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 27 atoms. PyMOL>color cyan,ss s Executive: Colored 25 atoms. PyMOL>color gray,ss ""+l Executive: Colored 2441 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: 1.93 sec. = 1862.0 frames/hour (1.93 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: 8.75 sec. = 411.6 frames/hour (10.68 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, 5.697819709777832, 6.5055723190307617, 5.4175887107849121, 3.5676643848419189, 4.9664821624755859, 5.0628786087036133, 5.1364798545837402, 5.7954444885253906, 4.7148728370666504, 6.8233885765075684, 5.6307487487792969, 7.9204292297363281, 4.9295563697814941, 4.6886892318725586, 5.2325043678283691, 5.6663498878479004, 5.037010669708252, 3.4607508182525635, 6.035980224609375] -> 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 = 11.821 "obj and name CA" index = 2 rmsd = 10.603 "obj and name CA" index = 3 rmsd = 8.625 "obj and name CA" index = 4 rmsd = 6.661 "obj and name CA" index = 5 rmsd = 4.935 "obj and name CA" index = 6 rmsd = 3.501 "obj and name CA" index = 7 rmsd = 1.749 "obj and name CA" index = 8 rmsd = 1.736 "obj and name CA" index = 9 rmsd = 1.545 "obj and name CA" index = 10 rmsd = 1.659 "obj and name CA" index = 11 rmsd = 1.646 "obj and name CA" index = 12 rmsd = 1.461 "obj and name CA" index = 13 rmsd = 1.522 "obj and name CA" index = 14 rmsd = 1.514 "obj and name CA" index = 15 rmsd = 1.645 "obj and name CA" index = 16 rmsd = 1.731 "obj and name CA" index = 17 rmsd = 1.689 "obj and name CA" index = 18 rmsd = 1.828 "obj and name CA" index = 19 rmsd = 1.405 "obj and name CA" index = 20 rmsd = 1.162 "obj and name CA" index = 21 rmsd = 1.071 "obj and name CA" index = 22 rmsd = 1.305 "obj and name CA" index = 23 rmsd = 1.594 "obj and name CA" index = 24 rmsd = 1.841 "obj and name CA" index = 25 rmsd = 2.255 "obj and name CA" index = 26 rmsd = 2.310 "obj and name CA" index = 27 rmsd = 3.075 "obj and name CA" index = 28 rmsd = 4.165 "obj and name CA" index = 29 rmsd = 3.288 "obj and name CA" index = 30 rmsd = 2.737 "obj and name CA" index = 31 rmsd = 2.392 "obj and name CA" index = 32 rmsd = 2.606 "obj and name CA" index = 33 rmsd = 2.577 "obj and name CA" index = 34 rmsd = 2.022 "obj and name CA" index = 35 rmsd = 1.790 "obj and name CA" index = 36 rmsd = 2.159 "obj and name CA" index = 37 rmsd = 2.080 "obj and name CA" index = 38 rmsd = 1.739 "obj and name CA" index = 39 rmsd = 1.624 "obj and name CA" index = 40 rmsd = 1.917 "obj and name CA" index = 41 rmsd = 1.892 "obj and name CA" index = 42 rmsd = 1.624 "obj and name CA" index = 43 rmsd = 2.061 "obj and name CA" index = 44 rmsd = 2.046 "obj and name CA" index = 45 rmsd = 1.795 "obj and name CA" index = 46 rmsd = 1.837 "obj and name CA" index = 47 rmsd = 2.363 "obj and name CA" index = 48 rmsd = 2.503 "obj and name CA" index = 49 rmsd = 2.647 "obj and name CA" index = 50 rmsd = 2.933 "obj and name CA" index = 51 rmsd = 2.428 "obj and name CA" index = 52 rmsd = 2.360 "obj and name CA" index = 53 rmsd = 1.735 "obj and name CA" index = 54 rmsd = 2.046 "obj and name CA" index = 55 rmsd = 1.850 "obj and name CA" index = 56 rmsd = 1.518 "obj and name CA" index = 57 rmsd = 1.091 "obj and name CA" index = 58 rmsd = 0.909 "obj and name CA" index = 59 rmsd = 1.073 "obj and name CA" index = 60 rmsd = 1.312 "obj and name CA" index = 61 rmsd = 1.855 "obj and name CA" index = 62 rmsd = 2.029 "obj and name CA" index = 63 rmsd = 2.563 "obj and name CA" index = 64 rmsd = 2.601 "obj and name CA" index = 65 rmsd = 3.711 "obj and name CA" index = 66 rmsd = 3.532 "obj and name CA" index = 67 rmsd = 3.467 "obj and name CA" index = 68 rmsd = 2.760 "obj and name CA" index = 69 rmsd = 2.371 "obj and name CA" index = 70 rmsd = 2.043 "obj and name CA" index = 71 rmsd = 1.653 "obj and name CA" index = 72 rmsd = 1.355 "obj and name CA" index = 73 rmsd = 1.239 "obj and name CA" index = 74 rmsd = 1.001 "obj and name CA" index = 75 rmsd = 1.098 "obj and name CA" index = 76 rmsd = 1.516 "obj and name CA" index = 77 rmsd = 1.708 "obj and name CA" index = 78 rmsd = 2.438 "obj and name CA" index = 79 rmsd = 2.740 "obj and name CA" index = 80 rmsd = 2.376 "obj and name CA" index = 81 rmsd = 2.108 "obj and name CA" index = 82 rmsd = 2.238 "obj and name CA" index = 83 rmsd = 2.064 "obj and name CA" index = 84 rmsd = 2.103 "obj and name CA" index = 85 rmsd = 2.212 "obj and name CA" index = 86 rmsd = 1.924 "obj and name CA" index = 87 rmsd = 1.216 "obj and name CA" index = 88 rmsd = 1.591 "obj and name CA" index = 89 rmsd = 1.828 "obj and name CA" index = 90 rmsd = 2.231 "obj and name CA" index = 91 rmsd = 1.883 "obj and name CA" index = 92 rmsd = 1.763 "obj and name CA" index = 93 rmsd = 2.131 "obj and name CA" index = 94 rmsd = 1.840 "obj and name CA" index = 95 rmsd = 1.769 "obj and name CA" index = 96 rmsd = 1.529 "obj and name CA" index = 97 rmsd = 1.393 "obj and name CA" index = 98 rmsd = 1.333 "obj and name CA" index = 99 rmsd = 1.199 "obj and name CA" index = 100 rmsd = 1.122 "obj and name CA" index = 101 rmsd = 1.147 "obj and name CA" index = 102 rmsd = 1.327 "obj and name CA" index = 103 rmsd = 1.543 "obj and name CA" index = 104 rmsd = 1.853 "obj and name CA" index = 105 rmsd = 2.193 "obj and name CA" index = 106 rmsd = 2.076 "obj and name CA" index = 107 rmsd = 2.613 "obj and name CA" index = 108 rmsd = 2.429 "obj and name CA" index = 109 rmsd = 1.856 "obj and name CA" index = 110 rmsd = 1.651 "obj and name CA" index = 111 rmsd = 1.933 "obj and name CA" index = 112 rmsd = 1.570 "obj and name CA" index = 113 rmsd = 1.376 "obj and name CA" index = 114 rmsd = 1.709 "obj and name CA" index = 115 rmsd = 1.735 "obj and name CA" index = 116 rmsd = 1.466 "obj and name CA" index = 117 rmsd = 1.573 "obj and name CA" index = 118 rmsd = 1.782 "obj and name CA" index = 119 rmsd = 1.638 "obj and name CA" index = 120 rmsd = 1.702 "obj and name CA" index = 121 rmsd = 2.030 "obj and name CA" index = 122 rmsd = 2.016 "obj and name CA" index = 123 rmsd = 1.868 "obj and name CA" index = 124 rmsd = 2.200 "obj and name CA" index = 125 rmsd = 2.264 "obj and name CA" index = 126 rmsd = 3.186 "obj and name CA" index = 127 rmsd = 3.757 "obj and name CA" index = 128 rmsd = 4.213 "obj and name CA" index = 129 rmsd = 4.508 "obj and name CA" index = 130 rmsd = 2.583 "obj and name CA" index = 131 rmsd = 1.724 "obj and name CA" index = 132 rmsd = 1.258 "obj and name CA" index = 133 rmsd = 1.010 "obj and name CA" index = 134 rmsd = 1.060 "obj and name CA" index = 135 rmsd = 1.398 "obj and name CA" index = 136 rmsd = 2.108 "obj and name CA" index = 137 rmsd = 2.591 "obj and name CA" index = 138 rmsd = 3.005 "obj and name CA" index = 139 rmsd = 3.537 "obj and name CA" index = 140 rmsd = 4.557 "obj and name CA" index = 141 rmsd = 3.391 "obj and name CA" index = 142 rmsd = 2.692 "obj and name CA" index = 143 rmsd = 2.886 "obj and name CA" index = 144 rmsd = 3.159 "obj and name CA" index = 145 rmsd = 3.123 "obj and name CA" index = 146 rmsd = 2.401 "obj and name CA" index = 147 rmsd = 1.634 "obj and name CA" index = 148 rmsd = 1.343 "obj and name CA" index = 149 rmsd = 1.135 "obj and name CA" index = 150 rmsd = 1.052 "obj and name CA" index = 151 rmsd = 0.965 "obj and name CA" index = 152 rmsd = 1.090 "obj and name CA" index = 153 rmsd = 1.171 "obj and name CA" index = 154 rmsd = 1.979 "obj and name CA" index = 155 rmsd = 2.103 "obj and name CA" index = 156 rmsd = 4.104 "obj and name CA" index = 157 rmsd = 5.089 "obj and name CA" index = 158 rmsd = 4.908 "obj and name CA" index = 159 rmsd = 6.208 "obj and name CA" index = 160 rmsd = 7.552 "obj and name CA" index = 161 rmsd = 8.707 "obj and name CA" index = 162 rmsd = 10.604 "obj and name CA" index = 163 rmsd = 12.149 "obj and name CA" index = 164 rmsd = 13.932 "obj and name CA" index = 165 rmsd = 15.934 "obj and name CA" index = 166 rmsd = 18.388 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 81 atoms. PyMOL>color cyan,ss s Executive: Colored 75 atoms. PyMOL>color gray,ss ""+l Executive: Colored 4990 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: 2.63 sec. = 1367.7 frames/hour (13.31 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit