PyMOL>load ./selSi.pdb,obj HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 25-JAN-08 2K07 TITLE SOLUTION NMR STRUCTURE OF HUMAN E2-LIKE UBIQUITIN-FOLD TITLE 2 MODIFIER CONJUGATING ENZYME 1 (UFC1). NORTHEAST STRUCTURAL TITLE 3 GENOMICS CONSORTIUM TARGET HR41 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UFM1-CONJUGATING ENZYME 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UBIQUITIN-FOLD MODIFIER-CONJUGATING ENZYME 1; COMPND 5 ENGINEERED: YES ObjectMolecule: Read secondary structure assignments. 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 1164 atoms. PyMOL>color cyan,ss s Executive: Colored 444 atoms. PyMOL>color gray,ss ""+l Executive: Colored 1280 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: 1.50 sec. = 2406.8 frames/hour (1.50 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 525 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 525 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: 5.36 sec. = 671.7 frames/hour (6.86 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, 5.299598217010498, 2.9181933403015137, 5.8065805435180664, 4.612093448638916, 3.7784023284912109, 3.5888326168060303, 3.8136320114135742, 3.2175180912017822, 3.7986056804656982, 4.3700518608093262, 3.7994394302368164, 4.6332759857177734, 2.61016845703125, 5.5285477638244629, 5.2166104316711426, 3.2154586315155029, 5.0813694000244141, 3.3437948226928711, 5.3204755783081055] -> atom index_map = [None, 2, 21, 31, 43, 58, 68, 82, 106, 130, 146, 162, 173, 188, 207, 221, 237, 256, 278, 292, 306, 316, 323, 337, 361, 373, 397, 412, 431, 455, 471, 488, 512, 531, 553, 568, 583, 604, 621, 632, 651, 670, 694, 715, 731, 746, 760, 774, 796, 810, 820, 832, 846, 858, 882, 902, 926, 945, 960, 971, 985, 1007, 1022, 1029, 1043, 1067, 1091, 1111, 1118, 1140, 1151, 1175, 1196, 1215, 1233, 1245, 1264, 1283, 1305, 1326, 1341, 1361, 1373, 1392, 1407, 1427, 1439, 1458, 1472, 1491, 1505, 1526, 1540, 1554, 1568, 1578, 1592, 1607, 1626, 1636, 1652, 1666, 1681, 1700, 1712, 1719, 1741, 1755, 1765, 1787, 1804, 1825, 1849, 1856, 1863, 1885, 1904, 1915, 1934, 1948, 1960, 1978, 1998, 2020, 2034, 2053, 2077, 2087, 2111, 2125, 2141, 2155, 2177, 2197, 2204, 2223, 2233, 2251, 2270, 2287, 2297, 2316, 2323, 2342, 2349, 2363, 2387, 2406, 2416, 2432, 2447, 2466, 2480, 2492, 2511, 2530, 2547, 2569, 2576, 2592, 2611, 2628, 2646, 2668, 2683, 2705, 2716, 2730, 2747, 2766, 2781, 2799, 2817, 2835, 2853, 2871] "obj and name CA" index = 1 rmsd = 5.342 "obj and name CA" index = 2 rmsd = 3.763 "obj and name CA" index = 3 rmsd = 2.346 "obj and name CA" index = 4 rmsd = 2.387 "obj and name CA" index = 5 rmsd = 2.201 "obj and name CA" index = 6 rmsd = 1.800 "obj and name CA" index = 7 rmsd = 1.798 "obj and name CA" index = 8 rmsd = 1.814 "obj and name CA" index = 9 rmsd = 1.590 "obj and name CA" index = 10 rmsd = 1.403 "obj and name CA" index = 11 rmsd = 1.492 "obj and name CA" index = 12 rmsd = 1.456 "obj and name CA" index = 13 rmsd = 1.124 "obj and name CA" index = 14 rmsd = 1.162 "obj and name CA" index = 15 rmsd = 0.970 "obj and name CA" index = 16 rmsd = 1.083 "obj and name CA" index = 17 rmsd = 1.572 "obj and name CA" index = 18 rmsd = 1.465 "obj and name CA" index = 19 rmsd = 1.479 "obj and name CA" index = 20 rmsd = 1.646 "obj and name CA" index = 21 rmsd = 1.577 "obj and name CA" index = 22 rmsd = 1.420 "obj and name CA" index = 23 rmsd = 1.832 "obj and name CA" index = 24 rmsd = 1.820 "obj and name CA" index = 25 rmsd = 1.827 "obj and name CA" index = 26 rmsd = 1.970 "obj and name CA" index = 27 rmsd = 1.686 "obj and name CA" index = 28 rmsd = 1.449 "obj and name CA" index = 29 rmsd = 1.627 "obj and name CA" index = 30 rmsd = 1.490 "obj and name CA" index = 31 rmsd = 1.250 "obj and name CA" index = 32 rmsd = 1.315 "obj and name CA" index = 33 rmsd = 1.417 "obj and name CA" index = 34 rmsd = 1.259 "obj and name CA" index = 35 rmsd = 1.108 "obj and name CA" index = 36 rmsd = 1.350 "obj and name CA" index = 37 rmsd = 1.469 "obj and name CA" index = 38 rmsd = 1.245 "obj and name CA" index = 39 rmsd = 1.259 "obj and name CA" index = 40 rmsd = 1.619 "obj and name CA" index = 41 rmsd = 1.650 "obj and name CA" index = 42 rmsd = 1.572 "obj and name CA" index = 43 rmsd = 1.793 "obj and name CA" index = 44 rmsd = 2.029 "obj and name CA" index = 45 rmsd = 1.893 "obj and name CA" index = 46 rmsd = 2.044 "obj and name CA" index = 47 rmsd = 2.234 "obj and name CA" index = 48 rmsd = 2.370 "obj and name CA" index = 49 rmsd = 2.353 "obj and name CA" index = 50 rmsd = 2.536 "obj and name CA" index = 51 rmsd = 2.218 "obj and name CA" index = 52 rmsd = 2.090 "obj and name CA" index = 53 rmsd = 2.113 "obj and name CA" index = 54 rmsd = 1.680 "obj and name CA" index = 55 rmsd = 1.675 "obj and name CA" index = 56 rmsd = 1.428 "obj and name CA" index = 57 rmsd = 1.505 "obj and name CA" index = 58 rmsd = 1.327 "obj and name CA" index = 59 rmsd = 1.533 "obj and name CA" index = 60 rmsd = 1.842 "obj and name CA" index = 61 rmsd = 1.681 "obj and name CA" index = 62 rmsd = 1.359 "obj and name CA" index = 63 rmsd = 1.300 "obj and name CA" index = 64 rmsd = 1.158 "obj and name CA" index = 65 rmsd = 1.070 "obj and name CA" index = 66 rmsd = 1.219 "obj and name CA" index = 67 rmsd = 1.509 "obj and name CA" index = 68 rmsd = 1.620 "obj and name CA" index = 69 rmsd = 1.710 "obj and name CA" index = 70 rmsd = 2.210 "obj and name CA" index = 71 rmsd = 2.522 "obj and name CA" index = 72 rmsd = 2.790 "obj and name CA" index = 73 rmsd = 3.060 "obj and name CA" index = 74 rmsd = 3.364 "obj and name CA" index = 75 rmsd = 3.234 "obj and name CA" index = 76 rmsd = 2.805 "obj and name CA" index = 77 rmsd = 2.529 "obj and name CA" index = 78 rmsd = 2.264 "obj and name CA" index = 79 rmsd = 1.906 "obj and name CA" index = 80 rmsd = 1.780 "obj and name CA" index = 81 rmsd = 1.595 "obj and name CA" index = 82 rmsd = 1.284 "obj and name CA" index = 83 rmsd = 1.125 "obj and name CA" index = 84 rmsd = 0.967 "obj and name CA" index = 85 rmsd = 0.986 "obj and name CA" index = 86 rmsd = 0.937 "obj and name CA" index = 87 rmsd = 1.081 "obj and name CA" index = 88 rmsd = 1.341 "obj and name CA" index = 89 rmsd = 1.301 "obj and name CA" index = 90 rmsd = 1.034 "obj and name CA" index = 91 rmsd = 1.077 "obj and name CA" index = 92 rmsd = 1.330 "obj and name CA" index = 93 rmsd = 1.163 "obj and name CA" index = 94 rmsd = 0.795 "obj and name CA" index = 95 rmsd = 1.012 "obj and name CA" index = 96 rmsd = 1.026 "obj and name CA" index = 97 rmsd = 0.901 "obj and name CA" index = 98 rmsd = 0.980 "obj and name CA" index = 99 rmsd = 1.226 "obj and name CA" index = 100 rmsd = 1.466 "obj and name CA" index = 101 rmsd = 1.673 "obj and name CA" index = 102 rmsd = 1.576 "obj and name CA" index = 103 rmsd = 1.790 "obj and name CA" index = 104 rmsd = 2.210 "obj and name CA" index = 105 rmsd = 2.336 "obj and name CA" index = 106 rmsd = 2.018 "obj and name CA" index = 107 rmsd = 2.548 "obj and name CA" index = 108 rmsd = 2.967 "obj and name CA" index = 109 rmsd = 2.062 "obj and name CA" index = 110 rmsd = 2.108 "obj and name CA" index = 111 rmsd = 2.311 "obj and name CA" index = 112 rmsd = 1.898 "obj and name CA" index = 113 rmsd = 1.486 "obj and name CA" index = 114 rmsd = 1.282 "obj and name CA" index = 115 rmsd = 1.188 "obj and name CA" index = 116 rmsd = 1.494 "obj and name CA" index = 117 rmsd = 1.281 "obj and name CA" index = 118 rmsd = 1.367 "obj and name CA" index = 119 rmsd = 1.471 "obj and name CA" index = 120 rmsd = 1.493 "obj and name CA" index = 121 rmsd = 1.150 "obj and name CA" index = 122 rmsd = 1.308 "obj and name CA" index = 123 rmsd = 1.519 "obj and name CA" index = 124 rmsd = 1.227 "obj and name CA" index = 125 rmsd = 0.903 "obj and name CA" index = 126 rmsd = 1.280 "obj and name CA" index = 127 rmsd = 1.452 "obj and name CA" index = 128 rmsd = 1.206 "obj and name CA" index = 129 rmsd = 1.108 "obj and name CA" index = 130 rmsd = 1.092 "obj and name CA" index = 131 rmsd = 1.065 "obj and name CA" index = 132 rmsd = 0.842 "obj and name CA" index = 133 rmsd = 0.867 "obj and name CA" index = 134 rmsd = 0.722 "obj and name CA" index = 135 rmsd = 0.816 "obj and name CA" index = 136 rmsd = 0.774 "obj and name CA" index = 137 rmsd = 0.717 "obj and name CA" index = 138 rmsd = 0.904 "obj and name CA" index = 139 rmsd = 1.054 "obj and name CA" index = 140 rmsd = 0.963 "obj and name CA" index = 141 rmsd = 0.871 "obj and name CA" index = 142 rmsd = 0.986 "obj and name CA" index = 143 rmsd = 1.404 "obj and name CA" index = 144 rmsd = 1.449 "obj and name CA" index = 145 rmsd = 1.273 "obj and name CA" index = 146 rmsd = 1.575 "obj and name CA" index = 147 rmsd = 1.987 "obj and name CA" index = 148 rmsd = 1.946 "obj and name CA" index = 149 rmsd = 1.914 "obj and name CA" index = 150 rmsd = 1.911 "obj and name CA" index = 151 rmsd = 2.368 "obj and name CA" index = 152 rmsd = 2.410 "obj and name CA" index = 153 rmsd = 2.206 "obj and name CA" index = 154 rmsd = 2.353 "obj and name CA" index = 155 rmsd = 2.615 "obj and name CA" index = 156 rmsd = 2.626 "obj and name CA" index = 157 rmsd = 2.764 "obj and name CA" index = 158 rmsd = 2.595 "obj and name CA" index = 159 rmsd = 2.499 "obj and name CA" index = 160 rmsd = 3.106 "obj and name CA" index = 161 rmsd = 3.589 "obj and name CA" index = 162 rmsd = 3.816 "obj and name CA" index = 163 rmsd = 3.492 "obj and name CA" index = 164 rmsd = 4.310 "obj and name CA" index = 165 rmsd = 4.771 "obj and name CA" index = 166 rmsd = 5.491 "obj and name CA" index = 167 rmsd = 5.985 "obj and name CA" index = 168 rmsd = 6.996 "obj and name CA" index = 169 rmsd = 8.596 "obj and name CA" index = 170 rmsd = 11.029 "obj and name CA" index = 171 rmsd = 13.044 "obj and name CA" index = 172 rmsd = 14.537 "obj and name CA" index = 173 rmsd = 16.347 "obj and name CA" index = 174 rmsd = 17.869 "obj and name CA" index = 175 rmsd = 20.092 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 2393 atoms. PyMOL>color cyan,ss s Executive: Colored 903 atoms. PyMOL>color gray,ss ""+l Executive: Colored 2655 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: 2.21 sec. = 1631.4 frames/hour (9.06 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit