PyMOL>load ./selSi.pdb,obj HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 01-APR-08 2K2E TITLE SOLUTION NMR STRUCTURE OF BORDETELLA PERTUSSIS PROTEIN TITLE 2 BP2786, A MTH938-LIKE DOMAIN. NORTHEAST STRUCTURAL TITLE 3 GENOMICS CONSORTIUM TARGET BER31 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN BP2786; COMPND 3 CHAIN: A; 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 603 atoms. PyMOL>color cyan,ss s Executive: Colored 434 atoms. PyMOL>color gray,ss ""+l Executive: Colored 1330 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: 1.55 sec. = 2323.4 frames/hour (1.55 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 474 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 474 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: 5.46 sec. = 659.5 frames/hour (7.01 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, 6.1107206344604492, 5.2386479377746582, 6.0445189476013184, 4.7093572616577148, 8.894108772277832, 6.4562888145446777, 5.9758725166320801, 6.2425117492675781, 5.7862615585327148, 6.5868759155273438, 6.2918977737426758, 8.4903278350830078, 7.6823701858520508, 10.432140350341797, 6.6925902366638184, 6.5410585403442383, 9.7328176498413086, 4.2493171691894531, 7.2332096099853516] -> atom index_map = [None, 2, 21, 43, 62, 80, 94, 106, 120, 130, 144, 154, 173, 187, 201, 217, 231, 241, 262, 269, 281, 288, 309, 328, 343, 359, 373, 390, 406, 430, 450, 461, 479, 489, 508, 518, 538, 548, 562, 577, 584, 598, 614, 624, 635, 659, 673, 689, 706, 730, 744, 754, 766, 785, 799, 809, 820, 839, 858, 875, 892, 902, 912, 919, 938, 948, 963, 979, 995, 1019, 1031, 1045, 1064, 1074, 1094, 1113, 1125, 1140, 1154, 1169, 1179, 1186, 1196, 1203, 1213, 1237, 1251, 1261, 1275, 1285, 1299, 1314, 1330, 1349, 1368, 1384, 1391, 1405, 1412, 1436, 1460, 1477, 1495, 1514, 1533, 1540, 1554, 1569, 1586, 1602, 1626, 1640, 1659, 1678, 1688, 1705, 1712, 1728, 1735, 1751, 1766, 1776, 1793, 1805, 1819, 1836, 1846, 1856, 1866, 1890, 1904, 1925, 1939, 1958, 1977, 1994, 2004, 2019, 2026, 2050, 2074, 2090, 2106, 2122, 2132, 2151, 2170, 2184, 2196, 2203, 2215, 2226, 2245, 2260, 2278, 2296, 2314, 2332, 2350] "obj and name CA" index = 1 rmsd = 15.256 "obj and name CA" index = 2 rmsd = 13.960 "obj and name CA" index = 3 rmsd = 12.605 "obj and name CA" index = 4 rmsd = 11.844 "obj and name CA" index = 5 rmsd = 10.450 "obj and name CA" index = 6 rmsd = 8.258 "obj and name CA" index = 7 rmsd = 6.417 "obj and name CA" index = 8 rmsd = 4.571 "obj and name CA" index = 9 rmsd = 3.624 "obj and name CA" index = 10 rmsd = 2.819 "obj and name CA" index = 11 rmsd = 2.473 "obj and name CA" index = 12 rmsd = 2.090 "obj and name CA" index = 13 rmsd = 2.060 "obj and name CA" index = 14 rmsd = 1.954 "obj and name CA" index = 15 rmsd = 2.479 "obj and name CA" index = 16 rmsd = 2.497 "obj and name CA" index = 17 rmsd = 2.440 "obj and name CA" index = 18 rmsd = 3.195 "obj and name CA" index = 19 rmsd = 3.078 "obj and name CA" index = 20 rmsd = 2.785 "obj and name CA" index = 21 rmsd = 2.453 "obj and name CA" index = 22 rmsd = 2.012 "obj and name CA" index = 23 rmsd = 2.264 "obj and name CA" index = 24 rmsd = 2.126 "obj and name CA" index = 25 rmsd = 2.544 "obj and name CA" index = 26 rmsd = 3.054 "obj and name CA" index = 27 rmsd = 2.525 "obj and name CA" index = 28 rmsd = 2.499 "obj and name CA" index = 29 rmsd = 2.170 "obj and name CA" index = 30 rmsd = 2.312 "obj and name CA" index = 31 rmsd = 2.105 "obj and name CA" index = 32 rmsd = 1.623 "obj and name CA" index = 33 rmsd = 1.423 "obj and name CA" index = 34 rmsd = 1.207 "obj and name CA" index = 35 rmsd = 1.352 "obj and name CA" index = 36 rmsd = 1.492 "obj and name CA" index = 37 rmsd = 1.894 "obj and name CA" index = 38 rmsd = 2.122 "obj and name CA" index = 39 rmsd = 2.090 "obj and name CA" index = 40 rmsd = 2.034 "obj and name CA" index = 41 rmsd = 1.834 "obj and name CA" index = 42 rmsd = 1.895 "obj and name CA" index = 43 rmsd = 2.039 "obj and name CA" index = 44 rmsd = 1.945 "obj and name CA" index = 45 rmsd = 2.348 "obj and name CA" index = 46 rmsd = 2.099 "obj and name CA" index = 47 rmsd = 2.315 "obj and name CA" index = 48 rmsd = 2.290 "obj and name CA" index = 49 rmsd = 1.997 "obj and name CA" index = 50 rmsd = 2.552 "obj and name CA" index = 51 rmsd = 2.546 "obj and name CA" index = 52 rmsd = 2.022 "obj and name CA" index = 53 rmsd = 2.364 "obj and name CA" index = 54 rmsd = 2.273 "obj and name CA" index = 55 rmsd = 2.388 "obj and name CA" index = 56 rmsd = 2.068 "obj and name CA" index = 57 rmsd = 1.713 "obj and name CA" index = 58 rmsd = 1.976 "obj and name CA" index = 59 rmsd = 2.007 "obj and name CA" index = 60 rmsd = 1.567 "obj and name CA" index = 61 rmsd = 1.651 "obj and name CA" index = 62 rmsd = 2.054 "obj and name CA" index = 63 rmsd = 2.337 "obj and name CA" index = 64 rmsd = 2.933 "obj and name CA" index = 65 rmsd = 3.684 "obj and name CA" index = 66 rmsd = 3.915 "obj and name CA" index = 67 rmsd = 4.702 "obj and name CA" index = 68 rmsd = 5.934 "obj and name CA" index = 69 rmsd = 5.957 "obj and name CA" index = 70 rmsd = 6.526 "obj and name CA" index = 71 rmsd = 7.337 "obj and name CA" index = 72 rmsd = 7.791 "obj and name CA" index = 73 rmsd = 7.943 "obj and name CA" index = 74 rmsd = 8.364 "obj and name CA" index = 75 rmsd = 8.403 "obj and name CA" index = 76 rmsd = 7.771 "obj and name CA" index = 77 rmsd = 7.788 "obj and name CA" index = 78 rmsd = 7.625 "obj and name CA" index = 79 rmsd = 7.769 "obj and name CA" index = 80 rmsd = 7.516 "obj and name CA" index = 81 rmsd = 7.391 "obj and name CA" index = 82 rmsd = 6.387 "obj and name CA" index = 83 rmsd = 5.899 "obj and name CA" index = 84 rmsd = 4.410 "obj and name CA" index = 85 rmsd = 3.701 "obj and name CA" index = 86 rmsd = 3.538 "obj and name CA" index = 87 rmsd = 2.955 "obj and name CA" index = 88 rmsd = 2.229 "obj and name CA" index = 89 rmsd = 1.863 "obj and name CA" index = 90 rmsd = 1.933 "obj and name CA" index = 91 rmsd = 1.488 "obj and name CA" index = 92 rmsd = 1.148 "obj and name CA" index = 93 rmsd = 0.965 "obj and name CA" index = 94 rmsd = 0.861 "obj and name CA" index = 95 rmsd = 0.998 "obj and name CA" index = 96 rmsd = 1.292 "obj and name CA" index = 97 rmsd = 1.929 "obj and name CA" index = 98 rmsd = 1.812 "obj and name CA" index = 99 rmsd = 2.177 "obj and name CA" index = 100 rmsd = 2.023 "obj and name CA" index = 101 rmsd = 2.119 "obj and name CA" index = 102 rmsd = 2.113 "obj and name CA" index = 103 rmsd = 1.934 "obj and name CA" index = 104 rmsd = 2.385 "obj and name CA" index = 105 rmsd = 2.633 "obj and name CA" index = 106 rmsd = 2.719 "obj and name CA" index = 107 rmsd = 2.293 "obj and name CA" index = 108 rmsd = 2.192 "obj and name CA" index = 109 rmsd = 2.720 "obj and name CA" index = 110 rmsd = 2.567 "obj and name CA" index = 111 rmsd = 2.078 "obj and name CA" index = 112 rmsd = 2.319 "obj and name CA" index = 113 rmsd = 2.736 "obj and name CA" index = 114 rmsd = 2.486 "obj and name CA" index = 115 rmsd = 2.402 "obj and name CA" index = 116 rmsd = 1.899 "obj and name CA" index = 117 rmsd = 1.813 "obj and name CA" index = 118 rmsd = 1.432 "obj and name CA" index = 119 rmsd = 1.373 "obj and name CA" index = 120 rmsd = 1.308 "obj and name CA" index = 121 rmsd = 1.339 "obj and name CA" index = 122 rmsd = 1.453 "obj and name CA" index = 123 rmsd = 1.337 "obj and name CA" index = 124 rmsd = 1.653 "obj and name CA" index = 125 rmsd = 1.689 "obj and name CA" index = 126 rmsd = 1.301 "obj and name CA" index = 127 rmsd = 1.482 "obj and name CA" index = 128 rmsd = 1.873 "obj and name CA" index = 129 rmsd = 1.777 "obj and name CA" index = 130 rmsd = 1.542 "obj and name CA" index = 131 rmsd = 2.003 "obj and name CA" index = 132 rmsd = 2.307 "obj and name CA" index = 133 rmsd = 2.064 "obj and name CA" index = 134 rmsd = 2.053 "obj and name CA" index = 135 rmsd = 2.646 "obj and name CA" index = 136 rmsd = 2.739 "obj and name CA" index = 137 rmsd = 2.604 "obj and name CA" index = 138 rmsd = 2.357 "obj and name CA" index = 139 rmsd = 1.904 "obj and name CA" index = 140 rmsd = 1.475 "obj and name CA" index = 141 rmsd = 1.153 "obj and name CA" index = 142 rmsd = 0.936 "obj and name CA" index = 143 rmsd = 0.879 "obj and name CA" index = 144 rmsd = 1.034 "obj and name CA" index = 145 rmsd = 1.354 "obj and name CA" index = 146 rmsd = 1.976 "obj and name CA" index = 147 rmsd = 2.877 "obj and name CA" index = 148 rmsd = 3.453 "obj and name CA" index = 149 rmsd = 4.046 "obj and name CA" index = 150 rmsd = 4.328 "obj and name CA" index = 151 rmsd = 5.414 "obj and name CA" index = 152 rmsd = 6.285 "obj and name CA" index = 153 rmsd = 7.300 "obj and name CA" index = 154 rmsd = 9.511 "obj and name CA" index = 155 rmsd = 11.158 "obj and name CA" index = 156 rmsd = 11.870 "obj and name CA" index = 157 rmsd = 12.900 "obj and name CA" index = 158 rmsd = 13.517 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 1236 atoms. PyMOL>color cyan,ss s Executive: Colored 892 atoms. PyMOL>color gray,ss ""+l Executive: Colored 2764 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: 1.93 sec. = 1866.2 frames/hour (8.94 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit