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 48 atoms. PyMOL>color cyan,ss s Executive: Colored 64 atoms. PyMOL>color gray,ss ""+l Executive: Colored 2746 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: 1.95 sec. = 1846.9 frames/hour (1.95 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 528 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 528 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: 6.56 sec. = 548.6 frames/hour (8.51 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, 1.4357225894927979, 2.1599204540252686, 1.621501088142395, 1.2740893363952637, 1.3005588054656982, 2.1138062477111816, 1.7652990818023682, 1.7722147703170776, 2.0424489974975586, 1.7057006359100342, 2.2066984176635742, 2.305311918258667, 1.143712043762207, 2.9305243492126465, 1.8312886953353882, 1.972929835319519, 2.4440464973449707, 1.6530388593673706, 2.0467798709869385] -> atom index_map = [None, 2, 21, 35, 47, 67, 86, 96, 103, 122, 146, 165, 181, 188, 203, 215, 237, 251, 258, 275, 289, 303, 320, 339, 353, 360, 376, 395, 406, 428, 448, 460, 474, 488, 507, 531, 545, 564, 580, 599, 613, 623, 645, 657, 664, 683, 703, 717, 728, 742, 761, 778, 797, 817, 833, 855, 869, 883, 895, 917, 936, 950, 964, 983, 1000, 1012, 1034, 1053, 1077, 1099, 1115, 1132, 1139, 1155, 1175, 1189, 1205, 1220, 1244, 1263, 1274, 1288, 1307, 1322, 1339, 1356, 1373, 1390, 1407, 1425, 1444, 1458, 1470, 1490, 1509, 1519, 1526, 1545, 1569, 1588, 1604, 1611, 1626, 1638, 1660, 1674, 1681, 1698, 1712, 1726, 1743, 1762, 1776, 1783, 1799, 1818, 1829, 1851, 1871, 1883, 1897, 1911, 1930, 1954, 1968, 1987, 2003, 2022, 2036, 2046, 2068, 2080, 2087, 2106, 2126, 2140, 2151, 2165, 2184, 2201, 2220, 2240, 2256, 2278, 2292, 2306, 2318, 2340, 2359, 2373, 2387, 2406, 2423, 2435, 2457, 2476, 2500, 2522, 2538, 2555, 2562, 2578, 2598, 2612, 2628, 2643, 2667, 2686, 2697, 2711, 2730, 2745, 2762, 2779, 2796, 2813, 2830] "obj and name CA" index = 1 rmsd = 3.201 "obj and name CA" index = 2 rmsd = 1.114 "obj and name CA" index = 3 rmsd = 0.864 "obj and name CA" index = 4 rmsd = 0.715 "obj and name CA" index = 5 rmsd = 0.613 "obj and name CA" index = 6 rmsd = 0.520 "obj and name CA" index = 7 rmsd = 0.442 "obj and name CA" index = 8 rmsd = 0.419 "obj and name CA" index = 9 rmsd = 0.424 "obj and name CA" index = 10 rmsd = 0.456 "obj and name CA" index = 11 rmsd = 0.520 "obj and name CA" index = 12 rmsd = 0.587 "obj and name CA" index = 13 rmsd = 0.683 "obj and name CA" index = 14 rmsd = 0.743 "obj and name CA" index = 15 rmsd = 0.755 "obj and name CA" index = 16 rmsd = 1.384 "obj and name CA" index = 17 rmsd = 0.618 "obj and name CA" index = 18 rmsd = 0.487 "obj and name CA" index = 19 rmsd = 0.422 "obj and name CA" index = 20 rmsd = 0.456 "obj and name CA" index = 21 rmsd = 0.489 "obj and name CA" index = 22 rmsd = 0.441 "obj and name CA" index = 23 rmsd = 0.551 "obj and name CA" index = 24 rmsd = 0.562 "obj and name CA" index = 25 rmsd = 0.551 "obj and name CA" index = 26 rmsd = 0.439 "obj and name CA" index = 27 rmsd = 0.622 "obj and name CA" index = 28 rmsd = 0.737 "obj and name CA" index = 29 rmsd = 0.632 "obj and name CA" index = 30 rmsd = 0.758 "obj and name CA" index = 31 rmsd = 0.520 "obj and name CA" index = 32 rmsd = 0.478 "obj and name CA" index = 33 rmsd = 0.367 "obj and name CA" index = 34 rmsd = 0.390 "obj and name CA" index = 35 rmsd = 0.379 "obj and name CA" index = 36 rmsd = 0.358 "obj and name CA" index = 37 rmsd = 0.291 "obj and name CA" index = 38 rmsd = 0.352 "obj and name CA" index = 39 rmsd = 0.501 "obj and name CA" index = 40 rmsd = 0.630 "obj and name CA" index = 41 rmsd = 0.867 "obj and name CA" index = 42 rmsd = 0.936 "obj and name CA" index = 43 rmsd = 0.842 "obj and name CA" index = 44 rmsd = 0.665 "obj and name CA" index = 45 rmsd = 0.491 "obj and name CA" index = 46 rmsd = 0.401 "obj and name CA" index = 47 rmsd = 0.356 "obj and name CA" index = 48 rmsd = 0.353 "obj and name CA" index = 49 rmsd = 0.354 "obj and name CA" index = 50 rmsd = 0.396 "obj and name CA" index = 51 rmsd = 0.441 "obj and name CA" index = 52 rmsd = 0.563 "obj and name CA" index = 53 rmsd = 0.636 "obj and name CA" index = 54 rmsd = 0.788 "obj and name CA" index = 55 rmsd = 0.750 "obj and name CA" index = 56 rmsd = 0.765 "obj and name CA" index = 57 rmsd = 0.850 "obj and name CA" index = 58 rmsd = 0.780 "obj and name CA" index = 59 rmsd = 0.644 "obj and name CA" index = 60 rmsd = 0.665 "obj and name CA" index = 61 rmsd = 0.725 "obj and name CA" index = 62 rmsd = 0.597 "obj and name CA" index = 63 rmsd = 0.579 "obj and name CA" index = 64 rmsd = 0.685 "obj and name CA" index = 65 rmsd = 0.692 "obj and name CA" index = 66 rmsd = 0.603 "obj and name CA" index = 67 rmsd = 0.693 "obj and name CA" index = 68 rmsd = 0.826 "obj and name CA" index = 69 rmsd = 0.727 "obj and name CA" index = 70 rmsd = 0.833 "obj and name CA" index = 71 rmsd = 0.799 "obj and name CA" index = 72 rmsd = 0.671 "obj and name CA" index = 73 rmsd = 0.743 "obj and name CA" index = 74 rmsd = 0.652 "obj and name CA" index = 75 rmsd = 0.563 "obj and name CA" index = 76 rmsd = 0.555 "obj and name CA" index = 77 rmsd = 0.547 "obj and name CA" index = 78 rmsd = 0.529 "obj and name CA" index = 79 rmsd = 0.757 "obj and name CA" index = 80 rmsd = 0.755 "obj and name CA" index = 81 rmsd = 0.735 "obj and name CA" index = 82 rmsd = 1.085 "obj and name CA" index = 83 rmsd = 0.882 "obj and name CA" index = 84 rmsd = 1.988 "obj and name CA" index = 85 rmsd = 3.273 "obj and name CA" index = 86 rmsd = 5.311 "obj and name CA" index = 87 rmsd = 7.523 "obj and name CA" index = 88 rmsd = 9.597 "obj and name CA" index = 89 rmsd = 3.201 "obj and name CA" index = 90 rmsd = 1.114 "obj and name CA" index = 91 rmsd = 0.864 "obj and name CA" index = 92 rmsd = 0.715 "obj and name CA" index = 93 rmsd = 0.613 "obj and name CA" index = 94 rmsd = 0.519 "obj and name CA" index = 95 rmsd = 0.442 "obj and name CA" index = 96 rmsd = 0.419 "obj and name CA" index = 97 rmsd = 0.424 "obj and name CA" index = 98 rmsd = 0.457 "obj and name CA" index = 99 rmsd = 0.521 "obj and name CA" index = 100 rmsd = 0.588 "obj and name CA" index = 101 rmsd = 0.683 "obj and name CA" index = 102 rmsd = 0.743 "obj and name CA" index = 103 rmsd = 0.755 "obj and name CA" index = 104 rmsd = 1.384 "obj and name CA" index = 105 rmsd = 0.618 "obj and name CA" index = 106 rmsd = 0.487 "obj and name CA" index = 107 rmsd = 0.422 "obj and name CA" index = 108 rmsd = 0.456 "obj and name CA" index = 109 rmsd = 0.489 "obj and name CA" index = 110 rmsd = 0.441 "obj and name CA" index = 111 rmsd = 0.550 "obj and name CA" index = 112 rmsd = 0.562 "obj and name CA" index = 113 rmsd = 0.551 "obj and name CA" index = 114 rmsd = 0.440 "obj and name CA" index = 115 rmsd = 0.622 "obj and name CA" index = 116 rmsd = 0.738 "obj and name CA" index = 117 rmsd = 0.633 "obj and name CA" index = 118 rmsd = 0.758 "obj and name CA" index = 119 rmsd = 0.520 "obj and name CA" index = 120 rmsd = 0.478 "obj and name CA" index = 121 rmsd = 0.367 "obj and name CA" index = 122 rmsd = 0.390 "obj and name CA" index = 123 rmsd = 0.378 "obj and name CA" index = 124 rmsd = 0.358 "obj and name CA" index = 125 rmsd = 0.291 "obj and name CA" index = 126 rmsd = 0.352 "obj and name CA" index = 127 rmsd = 0.501 "obj and name CA" index = 128 rmsd = 0.631 "obj and name CA" index = 129 rmsd = 0.868 "obj and name CA" index = 130 rmsd = 0.937 "obj and name CA" index = 131 rmsd = 0.842 "obj and name CA" index = 132 rmsd = 0.665 "obj and name CA" index = 133 rmsd = 0.491 "obj and name CA" index = 134 rmsd = 0.401 "obj and name CA" index = 135 rmsd = 0.356 "obj and name CA" index = 136 rmsd = 0.353 "obj and name CA" index = 137 rmsd = 0.354 "obj and name CA" index = 138 rmsd = 0.396 "obj and name CA" index = 139 rmsd = 0.441 "obj and name CA" index = 140 rmsd = 0.563 "obj and name CA" index = 141 rmsd = 0.636 "obj and name CA" index = 142 rmsd = 0.788 "obj and name CA" index = 143 rmsd = 0.750 "obj and name CA" index = 144 rmsd = 0.765 "obj and name CA" index = 145 rmsd = 0.850 "obj and name CA" index = 146 rmsd = 0.780 "obj and name CA" index = 147 rmsd = 0.644 "obj and name CA" index = 148 rmsd = 0.665 "obj and name CA" index = 149 rmsd = 0.725 "obj and name CA" index = 150 rmsd = 0.598 "obj and name CA" index = 151 rmsd = 0.580 "obj and name CA" index = 152 rmsd = 0.685 "obj and name CA" index = 153 rmsd = 0.692 "obj and name CA" index = 154 rmsd = 0.604 "obj and name CA" index = 155 rmsd = 0.694 "obj and name CA" index = 156 rmsd = 0.827 "obj and name CA" index = 157 rmsd = 0.728 "obj and name CA" index = 158 rmsd = 0.834 "obj and name CA" index = 159 rmsd = 0.800 "obj and name CA" index = 160 rmsd = 0.671 "obj and name CA" index = 161 rmsd = 0.744 "obj and name CA" index = 162 rmsd = 0.653 "obj and name CA" index = 163 rmsd = 0.564 "obj and name CA" index = 164 rmsd = 0.555 "obj and name CA" index = 165 rmsd = 0.547 "obj and name CA" index = 166 rmsd = 0.529 "obj and name CA" index = 167 rmsd = 0.756 "obj and name CA" index = 168 rmsd = 0.755 "obj and name CA" index = 169 rmsd = 0.735 "obj and name CA" index = 170 rmsd = 1.085 "obj and name CA" index = 171 rmsd = 0.882 "obj and name CA" index = 172 rmsd = 1.988 "obj and name CA" index = 173 rmsd = 3.273 "obj and name CA" index = 174 rmsd = 5.312 "obj and name CA" index = 175 rmsd = 7.524 "obj and name CA" index = 176 rmsd = 9.597 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 144 atoms. PyMOL>color cyan,ss s Executive: Colored 192 atoms. PyMOL>color gray,ss ""+l Executive: Colored 5544 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: 2.43 sec. = 1481.5 frames/hour (10.94 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit