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 19 atoms. PyMOL>color cyan,ss s Executive: Colored 17 atoms. PyMOL>color gray,ss ""+l Executive: Colored 2410 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: 1.84 sec. = 1957.9 frames/hour (1.84 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 465 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 465 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: 7.99 sec. = 450.5 frames/hour (9.83 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, 8.4737558364868164, 8.0980024337768555, 8.4415683746337891, 7.318659782409668, 8.5214357376098633, 7.8931427001953125, 10.662240982055664, 9.5367870330810547, 7.1478352546691895, 8.3732414245605469, 7.3869433403015137, 7.1774587631225586, 9.7871875762939453, 8.9404773712158203, 8.3493452072143555, 7.7568936347961426, 8.742340087890625, 6.9564323425292969, 6.2418322563171387] -> atom index_map = [None, 2, 21, 28, 43, 57, 73, 89, 113, 125, 135, 151, 165, 184, 191, 213, 227, 237, 252, 269, 288, 309, 319, 335, 359, 383, 395, 414, 428, 435, 454, 468, 487, 506, 523, 537, 554, 573, 597, 608, 624, 639, 655, 674, 686, 698, 720, 744, 755, 779, 803, 817, 833, 848, 858, 872, 882, 896, 915, 922, 932, 948, 959, 983, 998, 1008, 1023, 1042, 1056, 1066, 1078, 1093, 1107, 1114, 1136, 1160, 1179, 1189, 1213, 1237, 1248, 1267, 1281, 1288, 1298, 1322, 1341, 1356, 1370, 1381, 1388, 1403, 1419, 1438, 1458, 1482, 1496, 1506, 1520, 1527, 1537, 1561, 1568, 1582, 1597, 1613, 1629, 1645, 1669, 1688, 1702, 1723, 1747, 1761, 1775, 1782, 1789, 1800, 1810, 1817, 1827, 1843, 1862, 1872, 1896, 1913, 1933, 1947, 1964, 1979, 1993, 2004, 2021, 2038, 2057, 2081, 2093, 2105, 2124, 2141, 2165, 2185, 2207, 2231, 2246, 2263, 2278, 2297, 2304, 2323, 2338, 2355, 2372, 2389, 2406, 2423] "obj and name CA" index = 1 rmsd = 8.138 "obj and name CA" index = 2 rmsd = 6.444 "obj and name CA" index = 3 rmsd = 5.163 "obj and name CA" index = 4 rmsd = 4.544 "obj and name CA" index = 5 rmsd = 3.704 "obj and name CA" index = 6 rmsd = 3.209 "obj and name CA" index = 7 rmsd = 2.869 "obj and name CA" index = 8 rmsd = 2.931 "obj and name CA" index = 9 rmsd = 2.660 "obj and name CA" index = 10 rmsd = 2.711 "obj and name CA" index = 11 rmsd = 2.730 "obj and name CA" index = 12 rmsd = 2.757 "obj and name CA" index = 13 rmsd = 3.093 "obj and name CA" index = 14 rmsd = 2.858 "obj and name CA" index = 15 rmsd = 2.831 "obj and name CA" index = 16 rmsd = 2.414 "obj and name CA" index = 17 rmsd = 2.815 "obj and name CA" index = 18 rmsd = 2.897 "obj and name CA" index = 19 rmsd = 2.234 "obj and name CA" index = 20 rmsd = 2.207 "obj and name CA" index = 21 rmsd = 2.840 "obj and name CA" index = 22 rmsd = 3.087 "obj and name CA" index = 23 rmsd = 3.543 "obj and name CA" index = 24 rmsd = 4.122 "obj and name CA" index = 25 rmsd = 4.706 "obj and name CA" index = 26 rmsd = 4.041 "obj and name CA" index = 27 rmsd = 4.988 "obj and name CA" index = 28 rmsd = 5.381 "obj and name CA" index = 29 rmsd = 4.580 "obj and name CA" index = 30 rmsd = 5.648 "obj and name CA" index = 31 rmsd = 5.211 "obj and name CA" index = 32 rmsd = 5.077 "obj and name CA" index = 33 rmsd = 6.795 "obj and name CA" index = 34 rmsd = 7.711 "obj and name CA" index = 35 rmsd = 8.800 "obj and name CA" index = 36 rmsd = 8.574 "obj and name CA" index = 37 rmsd = 8.391 "obj and name CA" index = 38 rmsd = 8.017 "obj and name CA" index = 39 rmsd = 6.253 "obj and name CA" index = 40 rmsd = 6.609 "obj and name CA" index = 41 rmsd = 5.176 "obj and name CA" index = 42 rmsd = 5.417 "obj and name CA" index = 43 rmsd = 5.956 "obj and name CA" index = 44 rmsd = 5.256 "obj and name CA" index = 45 rmsd = 4.587 "obj and name CA" index = 46 rmsd = 3.875 "obj and name CA" index = 47 rmsd = 3.904 "obj and name CA" index = 48 rmsd = 5.043 "obj and name CA" index = 49 rmsd = 5.580 "obj and name CA" index = 50 rmsd = 6.386 "obj and name CA" index = 51 rmsd = 6.322 "obj and name CA" index = 52 rmsd = 8.225 "obj and name CA" index = 53 rmsd = 7.817 "obj and name CA" index = 54 rmsd = 7.400 "obj and name CA" index = 55 rmsd = 6.988 "obj and name CA" index = 56 rmsd = 5.177 "obj and name CA" index = 57 rmsd = 5.927 "obj and name CA" index = 58 rmsd = 7.999 "obj and name CA" index = 59 rmsd = 7.887 "obj and name CA" index = 60 rmsd = 6.201 "obj and name CA" index = 61 rmsd = 5.558 "obj and name CA" index = 62 rmsd = 5.219 "obj and name CA" index = 63 rmsd = 3.846 "obj and name CA" index = 64 rmsd = 3.201 "obj and name CA" index = 65 rmsd = 2.970 "obj and name CA" index = 66 rmsd = 2.344 "obj and name CA" index = 67 rmsd = 2.436 "obj and name CA" index = 68 rmsd = 2.229 "obj and name CA" index = 69 rmsd = 2.331 "obj and name CA" index = 70 rmsd = 2.528 "obj and name CA" index = 71 rmsd = 3.026 "obj and name CA" index = 72 rmsd = 2.352 "obj and name CA" index = 73 rmsd = 2.109 "obj and name CA" index = 74 rmsd = 1.697 "obj and name CA" index = 75 rmsd = 1.548 "obj and name CA" index = 76 rmsd = 1.690 "obj and name CA" index = 77 rmsd = 1.934 "obj and name CA" index = 78 rmsd = 2.682 "obj and name CA" index = 79 rmsd = 3.828 "obj and name CA" index = 80 rmsd = 3.792 "obj and name CA" index = 81 rmsd = 4.567 "obj and name CA" index = 82 rmsd = 4.961 "obj and name CA" index = 83 rmsd = 4.605 "obj and name CA" index = 84 rmsd = 5.047 "obj and name CA" index = 85 rmsd = 4.406 "obj and name CA" index = 86 rmsd = 4.522 "obj and name CA" index = 87 rmsd = 3.335 "obj and name CA" index = 88 rmsd = 2.830 "obj and name CA" index = 89 rmsd = 2.469 "obj and name CA" index = 90 rmsd = 1.766 "obj and name CA" index = 91 rmsd = 1.561 "obj and name CA" index = 92 rmsd = 1.625 "obj and name CA" index = 93 rmsd = 1.795 "obj and name CA" index = 94 rmsd = 2.147 "obj and name CA" index = 95 rmsd = 2.408 "obj and name CA" index = 96 rmsd = 2.540 "obj and name CA" index = 97 rmsd = 2.977 "obj and name CA" index = 98 rmsd = 3.655 "obj and name CA" index = 99 rmsd = 3.646 "obj and name CA" index = 100 rmsd = 3.579 "obj and name CA" index = 101 rmsd = 2.989 "obj and name CA" index = 102 rmsd = 2.414 "obj and name CA" index = 103 rmsd = 2.295 "obj and name CA" index = 104 rmsd = 1.981 "obj and name CA" index = 105 rmsd = 2.062 "obj and name CA" index = 106 rmsd = 2.133 "obj and name CA" index = 107 rmsd = 2.368 "obj and name CA" index = 108 rmsd = 2.596 "obj and name CA" index = 109 rmsd = 2.963 "obj and name CA" index = 110 rmsd = 3.413 "obj and name CA" index = 111 rmsd = 3.535 "obj and name CA" index = 112 rmsd = 4.009 "obj and name CA" index = 113 rmsd = 5.573 "obj and name CA" index = 114 rmsd = 6.846 "obj and name CA" index = 115 rmsd = 7.988 "obj and name CA" index = 116 rmsd = 8.399 "obj and name CA" index = 117 rmsd = 8.282 "obj and name CA" index = 118 rmsd = 7.369 "obj and name CA" index = 119 rmsd = 7.820 "obj and name CA" index = 120 rmsd = 8.652 "obj and name CA" index = 121 rmsd = 8.360 "obj and name CA" index = 122 rmsd = 8.143 "obj and name CA" index = 123 rmsd = 9.511 "obj and name CA" index = 124 rmsd = 10.290 "obj and name CA" index = 125 rmsd = 10.080 "obj and name CA" index = 126 rmsd = 9.438 "obj and name CA" index = 127 rmsd = 8.988 "obj and name CA" index = 128 rmsd = 7.722 "obj and name CA" index = 129 rmsd = 7.508 "obj and name CA" index = 130 rmsd = 7.341 "obj and name CA" index = 131 rmsd = 6.985 "obj and name CA" index = 132 rmsd = 5.685 "obj and name CA" index = 133 rmsd = 3.603 "obj and name CA" index = 134 rmsd = 3.629 "obj and name CA" index = 135 rmsd = 4.141 "obj and name CA" index = 136 rmsd = 3.910 "obj and name CA" index = 137 rmsd = 2.835 "obj and name CA" index = 138 rmsd = 3.363 "obj and name CA" index = 139 rmsd = 3.829 "obj and name CA" index = 140 rmsd = 3.138 "obj and name CA" index = 141 rmsd = 3.000 "obj and name CA" index = 142 rmsd = 4.092 "obj and name CA" index = 143 rmsd = 4.113 "obj and name CA" index = 144 rmsd = 3.604 "obj and name CA" index = 145 rmsd = 4.353 "obj and name CA" index = 146 rmsd = 5.139 "obj and name CA" index = 147 rmsd = 4.940 "obj and name CA" index = 148 rmsd = 5.587 "obj and name CA" index = 149 rmsd = 7.115 "obj and name CA" index = 150 rmsd = 8.778 "obj and name CA" index = 151 rmsd = 10.361 "obj and name CA" index = 152 rmsd = 12.467 "obj and name CA" index = 153 rmsd = 14.337 "obj and name CA" index = 154 rmsd = 16.294 "obj and name CA" index = 155 rmsd = 17.918 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 57 atoms. PyMOL>color cyan,ss s Executive: Colored 51 atoms. PyMOL>color gray,ss ""+l Executive: Colored 4932 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: 1.66 sec. = 2162.6 frames/hour (11.50 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit