PyMOL>load ./selSi.pdb,obj HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 31-MAR-10 2KW5 TITLE SOLUTION NMR STRUCTURE OF THE SLR1183 PROTEIN FROM TITLE 2 SYNECHOCYSTIS SP. PCC 6803, NORTHEAST STRUCTURAL GENOMICS TITLE 3 CONSORTIUM TARGET SGR145 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SLR1183 PROTEIN; 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 1047 atoms. PyMOL>color cyan,ss s Executive: Colored 704 atoms. PyMOL>color gray,ss ""+l Executive: Colored 1390 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: 1.33 sec. = 2706.4 frames/hour (1.33 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 606 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 606 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: 5.27 sec. = 682.6 frames/hour (6.60 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, 9.5847339630126953, 5.0189657211303711, 6.3551387786865234, 8.0549907684326172, 8.5665111541748047, 3.9085023403167725, 3.5258626937866211, 6.1114897727966309, 4.5121831893920898, 7.5481767654418945, 6.1499738693237305, 5.5020918846130371, 3.2339558601379395, 4.9951457977294922, 3.7318291664123535, 6.5801424980163574, 5.9605088233947754, 5.8059573173522949, 3.8055849075317383] -> atom index_map = [None, 2, 21, 45, 57, 72, 96, 116, 127, 144, 155, 170, 191, 207, 228, 235, 249, 264, 278, 292, 304, 324, 343, 359, 370, 386, 396, 410, 427, 446, 460, 477, 484, 506, 525, 544, 555, 574, 584, 599, 606, 621, 628, 652, 666, 676, 687, 707, 726, 736, 747, 766, 773, 794, 809, 825, 839, 849, 865, 877, 894, 905, 916, 932, 939, 958, 968, 990, 1000, 1022, 1039, 1058, 1068, 1085, 1100, 1122, 1129, 1145, 1167, 1186, 1200, 1214, 1230, 1247, 1258, 1272, 1291, 1301, 1313, 1333, 1345, 1364, 1380, 1390, 1402, 1412, 1436, 1451, 1458, 1477, 1493, 1504, 1523, 1543, 1554, 1572, 1591, 1605, 1616, 1627, 1646, 1670, 1687, 1704, 1723, 1744, 1758, 1780, 1796, 1817, 1834, 1841, 1860, 1882, 1896, 1903, 1910, 1926, 1946, 1965, 1984, 1999, 2006, 2026, 2036, 2050, 2065, 2082, 2101, 2118, 2139, 2153, 2167, 2174, 2181, 2195, 2217, 2229, 2248, 2260, 2279, 2298, 2312, 2334, 2353, 2368, 2382, 2401, 2418, 2429, 2444, 2463, 2477, 2488, 2507, 2521, 2545, 2564, 2583, 2593, 2607, 2621, 2640, 2655, 2679, 2693, 2712, 2724, 2739, 2746, 2756, 2777, 2795, 2812, 2819, 2841, 2851, 2861, 2880, 2899, 2916, 2935, 2954, 2961, 2978, 3000, 3019, 3034, 3052, 3070, 3088, 3106, 3124] "obj and name CA" index = 1 rmsd = 22.757 "obj and name CA" index = 2 rmsd = 21.133 "obj and name CA" index = 3 rmsd = 18.850 "obj and name CA" index = 4 rmsd = 17.627 "obj and name CA" index = 5 rmsd = 15.974 "obj and name CA" index = 6 rmsd = 14.602 "obj and name CA" index = 7 rmsd = 12.533 "obj and name CA" index = 8 rmsd = 11.169 "obj and name CA" index = 9 rmsd = 9.984 "obj and name CA" index = 10 rmsd = 8.597 "obj and name CA" index = 11 rmsd = 7.606 "obj and name CA" index = 12 rmsd = 6.565 "obj and name CA" index = 13 rmsd = 5.651 "obj and name CA" index = 14 rmsd = 5.350 "obj and name CA" index = 15 rmsd = 3.841 "obj and name CA" index = 16 rmsd = 3.854 "obj and name CA" index = 17 rmsd = 2.914 "obj and name CA" index = 18 rmsd = 3.470 "obj and name CA" index = 19 rmsd = 2.700 "obj and name CA" index = 20 rmsd = 2.184 "obj and name CA" index = 21 rmsd = 2.124 "obj and name CA" index = 22 rmsd = 2.619 "obj and name CA" index = 23 rmsd = 2.435 "obj and name CA" index = 24 rmsd = 2.097 "obj and name CA" index = 25 rmsd = 2.455 "obj and name CA" index = 26 rmsd = 2.828 "obj and name CA" index = 27 rmsd = 2.529 "obj and name CA" index = 28 rmsd = 2.449 "obj and name CA" index = 29 rmsd = 2.838 "obj and name CA" index = 30 rmsd = 3.186 "obj and name CA" index = 31 rmsd = 3.113 "obj and name CA" index = 32 rmsd = 2.820 "obj and name CA" index = 33 rmsd = 2.342 "obj and name CA" index = 34 rmsd = 1.956 "obj and name CA" index = 35 rmsd = 1.694 "obj and name CA" index = 36 rmsd = 1.424 "obj and name CA" index = 37 rmsd = 1.767 "obj and name CA" index = 38 rmsd = 2.794 "obj and name CA" index = 39 rmsd = 3.276 "obj and name CA" index = 40 rmsd = 3.070 "obj and name CA" index = 41 rmsd = 2.455 "obj and name CA" index = 42 rmsd = 2.467 "obj and name CA" index = 43 rmsd = 2.114 "obj and name CA" index = 44 rmsd = 2.308 "obj and name CA" index = 45 rmsd = 2.766 "obj and name CA" index = 46 rmsd = 2.692 "obj and name CA" index = 47 rmsd = 2.614 "obj and name CA" index = 48 rmsd = 3.072 "obj and name CA" index = 49 rmsd = 3.350 "obj and name CA" index = 50 rmsd = 3.321 "obj and name CA" index = 51 rmsd = 3.696 "obj and name CA" index = 52 rmsd = 3.290 "obj and name CA" index = 53 rmsd = 3.230 "obj and name CA" index = 54 rmsd = 2.645 "obj and name CA" index = 55 rmsd = 2.461 "obj and name CA" index = 56 rmsd = 2.174 "obj and name CA" index = 57 rmsd = 1.931 "obj and name CA" index = 58 rmsd = 2.037 "obj and name CA" index = 59 rmsd = 2.450 "obj and name CA" index = 60 rmsd = 2.750 "obj and name CA" index = 61 rmsd = 3.077 "obj and name CA" index = 62 rmsd = 3.244 "obj and name CA" index = 63 rmsd = 2.873 "obj and name CA" index = 64 rmsd = 2.826 "obj and name CA" index = 65 rmsd = 3.400 "obj and name CA" index = 66 rmsd = 3.393 "obj and name CA" index = 67 rmsd = 3.069 "obj and name CA" index = 68 rmsd = 3.445 "obj and name CA" index = 69 rmsd = 3.883 "obj and name CA" index = 70 rmsd = 3.896 "obj and name CA" index = 71 rmsd = 3.806 "obj and name CA" index = 72 rmsd = 4.330 "obj and name CA" index = 73 rmsd = 4.499 "obj and name CA" index = 74 rmsd = 4.421 "obj and name CA" index = 75 rmsd = 4.613 "obj and name CA" index = 76 rmsd = 4.154 "obj and name CA" index = 77 rmsd = 3.862 "obj and name CA" index = 78 rmsd = 3.189 "obj and name CA" index = 79 rmsd = 2.942 "obj and name CA" index = 80 rmsd = 2.722 "obj and name CA" index = 81 rmsd = 2.406 "obj and name CA" index = 82 rmsd = 2.428 "obj and name CA" index = 83 rmsd = 2.438 "obj and name CA" index = 84 rmsd = 2.157 "obj and name CA" index = 85 rmsd = 1.825 "obj and name CA" index = 86 rmsd = 2.193 "obj and name CA" index = 87 rmsd = 2.297 "obj and name CA" index = 88 rmsd = 2.000 "obj and name CA" index = 89 rmsd = 1.658 "obj and name CA" index = 90 rmsd = 1.658 "obj and name CA" index = 91 rmsd = 2.117 "obj and name CA" index = 92 rmsd = 2.305 "obj and name CA" index = 93 rmsd = 2.660 "obj and name CA" index = 94 rmsd = 2.749 "obj and name CA" index = 95 rmsd = 2.543 "obj and name CA" index = 96 rmsd = 2.698 "obj and name CA" index = 97 rmsd = 2.296 "obj and name CA" index = 98 rmsd = 1.760 "obj and name CA" index = 99 rmsd = 1.504 "obj and name CA" index = 100 rmsd = 1.123 "obj and name CA" index = 101 rmsd = 1.161 "obj and name CA" index = 102 rmsd = 1.201 "obj and name CA" index = 103 rmsd = 1.280 "obj and name CA" index = 104 rmsd = 1.374 "obj and name CA" index = 105 rmsd = 1.398 "obj and name CA" index = 106 rmsd = 1.808 "obj and name CA" index = 107 rmsd = 2.060 "obj and name CA" index = 108 rmsd = 2.140 "obj and name CA" index = 109 rmsd = 1.725 "obj and name CA" index = 110 rmsd = 1.500 "obj and name CA" index = 111 rmsd = 1.978 "obj and name CA" index = 112 rmsd = 1.951 "obj and name CA" index = 113 rmsd = 1.431 "obj and name CA" index = 114 rmsd = 1.502 "obj and name CA" index = 115 rmsd = 1.987 "obj and name CA" index = 116 rmsd = 1.786 "obj and name CA" index = 117 rmsd = 1.392 "obj and name CA" index = 118 rmsd = 1.644 "obj and name CA" index = 119 rmsd = 1.949 "obj and name CA" index = 120 rmsd = 1.723 "obj and name CA" index = 121 rmsd = 1.707 "obj and name CA" index = 122 rmsd = 2.586 "obj and name CA" index = 123 rmsd = 2.445 "obj and name CA" index = 124 rmsd = 2.284 "obj and name CA" index = 125 rmsd = 1.839 "obj and name CA" index = 126 rmsd = 1.563 "obj and name CA" index = 127 rmsd = 1.086 "obj and name CA" index = 128 rmsd = 0.990 "obj and name CA" index = 129 rmsd = 0.784 "obj and name CA" index = 130 rmsd = 1.026 "obj and name CA" index = 131 rmsd = 1.426 "obj and name CA" index = 132 rmsd = 1.385 "obj and name CA" index = 133 rmsd = 1.738 "obj and name CA" index = 134 rmsd = 2.169 "obj and name CA" index = 135 rmsd = 2.274 "obj and name CA" index = 136 rmsd = 2.428 "obj and name CA" index = 137 rmsd = 2.635 "obj and name CA" index = 138 rmsd = 3.024 "obj and name CA" index = 139 rmsd = 3.719 "obj and name CA" index = 140 rmsd = 4.310 "obj and name CA" index = 141 rmsd = 5.962 "obj and name CA" index = 142 rmsd = 5.899 "obj and name CA" index = 143 rmsd = 4.244 "obj and name CA" index = 144 rmsd = 3.498 "obj and name CA" index = 145 rmsd = 2.522 "obj and name CA" index = 146 rmsd = 2.941 "obj and name CA" index = 147 rmsd = 2.342 "obj and name CA" index = 148 rmsd = 2.487 "obj and name CA" index = 149 rmsd = 2.023 "obj and name CA" index = 150 rmsd = 1.793 "obj and name CA" index = 151 rmsd = 1.860 "obj and name CA" index = 152 rmsd = 1.578 "obj and name CA" index = 153 rmsd = 1.431 "obj and name CA" index = 154 rmsd = 1.918 "obj and name CA" index = 155 rmsd = 1.801 "obj and name CA" index = 156 rmsd = 1.372 "obj and name CA" index = 157 rmsd = 1.591 "obj and name CA" index = 158 rmsd = 1.956 "obj and name CA" index = 159 rmsd = 1.727 "obj and name CA" index = 160 rmsd = 1.626 "obj and name CA" index = 161 rmsd = 2.056 "obj and name CA" index = 162 rmsd = 2.180 "obj and name CA" index = 163 rmsd = 1.739 "obj and name CA" index = 164 rmsd = 1.902 "obj and name CA" index = 165 rmsd = 1.729 "obj and name CA" index = 166 rmsd = 2.008 "obj and name CA" index = 167 rmsd = 1.716 "obj and name CA" index = 168 rmsd = 1.581 "obj and name CA" index = 169 rmsd = 1.800 "obj and name CA" index = 170 rmsd = 1.741 "obj and name CA" index = 171 rmsd = 1.607 "obj and name CA" index = 172 rmsd = 1.772 "obj and name CA" index = 173 rmsd = 2.056 "obj and name CA" index = 174 rmsd = 2.413 "obj and name CA" index = 175 rmsd = 2.843 "obj and name CA" index = 176 rmsd = 3.572 "obj and name CA" index = 177 rmsd = 4.044 "obj and name CA" index = 178 rmsd = 4.874 "obj and name CA" index = 179 rmsd = 5.550 "obj and name CA" index = 180 rmsd = 5.370 "obj and name CA" index = 181 rmsd = 4.855 "obj and name CA" index = 182 rmsd = 3.998 "obj and name CA" index = 183 rmsd = 3.025 "obj and name CA" index = 184 rmsd = 2.436 "obj and name CA" index = 185 rmsd = 2.164 "obj and name CA" index = 186 rmsd = 1.774 "obj and name CA" index = 187 rmsd = 1.504 "obj and name CA" index = 188 rmsd = 1.357 "obj and name CA" index = 189 rmsd = 1.244 "obj and name CA" index = 190 rmsd = 1.157 "obj and name CA" index = 191 rmsd = 1.396 "obj and name CA" index = 192 rmsd = 1.507 "obj and name CA" index = 193 rmsd = 1.984 "obj and name CA" index = 194 rmsd = 2.291 "obj and name CA" index = 195 rmsd = 2.600 "obj and name CA" index = 196 rmsd = 3.280 "obj and name CA" index = 197 rmsd = 5.067 "obj and name CA" index = 198 rmsd = 6.083 "obj and name CA" index = 199 rmsd = 7.733 "obj and name CA" index = 200 rmsd = 10.012 "obj and name CA" index = 201 rmsd = 12.078 "obj and name CA" index = 202 rmsd = 14.141 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 2148 atoms. PyMOL>color cyan,ss s Executive: Colored 1443 atoms. PyMOL>color gray,ss ""+l Executive: Colored 2893 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: 2.01 sec. = 1793.9 frames/hour (8.61 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit