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 PyMOL>color gray,ss ""+l Executive: Colored 2672 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: 1.68 sec. = 2147.9 frames/hour (1.68 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 480 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 480 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: 6.77 sec. = 532.0 frames/hour (8.44 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, 14.541286468505859, 12.479952812194824, 13.011494636535645, 15.356343269348145, 15.917599678039551, 15.39408016204834, 13.621443748474121, 12.47039794921875, 15.941495895385742, 14.32033634185791, 13.535151481628418, 12.65424919128418, 14.420782089233398, 14.434237480163574, 10.51653003692627, 12.129949569702148, 12.321807861328125, 12.332498550415039, 11.11329174041748] -> atom index_map = [None, 2, 21, 32, 47, 66, 86, 97, 113, 127, 148, 168, 187, 202, 216, 235, 257, 274, 291, 310, 325, 342, 356, 373, 384, 399, 411, 433, 452, 469, 479, 496, 510, 521, 542, 563, 587, 598, 614, 630, 641, 655, 674, 690, 707, 719, 736, 755, 769, 791, 805, 815, 831, 847, 866, 888, 912, 931, 948, 965, 984, 996, 1011, 1021, 1042, 1056, 1078, 1094, 1116, 1140, 1147, 1162, 1173, 1195, 1214, 1229, 1246, 1263, 1280, 1297, 1314, 1332, 1351, 1362, 1377, 1396, 1416, 1427, 1443, 1457, 1478, 1498, 1517, 1532, 1546, 1565, 1587, 1604, 1621, 1640, 1655, 1672, 1686, 1703, 1714, 1729, 1741, 1763, 1782, 1799, 1809, 1826, 1840, 1851, 1872, 1893, 1917, 1928, 1944, 1960, 1971, 1985, 2004, 2020, 2037, 2049, 2066, 2085, 2099, 2121, 2135, 2145, 2161, 2177, 2196, 2218, 2242, 2261, 2278, 2295, 2314, 2326, 2341, 2351, 2372, 2386, 2408, 2424, 2446, 2470, 2477, 2492, 2503, 2525, 2544, 2559, 2576, 2593, 2610, 2627, 2644] "obj and name CA" index = 1 rmsd = 8.845 "obj and name CA" index = 2 rmsd = 7.279 "obj and name CA" index = 3 rmsd = 5.744 "obj and name CA" index = 4 rmsd = 4.438 "obj and name CA" index = 5 rmsd = 4.662 "obj and name CA" index = 6 rmsd = 3.616 "obj and name CA" index = 7 rmsd = 2.829 "obj and name CA" index = 8 rmsd = 2.885 "obj and name CA" index = 9 rmsd = 2.403 "obj and name CA" index = 10 rmsd = 1.847 "obj and name CA" index = 11 rmsd = 1.713 "obj and name CA" index = 12 rmsd = 1.740 "obj and name CA" index = 13 rmsd = 2.403 "obj and name CA" index = 14 rmsd = 2.012 "obj and name CA" index = 15 rmsd = 1.938 "obj and name CA" index = 16 rmsd = 2.748 "obj and name CA" index = 17 rmsd = 3.526 "obj and name CA" index = 18 rmsd = 3.054 "obj and name CA" index = 19 rmsd = 2.913 "obj and name CA" index = 20 rmsd = 3.894 "obj and name CA" index = 21 rmsd = 5.161 "obj and name CA" index = 22 rmsd = 5.698 "obj and name CA" index = 23 rmsd = 6.489 "obj and name CA" index = 24 rmsd = 5.355 "obj and name CA" index = 25 rmsd = 4.656 "obj and name CA" index = 26 rmsd = 3.732 "obj and name CA" index = 27 rmsd = 3.777 "obj and name CA" index = 28 rmsd = 4.333 "obj and name CA" index = 29 rmsd = 3.690 "obj and name CA" index = 30 rmsd = 2.830 "obj and name CA" index = 31 rmsd = 3.853 "obj and name CA" index = 32 rmsd = 4.774 "obj and name CA" index = 33 rmsd = 3.638 "obj and name CA" index = 34 rmsd = 2.815 "obj and name CA" index = 35 rmsd = 4.182 "obj and name CA" index = 36 rmsd = 4.714 "obj and name CA" index = 37 rmsd = 3.308 "obj and name CA" index = 38 rmsd = 2.821 "obj and name CA" index = 39 rmsd = 4.312 "obj and name CA" index = 40 rmsd = 4.546 "obj and name CA" index = 41 rmsd = 3.034 "obj and name CA" index = 42 rmsd = 3.093 "obj and name CA" index = 43 rmsd = 4.675 "obj and name CA" index = 44 rmsd = 4.343 "obj and name CA" index = 45 rmsd = 3.882 "obj and name CA" index = 46 rmsd = 3.780 "obj and name CA" index = 47 rmsd = 3.563 "obj and name CA" index = 48 rmsd = 2.807 "obj and name CA" index = 49 rmsd = 2.097 "obj and name CA" index = 50 rmsd = 2.504 "obj and name CA" index = 51 rmsd = 2.556 "obj and name CA" index = 52 rmsd = 1.926 "obj and name CA" index = 53 rmsd = 1.664 "obj and name CA" index = 54 rmsd = 2.727 "obj and name CA" index = 55 rmsd = 2.043 "obj and name CA" index = 56 rmsd = 1.445 "obj and name CA" index = 57 rmsd = 2.615 "obj and name CA" index = 58 rmsd = 3.011 "obj and name CA" index = 59 rmsd = 1.865 "obj and name CA" index = 60 rmsd = 2.694 "obj and name CA" index = 61 rmsd = 3.755 "obj and name CA" index = 62 rmsd = 2.477 "obj and name CA" index = 63 rmsd = 2.505 "obj and name CA" index = 64 rmsd = 3.950 "obj and name CA" index = 65 rmsd = 3.740 "obj and name CA" index = 66 rmsd = 2.990 "obj and name CA" index = 67 rmsd = 3.979 "obj and name CA" index = 68 rmsd = 5.070 "obj and name CA" index = 69 rmsd = 4.340 "obj and name CA" index = 70 rmsd = 4.244 "obj and name CA" index = 71 rmsd = 5.632 "obj and name CA" index = 72 rmsd = 7.252 "obj and name CA" index = 73 rmsd = 8.178 "obj and name CA" index = 74 rmsd = 8.337 "obj and name CA" index = 75 rmsd = 9.787 "obj and name CA" index = 76 rmsd = 11.074 "obj and name CA" index = 77 rmsd = 12.479 "obj and name CA" index = 78 rmsd = 13.938 "obj and name CA" index = 79 rmsd = 15.917 "obj and name CA" index = 80 rmsd = 16.363 "obj and name CA" index = 81 rmsd = 8.846 "obj and name CA" index = 82 rmsd = 7.279 "obj and name CA" index = 83 rmsd = 5.744 "obj and name CA" index = 84 rmsd = 4.439 "obj and name CA" index = 85 rmsd = 4.662 "obj and name CA" index = 86 rmsd = 3.616 "obj and name CA" index = 87 rmsd = 2.830 "obj and name CA" index = 88 rmsd = 2.886 "obj and name CA" index = 89 rmsd = 2.403 "obj and name CA" index = 90 rmsd = 1.847 "obj and name CA" index = 91 rmsd = 1.713 "obj and name CA" index = 92 rmsd = 1.740 "obj and name CA" index = 93 rmsd = 2.403 "obj and name CA" index = 94 rmsd = 2.012 "obj and name CA" index = 95 rmsd = 1.937 "obj and name CA" index = 96 rmsd = 2.748 "obj and name CA" index = 97 rmsd = 3.526 "obj and name CA" index = 98 rmsd = 3.053 "obj and name CA" index = 99 rmsd = 2.912 "obj and name CA" index = 100 rmsd = 3.893 "obj and name CA" index = 101 rmsd = 5.161 "obj and name CA" index = 102 rmsd = 5.698 "obj and name CA" index = 103 rmsd = 6.489 "obj and name CA" index = 104 rmsd = 5.355 "obj and name CA" index = 105 rmsd = 4.656 "obj and name CA" index = 106 rmsd = 3.732 "obj and name CA" index = 107 rmsd = 3.776 "obj and name CA" index = 108 rmsd = 4.333 "obj and name CA" index = 109 rmsd = 3.690 "obj and name CA" index = 110 rmsd = 2.830 "obj and name CA" index = 111 rmsd = 3.853 "obj and name CA" index = 112 rmsd = 4.774 "obj and name CA" index = 113 rmsd = 3.638 "obj and name CA" index = 114 rmsd = 2.815 "obj and name CA" index = 115 rmsd = 4.183 "obj and name CA" index = 116 rmsd = 4.715 "obj and name CA" index = 117 rmsd = 3.308 "obj and name CA" index = 118 rmsd = 2.821 "obj and name CA" index = 119 rmsd = 4.312 "obj and name CA" index = 120 rmsd = 4.546 "obj and name CA" index = 121 rmsd = 3.034 "obj and name CA" index = 122 rmsd = 3.093 "obj and name CA" index = 123 rmsd = 4.675 "obj and name CA" index = 124 rmsd = 4.343 "obj and name CA" index = 125 rmsd = 3.883 "obj and name CA" index = 126 rmsd = 3.780 "obj and name CA" index = 127 rmsd = 3.563 "obj and name CA" index = 128 rmsd = 2.807 "obj and name CA" index = 129 rmsd = 2.097 "obj and name CA" index = 130 rmsd = 2.504 "obj and name CA" index = 131 rmsd = 2.557 "obj and name CA" index = 132 rmsd = 1.926 "obj and name CA" index = 133 rmsd = 1.664 "obj and name CA" index = 134 rmsd = 2.727 "obj and name CA" index = 135 rmsd = 2.044 "obj and name CA" index = 136 rmsd = 1.445 "obj and name CA" index = 137 rmsd = 2.615 "obj and name CA" index = 138 rmsd = 3.011 "obj and name CA" index = 139 rmsd = 1.866 "obj and name CA" index = 140 rmsd = 2.694 "obj and name CA" index = 141 rmsd = 3.755 "obj and name CA" index = 142 rmsd = 2.477 "obj and name CA" index = 143 rmsd = 2.504 "obj and name CA" index = 144 rmsd = 3.950 "obj and name CA" index = 145 rmsd = 3.739 "obj and name CA" index = 146 rmsd = 2.989 "obj and name CA" index = 147 rmsd = 3.978 "obj and name CA" index = 148 rmsd = 5.069 "obj and name CA" index = 149 rmsd = 4.339 "obj and name CA" index = 150 rmsd = 4.244 "obj and name CA" index = 151 rmsd = 5.632 "obj and name CA" index = 152 rmsd = 7.252 "obj and name CA" index = 153 rmsd = 8.177 "obj and name CA" index = 154 rmsd = 8.336 "obj and name CA" index = 155 rmsd = 9.786 "obj and name CA" index = 156 rmsd = 11.074 "obj and name CA" index = 157 rmsd = 12.478 "obj and name CA" index = 158 rmsd = 13.938 "obj and name CA" index = 159 rmsd = 15.917 "obj and name CA" index = 160 rmsd = 16.362 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 106 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 5386 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: 1.62 sec. = 2228.0 frames/hour (10.06 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit