PyMOL>load ./selSi.pdb,obj HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 03-SEP-07 2JUW TITLE NMR SOLUTION STRUCTURE OF HOMODIMER PROTEIN SO_2176 FROM SHEWANELLA TITLE 2 ONEIDENSIS. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET SOR77 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UPF0352 PROTEIN SO_2176; COMPND 3 CHAIN: A, B; COMPND 4 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 2086 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 456 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: 1.88 sec. = 1913.9 frames/hour (1.88 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: 5.71 sec. = 631.0 frames/hour (7.59 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, 3.1315834522247314, 2.9943602085113525, 2.8269717693328857, 3.1363067626953125, 2.394381046295166, 3.9291634559631348, 3.9289951324462891, 3.7305285930633545, 4.4818463325500488, 3.7903385162353516, 3.248929500579834, 3.4505050182342529, 4.0054521560668945, 3.0794610977172852, 2.9093844890594482, 3.2971136569976807, 4.3771195411682129, 3.4121832847595215, 3.6870570182800293] -> atom index_map = [None, 2, 21, 31, 50, 67, 78, 100, 121, 132, 146, 160, 177, 193, 208, 219, 238, 257, 267, 282, 301, 320, 336, 352, 371, 386, 408, 426, 448, 458, 472, 486, 498, 517, 528, 547, 564, 574, 593, 600, 614, 625, 641, 655, 673, 692, 711, 726, 750, 772, 788, 802, 813, 828, 839, 863, 880, 890, 906, 916, 931, 948, 968, 978, 1000, 1010, 1029, 1039, 1056, 1067, 1083, 1105, 1116, 1130, 1149, 1164, 1182, 1200, 1218, 1236, 1254, 1273, 1292, 1302, 1321, 1338, 1349, 1371, 1392, 1403, 1417, 1431, 1448, 1464, 1479, 1490, 1509, 1528, 1538, 1553, 1572, 1591, 1607, 1623, 1642, 1657, 1679, 1697, 1719, 1729, 1743, 1757, 1769, 1788, 1799, 1818, 1835, 1845, 1864, 1871, 1885, 1896, 1912, 1926, 1944, 1963, 1982, 1997, 2021, 2043, 2059, 2073, 2084, 2099, 2110, 2134, 2151, 2161, 2177, 2187, 2202, 2219, 2239, 2249, 2271, 2281, 2300, 2310, 2327, 2338, 2354, 2376, 2387, 2401, 2420, 2435, 2453, 2471, 2489, 2507, 2525] "obj and name CA" index = 1 rmsd = 9.189 "obj and name CA" index = 2 rmsd = 7.190 "obj and name CA" index = 3 rmsd = 5.821 "obj and name CA" index = 4 rmsd = 4.039 "obj and name CA" index = 5 rmsd = 3.061 "obj and name CA" index = 6 rmsd = 2.432 "obj and name CA" index = 7 rmsd = 1.531 "obj and name CA" index = 8 rmsd = 1.788 "obj and name CA" index = 9 rmsd = 1.811 "obj and name CA" index = 10 rmsd = 1.804 "obj and name CA" index = 11 rmsd = 1.433 "obj and name CA" index = 12 rmsd = 1.104 "obj and name CA" index = 13 rmsd = 1.125 "obj and name CA" index = 14 rmsd = 1.179 "obj and name CA" index = 15 rmsd = 0.895 "obj and name CA" index = 16 rmsd = 0.799 "obj and name CA" index = 17 rmsd = 0.964 "obj and name CA" index = 18 rmsd = 0.995 "obj and name CA" index = 19 rmsd = 0.793 "obj and name CA" index = 20 rmsd = 0.903 "obj and name CA" index = 21 rmsd = 1.085 "obj and name CA" index = 22 rmsd = 0.941 "obj and name CA" index = 23 rmsd = 0.909 "obj and name CA" index = 24 rmsd = 1.232 "obj and name CA" index = 25 rmsd = 1.197 "obj and name CA" index = 26 rmsd = 1.066 "obj and name CA" index = 27 rmsd = 1.214 "obj and name CA" index = 28 rmsd = 1.011 "obj and name CA" index = 29 rmsd = 1.137 "obj and name CA" index = 30 rmsd = 1.240 "obj and name CA" index = 31 rmsd = 1.230 "obj and name CA" index = 32 rmsd = 0.903 "obj and name CA" index = 33 rmsd = 0.791 "obj and name CA" index = 34 rmsd = 0.865 "obj and name CA" index = 35 rmsd = 0.928 "obj and name CA" index = 36 rmsd = 0.760 "obj and name CA" index = 37 rmsd = 0.723 "obj and name CA" index = 38 rmsd = 0.866 "obj and name CA" index = 39 rmsd = 0.868 "obj and name CA" index = 40 rmsd = 0.717 "obj and name CA" index = 41 rmsd = 0.713 "obj and name CA" index = 42 rmsd = 0.872 "obj and name CA" index = 43 rmsd = 0.961 "obj and name CA" index = 44 rmsd = 0.933 "obj and name CA" index = 45 rmsd = 1.037 "obj and name CA" index = 46 rmsd = 1.380 "obj and name CA" index = 47 rmsd = 1.413 "obj and name CA" index = 48 rmsd = 1.309 "obj and name CA" index = 49 rmsd = 1.242 "obj and name CA" index = 50 rmsd = 1.492 "obj and name CA" index = 51 rmsd = 1.468 "obj and name CA" index = 52 rmsd = 1.656 "obj and name CA" index = 53 rmsd = 1.392 "obj and name CA" index = 54 rmsd = 1.144 "obj and name CA" index = 55 rmsd = 1.245 "obj and name CA" index = 56 rmsd = 1.267 "obj and name CA" index = 57 rmsd = 1.058 "obj and name CA" index = 58 rmsd = 0.996 "obj and name CA" index = 59 rmsd = 1.190 "obj and name CA" index = 60 rmsd = 1.131 "obj and name CA" index = 61 rmsd = 0.894 "obj and name CA" index = 62 rmsd = 1.023 "obj and name CA" index = 63 rmsd = 1.334 "obj and name CA" index = 64 rmsd = 1.190 "obj and name CA" index = 65 rmsd = 0.913 "obj and name CA" index = 66 rmsd = 1.130 "obj and name CA" index = 67 rmsd = 1.394 "obj and name CA" index = 68 rmsd = 1.234 "obj and name CA" index = 69 rmsd = 1.106 "obj and name CA" index = 70 rmsd = 1.482 "obj and name CA" index = 71 rmsd = 1.775 "obj and name CA" index = 72 rmsd = 1.616 "obj and name CA" index = 73 rmsd = 1.892 "obj and name CA" index = 74 rmsd = 2.110 "obj and name CA" index = 75 rmsd = 3.159 "obj and name CA" index = 76 rmsd = 4.377 "obj and name CA" index = 77 rmsd = 5.830 "obj and name CA" index = 78 rmsd = 6.879 "obj and name CA" index = 79 rmsd = 8.587 "obj and name CA" index = 80 rmsd = 10.330 "obj and name CA" index = 81 rmsd = 9.000 "obj and name CA" index = 82 rmsd = 7.314 "obj and name CA" index = 83 rmsd = 5.007 "obj and name CA" index = 84 rmsd = 3.537 "obj and name CA" index = 85 rmsd = 2.619 "obj and name CA" index = 86 rmsd = 2.262 "obj and name CA" index = 87 rmsd = 1.451 "obj and name CA" index = 88 rmsd = 1.493 "obj and name CA" index = 89 rmsd = 1.528 "obj and name CA" index = 90 rmsd = 1.578 "obj and name CA" index = 91 rmsd = 1.250 "obj and name CA" index = 92 rmsd = 0.986 "obj and name CA" index = 93 rmsd = 1.225 "obj and name CA" index = 94 rmsd = 1.261 "obj and name CA" index = 95 rmsd = 0.877 "obj and name CA" index = 96 rmsd = 0.791 "obj and name CA" index = 97 rmsd = 0.957 "obj and name CA" index = 98 rmsd = 0.940 "obj and name CA" index = 99 rmsd = 0.730 "obj and name CA" index = 100 rmsd = 0.809 "obj and name CA" index = 101 rmsd = 0.934 "obj and name CA" index = 102 rmsd = 0.942 "obj and name CA" index = 103 rmsd = 0.874 "obj and name CA" index = 104 rmsd = 1.142 "obj and name CA" index = 105 rmsd = 1.313 "obj and name CA" index = 106 rmsd = 1.354 "obj and name CA" index = 107 rmsd = 1.337 "obj and name CA" index = 108 rmsd = 1.042 "obj and name CA" index = 109 rmsd = 1.082 "obj and name CA" index = 110 rmsd = 0.989 "obj and name CA" index = 111 rmsd = 1.025 "obj and name CA" index = 112 rmsd = 0.913 "obj and name CA" index = 113 rmsd = 0.767 "obj and name CA" index = 114 rmsd = 0.791 "obj and name CA" index = 115 rmsd = 0.901 "obj and name CA" index = 116 rmsd = 0.767 "obj and name CA" index = 117 rmsd = 0.589 "obj and name CA" index = 118 rmsd = 0.751 "obj and name CA" index = 119 rmsd = 0.869 "obj and name CA" index = 120 rmsd = 0.726 "obj and name CA" index = 121 rmsd = 0.765 "obj and name CA" index = 122 rmsd = 0.967 "obj and name CA" index = 123 rmsd = 1.015 "obj and name CA" index = 124 rmsd = 0.961 "obj and name CA" index = 125 rmsd = 1.087 "obj and name CA" index = 126 rmsd = 1.383 "obj and name CA" index = 127 rmsd = 1.572 "obj and name CA" index = 128 rmsd = 1.555 "obj and name CA" index = 129 rmsd = 1.427 "obj and name CA" index = 130 rmsd = 1.660 "obj and name CA" index = 131 rmsd = 1.553 "obj and name CA" index = 132 rmsd = 1.732 "obj and name CA" index = 133 rmsd = 1.526 "obj and name CA" index = 134 rmsd = 1.308 "obj and name CA" index = 135 rmsd = 1.456 "obj and name CA" index = 136 rmsd = 1.551 "obj and name CA" index = 137 rmsd = 1.207 "obj and name CA" index = 138 rmsd = 1.123 "obj and name CA" index = 139 rmsd = 1.372 "obj and name CA" index = 140 rmsd = 1.337 "obj and name CA" index = 141 rmsd = 1.056 "obj and name CA" index = 142 rmsd = 1.110 "obj and name CA" index = 143 rmsd = 1.342 "obj and name CA" index = 144 rmsd = 1.219 "obj and name CA" index = 145 rmsd = 0.990 "obj and name CA" index = 146 rmsd = 1.201 "obj and name CA" index = 147 rmsd = 1.338 "obj and name CA" index = 148 rmsd = 1.134 "obj and name CA" index = 149 rmsd = 1.134 "obj and name CA" index = 150 rmsd = 1.321 "obj and name CA" index = 151 rmsd = 1.422 "obj and name CA" index = 152 rmsd = 1.649 "obj and name CA" index = 153 rmsd = 1.774 "obj and name CA" index = 154 rmsd = 2.009 "obj and name CA" index = 155 rmsd = 3.192 "obj and name CA" index = 156 rmsd = 4.643 "obj and name CA" index = 157 rmsd = 5.410 "obj and name CA" index = 158 rmsd = 6.393 "obj and name CA" index = 159 rmsd = 8.621 "obj and name CA" index = 160 rmsd = 10.168 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 4292 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 952 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: 2.25 sec. = 1597.8 frames/hour (9.84 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit