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 Executive: Colored 24 atoms. PyMOL>color cyan,ss s Executive: Colored 23 atoms. PyMOL>color gray,ss ""+l Executive: Colored 2448 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: 1.89 sec. = 1905.0 frames/hour (1.89 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 498 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 498 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: 9.20 sec. = 391.2 frames/hour (11.09 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, 4.0513401031494141, 4.4235591888427734, 3.8245842456817627, 3.6586453914642334, 6.677457332611084, 6.0842366218566895, 5.9412894248962402, 3.3703451156616211, 4.2742185592651367, 6.3873372077941895, 6.7819147109985352, 7.5834331512451172, 5.4238104820251465, 3.051079273223877, 5.7776069641113281, 3.412590503692627, 7.6890311241149902, 6.1127643585205078, 4.3720316886901855] -> atom index_map = [None, 2, 21, 33, 53, 68, 79, 96, 116, 132, 143, 158, 177, 199, 214, 233, 243, 257, 273, 287, 297, 316, 335, 354, 378, 392, 409, 423, 433, 450, 461, 476, 495, 502, 513, 532, 552, 567, 577, 584, 605, 622, 634, 653, 672, 689, 708, 727, 737, 744, 761, 768, 790, 801, 815, 826, 833, 847, 861, 881, 891, 915, 936, 956, 963, 980, 991, 1001, 1008, 1022, 1042, 1057, 1073, 1088, 1108, 1115, 1135, 1149, 1165, 1180, 1187, 1194, 1210, 1225, 1232, 1243, 1250, 1274, 1290, 1306, 1320, 1327, 1346, 1360, 1374, 1385, 1392, 1414, 1424, 1434, 1445, 1456, 1475, 1496, 1515, 1522, 1536, 1557, 1564, 1579, 1598, 1613, 1623, 1639, 1660, 1672, 1682, 1701, 1718, 1740, 1764, 1780, 1792, 1804, 1818, 1825, 1845, 1857, 1876, 1887, 1894, 1909, 1919, 1940, 1955, 1974, 1995, 2014, 2026, 2040, 2054, 2064, 2079, 2093, 2103, 2117, 2129, 2146, 2165, 2189, 2203, 2227, 2243, 2254, 2273, 2290, 2309, 2326, 2341, 2352, 2371, 2386, 2403, 2420, 2437, 2454, 2471] "obj and name CA" index = 1 rmsd = 11.341 "obj and name CA" index = 2 rmsd = 10.557 "obj and name CA" index = 3 rmsd = 8.809 "obj and name CA" index = 4 rmsd = 6.759 "obj and name CA" index = 5 rmsd = 5.274 "obj and name CA" index = 6 rmsd = 3.532 "obj and name CA" index = 7 rmsd = 1.841 "obj and name CA" index = 8 rmsd = 1.734 "obj and name CA" index = 9 rmsd = 1.511 "obj and name CA" index = 10 rmsd = 1.696 "obj and name CA" index = 11 rmsd = 1.675 "obj and name CA" index = 12 rmsd = 1.528 "obj and name CA" index = 13 rmsd = 1.507 "obj and name CA" index = 14 rmsd = 1.446 "obj and name CA" index = 15 rmsd = 1.620 "obj and name CA" index = 16 rmsd = 1.761 "obj and name CA" index = 17 rmsd = 1.778 "obj and name CA" index = 18 rmsd = 1.868 "obj and name CA" index = 19 rmsd = 1.544 "obj and name CA" index = 20 rmsd = 1.245 "obj and name CA" index = 21 rmsd = 1.287 "obj and name CA" index = 22 rmsd = 1.477 "obj and name CA" index = 23 rmsd = 1.620 "obj and name CA" index = 24 rmsd = 1.860 "obj and name CA" index = 25 rmsd = 2.187 "obj and name CA" index = 26 rmsd = 2.331 "obj and name CA" index = 27 rmsd = 3.028 "obj and name CA" index = 28 rmsd = 3.896 "obj and name CA" index = 29 rmsd = 3.537 "obj and name CA" index = 30 rmsd = 2.952 "obj and name CA" index = 31 rmsd = 2.458 "obj and name CA" index = 32 rmsd = 2.633 "obj and name CA" index = 33 rmsd = 2.741 "obj and name CA" index = 34 rmsd = 2.463 "obj and name CA" index = 35 rmsd = 2.345 "obj and name CA" index = 36 rmsd = 2.351 "obj and name CA" index = 37 rmsd = 2.251 "obj and name CA" index = 38 rmsd = 2.027 "obj and name CA" index = 39 rmsd = 2.169 "obj and name CA" index = 40 rmsd = 2.109 "obj and name CA" index = 41 rmsd = 1.926 "obj and name CA" index = 42 rmsd = 1.789 "obj and name CA" index = 43 rmsd = 2.092 "obj and name CA" index = 44 rmsd = 1.852 "obj and name CA" index = 45 rmsd = 1.681 "obj and name CA" index = 46 rmsd = 1.571 "obj and name CA" index = 47 rmsd = 2.028 "obj and name CA" index = 48 rmsd = 2.388 "obj and name CA" index = 49 rmsd = 2.546 "obj and name CA" index = 50 rmsd = 2.606 "obj and name CA" index = 51 rmsd = 2.023 "obj and name CA" index = 52 rmsd = 2.129 "obj and name CA" index = 53 rmsd = 1.858 "obj and name CA" index = 54 rmsd = 2.306 "obj and name CA" index = 55 rmsd = 2.257 "obj and name CA" index = 56 rmsd = 2.044 "obj and name CA" index = 57 rmsd = 1.585 "obj and name CA" index = 58 rmsd = 1.380 "obj and name CA" index = 59 rmsd = 1.390 "obj and name CA" index = 60 rmsd = 1.340 "obj and name CA" index = 61 rmsd = 1.862 "obj and name CA" index = 62 rmsd = 1.900 "obj and name CA" index = 63 rmsd = 2.610 "obj and name CA" index = 64 rmsd = 2.388 "obj and name CA" index = 65 rmsd = 3.281 "obj and name CA" index = 66 rmsd = 3.578 "obj and name CA" index = 67 rmsd = 3.432 "obj and name CA" index = 68 rmsd = 2.771 "obj and name CA" index = 69 rmsd = 2.524 "obj and name CA" index = 70 rmsd = 2.064 "obj and name CA" index = 71 rmsd = 1.758 "obj and name CA" index = 72 rmsd = 1.499 "obj and name CA" index = 73 rmsd = 1.446 "obj and name CA" index = 74 rmsd = 1.379 "obj and name CA" index = 75 rmsd = 1.339 "obj and name CA" index = 76 rmsd = 1.573 "obj and name CA" index = 77 rmsd = 1.791 "obj and name CA" index = 78 rmsd = 2.544 "obj and name CA" index = 79 rmsd = 2.947 "obj and name CA" index = 80 rmsd = 2.703 "obj and name CA" index = 81 rmsd = 2.113 "obj and name CA" index = 82 rmsd = 2.148 "obj and name CA" index = 83 rmsd = 1.984 "obj and name CA" index = 84 rmsd = 2.250 "obj and name CA" index = 85 rmsd = 2.682 "obj and name CA" index = 86 rmsd = 2.255 "obj and name CA" index = 87 rmsd = 1.451 "obj and name CA" index = 88 rmsd = 1.625 "obj and name CA" index = 89 rmsd = 1.784 "obj and name CA" index = 90 rmsd = 2.150 "obj and name CA" index = 91 rmsd = 1.841 "obj and name CA" index = 92 rmsd = 1.760 "obj and name CA" index = 93 rmsd = 2.404 "obj and name CA" index = 94 rmsd = 2.076 "obj and name CA" index = 95 rmsd = 2.008 "obj and name CA" index = 96 rmsd = 1.746 "obj and name CA" index = 97 rmsd = 1.517 "obj and name CA" index = 98 rmsd = 1.432 "obj and name CA" index = 99 rmsd = 1.292 "obj and name CA" index = 100 rmsd = 1.331 "obj and name CA" index = 101 rmsd = 1.281 "obj and name CA" index = 102 rmsd = 1.648 "obj and name CA" index = 103 rmsd = 1.954 "obj and name CA" index = 104 rmsd = 2.527 "obj and name CA" index = 105 rmsd = 3.180 "obj and name CA" index = 106 rmsd = 2.873 "obj and name CA" index = 107 rmsd = 2.973 "obj and name CA" index = 108 rmsd = 2.475 "obj and name CA" index = 109 rmsd = 2.090 "obj and name CA" index = 110 rmsd = 2.243 "obj and name CA" index = 111 rmsd = 2.281 "obj and name CA" index = 112 rmsd = 1.818 "obj and name CA" index = 113 rmsd = 1.764 "obj and name CA" index = 114 rmsd = 1.956 "obj and name CA" index = 115 rmsd = 1.861 "obj and name CA" index = 116 rmsd = 1.624 "obj and name CA" index = 117 rmsd = 1.695 "obj and name CA" index = 118 rmsd = 1.950 "obj and name CA" index = 119 rmsd = 1.718 "obj and name CA" index = 120 rmsd = 1.671 "obj and name CA" index = 121 rmsd = 1.958 "obj and name CA" index = 122 rmsd = 2.123 "obj and name CA" index = 123 rmsd = 2.268 "obj and name CA" index = 124 rmsd = 2.176 "obj and name CA" index = 125 rmsd = 2.180 "obj and name CA" index = 126 rmsd = 3.022 "obj and name CA" index = 127 rmsd = 3.846 "obj and name CA" index = 128 rmsd = 4.107 "obj and name CA" index = 129 rmsd = 4.571 "obj and name CA" index = 130 rmsd = 2.512 "obj and name CA" index = 131 rmsd = 1.808 "obj and name CA" index = 132 rmsd = 1.404 "obj and name CA" index = 133 rmsd = 1.446 "obj and name CA" index = 134 rmsd = 1.514 "obj and name CA" index = 135 rmsd = 1.922 "obj and name CA" index = 136 rmsd = 2.301 "obj and name CA" index = 137 rmsd = 2.727 "obj and name CA" index = 138 rmsd = 3.338 "obj and name CA" index = 139 rmsd = 3.906 "obj and name CA" index = 140 rmsd = 5.207 "obj and name CA" index = 141 rmsd = 4.054 "obj and name CA" index = 142 rmsd = 3.545 "obj and name CA" index = 143 rmsd = 4.035 "obj and name CA" index = 144 rmsd = 4.093 "obj and name CA" index = 145 rmsd = 3.664 "obj and name CA" index = 146 rmsd = 3.076 "obj and name CA" index = 147 rmsd = 2.230 "obj and name CA" index = 148 rmsd = 1.729 "obj and name CA" index = 149 rmsd = 1.403 "obj and name CA" index = 150 rmsd = 1.244 "obj and name CA" index = 151 rmsd = 1.177 "obj and name CA" index = 152 rmsd = 1.329 "obj and name CA" index = 153 rmsd = 1.500 "obj and name CA" index = 154 rmsd = 2.322 "obj and name CA" index = 155 rmsd = 2.280 "obj and name CA" index = 156 rmsd = 4.254 "obj and name CA" index = 157 rmsd = 5.467 "obj and name CA" index = 158 rmsd = 5.496 "obj and name CA" index = 159 rmsd = 6.595 "obj and name CA" index = 160 rmsd = 8.154 "obj and name CA" index = 161 rmsd = 9.491 "obj and name CA" index = 162 rmsd = 11.252 "obj and name CA" index = 163 rmsd = 12.539 "obj and name CA" index = 164 rmsd = 14.161 "obj and name CA" index = 165 rmsd = 15.725 "obj and name CA" index = 166 rmsd = 18.057 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 72 atoms. PyMOL>color cyan,ss s Executive: Colored 69 atoms. PyMOL>color gray,ss ""+l Executive: Colored 5007 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: 2.54 sec. = 1417.6 frames/hour (13.63 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit