0.872 "obj and name CA" index = 88 rmsd = 0.871 "obj and name CA" index = 89 rmsd = 0.873 "obj and name CA" index = 90 rmsd = 0.945 "obj and name CA" index = 91 rmsd = 0.963 "obj and name CA" index = 92 rmsd = 0.868 "obj and name CA" index = 93 rmsd = 0.795 "obj and name CA" index = 94 rmsd = 0.741 "obj and name CA" index = 95 rmsd = 0.707 "obj and name CA" index = 96 rmsd = 0.677 "obj and name CA" index = 97 rmsd = 0.736 "obj and name CA" index = 98 rmsd = 0.699 "obj and name CA" index = 99 rmsd = 0.925 "obj and name CA" index = 100 rmsd = 1.533 "obj and name CA" index = 101 rmsd = 0.827 "obj and name CA" index = 102 rmsd = 0.780 "obj and name CA" index = 103 rmsd = 0.660 "obj and name CA" index = 104 rmsd = 0.670 "obj and name CA" index = 105 rmsd = 0.716 "obj and name CA" index = 106 rmsd = 0.771 "obj and name CA" index = 107 rmsd = 0.821 "obj and name CA" index = 108 rmsd = 0.911 "obj and name CA" index = 109 rmsd = 0.923 "obj and name CA" index = 110 rmsd = 0.814 "obj and name CA" index = 111 rmsd = 0.891 "obj and name CA" index = 112 rmsd = 1.512 "obj and name CA" index = 113 rmsd = 2.317 "obj and name CA" index = 114 rmsd = 3.031 "obj and name CA" index = 115 rmsd = 3.190 "obj and name CA" index = 116 rmsd = 2.475 "obj and name CA" index = 117 rmsd = 1.543 "obj and name CA" index = 118 rmsd = 1.884 "obj and name CA" index = 119 rmsd = 1.530 "obj and name CA" index = 120 rmsd = 0.785 "obj and name CA" index = 121 rmsd = 0.666 "obj and name CA" index = 122 rmsd = 0.605 "obj and name CA" index = 123 rmsd = 0.645 "obj and name CA" index = 124 rmsd = 0.714 "obj and name CA" index = 125 rmsd = 0.786 "obj and name CA" index = 126 rmsd = 0.845 "obj and name CA" index = 127 rmsd = 0.900 "obj and name CA" index = 128 rmsd = 0.895 "obj and name CA" index = 129 rmsd = 0.997 "obj and name CA" index = 130 rmsd = 0.898 "obj and name CA" index = 131 rmsd = 0.769 "obj and name CA" index = 132 rmsd = 0.704 "obj and name CA" index = 133 rmsd = 0.652 "obj and name CA" index = 134 rmsd = 1.160 "obj and name CA" index = 135 rmsd = 2.139 "obj and name CA" index = 136 rmsd = 3.636 "obj and name CA" index = 137 rmsd = 4.661 "obj and name CA" index = 138 rmsd = 6.484 "obj and name CA" index = 139 rmsd = 8.509 "obj and name CA" index = 140 rmsd = 10.115 "obj and name CA" index = 141 rmsd = 11.412 "obj and name CA" index = 142 rmsd = 12.510 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h PyMOL>color cyan,ss s Executive: Colored 228 atoms. PyMOL>color gray,ss ""+l Executive: Colored 4478 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: 2.32 sec. = 1555.0 frames/hour (9.89 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit