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 82 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 2435 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: 1.50 sec. = 2406.4 frames/hour (1.50 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: 5.04 sec. = 713.6 frames/hour (6.54 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, 5.8785767555236816, 6.0287480354309082, 6.1262273788452148, 6.8126659393310547, 7.2455177307128906, 8.9563627243041992, 3.8871293067932129, 10.557194709777832, 3.9883952140808105, 6.1438660621643066, 5.3653602600097656, 7.0910582542419434, 5.647038459777832, 4.8295245170593262, 9.0218257904052734, 6.7648797035217285, 10.990139007568359, 4.9220461845397949, 9.1785135269165039] -> atom index_map = [None, 2, 18, 35, 46, 67, 87, 101, 111, 121, 131, 153, 177, 194, 216, 237, 247, 264, 286, 300, 307, 326, 337, 347, 366, 381, 403, 417, 427, 443, 462, 484, 494, 504, 525, 549, 566, 585, 605, 620, 644, 656, 675, 689, 711, 721, 742, 753, 770, 781, 800, 811, 832, 851, 866, 877, 894, 910, 934, 948, 955, 967, 986, 997, 1014, 1036, 1051, 1071, 1087, 1111, 1135, 1154, 1164, 1186, 1197, 1211, 1230, 1251, 1275, 1297, 1314, 1334, 1354, 1369, 1383, 1403, 1422, 1436, 1447, 1471, 1481, 1500, 1515, 1534, 1544, 1564, 1588, 1605, 1624, 1643, 1650, 1674, 1681, 1695, 1706, 1717, 1741, 1756, 1771, 1787, 1804, 1826, 1847, 1867, 1878, 1897, 1913, 1924, 1935, 1942, 1949, 1968, 1982, 1992, 2011, 2027, 2039, 2049, 2068, 2084, 2096, 2107, 2124, 2139, 2160, 2170, 2182, 2203, 2223, 2230, 2245, 2260, 2274, 2290, 2304, 2325, 2344, 2368, 2375, 2394, 2409, 2426, 2443, 2460, 2477, 2494] "obj and name CA" index = 1 rmsd = 20.486 "obj and name CA" index = 2 rmsd = 18.999 "obj and name CA" index = 3 rmsd = 17.324 "obj and name CA" index = 4 rmsd = 16.117 "obj and name CA" index = 5 rmsd = 14.424 "obj and name CA" index = 6 rmsd = 12.457 "obj and name CA" index = 7 rmsd = 10.296 "obj and name CA" index = 8 rmsd = 8.386 "obj and name CA" index = 9 rmsd = 6.721 "obj and name CA" index = 10 rmsd = 5.674 "obj and name CA" index = 11 rmsd = 4.259 "obj and name CA" index = 12 rmsd = 3.593 "obj and name CA" index = 13 rmsd = 3.019 "obj and name CA" index = 14 rmsd = 2.708 "obj and name CA" index = 15 rmsd = 2.698 "obj and name CA" index = 16 rmsd = 2.474 "obj and name CA" index = 17 rmsd = 3.181 "obj and name CA" index = 18 rmsd = 3.680 "obj and name CA" index = 19 rmsd = 4.105 "obj and name CA" index = 20 rmsd = 3.502 "obj and name CA" index = 21 rmsd = 3.701 "obj and name CA" index = 22 rmsd = 3.743 "obj and name CA" index = 23 rmsd = 3.730 "obj and name CA" index = 24 rmsd = 3.247 "obj and name CA" index = 25 rmsd = 2.889 "obj and name CA" index = 26 rmsd = 3.019 "obj and name CA" index = 27 rmsd = 2.911 "obj and name CA" index = 28 rmsd = 2.360 "obj and name CA" index = 29 rmsd = 2.045 "obj and name CA" index = 30 rmsd = 2.259 "obj and name CA" index = 31 rmsd = 2.318 "obj and name CA" index = 32 rmsd = 1.742 "obj and name CA" index = 33 rmsd = 1.651 "obj and name CA" index = 34 rmsd = 2.133 "obj and name CA" index = 35 rmsd = 2.082 "obj and name CA" index = 36 rmsd = 1.682 "obj and name CA" index = 37 rmsd = 2.034 "obj and name CA" index = 38 rmsd = 2.434 "obj and name CA" index = 39 rmsd = 2.658 "obj and name CA" index = 40 rmsd = 3.666 "obj and name CA" index = 41 rmsd = 2.845 "obj and name CA" index = 42 rmsd = 3.488 "obj and name CA" index = 43 rmsd = 3.877 "obj and name CA" index = 44 rmsd = 4.095 "obj and name CA" index = 45 rmsd = 2.792 "obj and name CA" index = 46 rmsd = 2.805 "obj and name CA" index = 47 rmsd = 2.551 "obj and name CA" index = 48 rmsd = 2.305 "obj and name CA" index = 49 rmsd = 1.842 "obj and name CA" index = 50 rmsd = 2.107 "obj and name CA" index = 51 rmsd = 2.199 "obj and name CA" index = 52 rmsd = 1.800 "obj and name CA" index = 53 rmsd = 1.927 "obj and name CA" index = 54 rmsd = 2.387 "obj and name CA" index = 55 rmsd = 2.313 "obj and name CA" index = 56 rmsd = 2.233 "obj and name CA" index = 57 rmsd = 2.572 "obj and name CA" index = 58 rmsd = 2.829 "obj and name CA" index = 59 rmsd = 2.737 "obj and name CA" index = 60 rmsd = 2.729 "obj and name CA" index = 61 rmsd = 2.277 "obj and name CA" index = 62 rmsd = 2.153 "obj and name CA" index = 63 rmsd = 1.726 "obj and name CA" index = 64 rmsd = 1.459 "obj and name CA" index = 65 rmsd = 1.423 "obj and name CA" index = 66 rmsd = 1.292 "obj and name CA" index = 67 rmsd = 1.047 "obj and name CA" index = 68 rmsd = 1.106 "obj and name CA" index = 69 rmsd = 1.197 "obj and name CA" index = 70 rmsd = 1.073 "obj and name CA" index = 71 rmsd = 0.983 "obj and name CA" index = 72 rmsd = 1.282 "obj and name CA" index = 73 rmsd = 1.519 "obj and name CA" index = 74 rmsd = 2.111 "obj and name CA" index = 75 rmsd = 1.966 "obj and name CA" index = 76 rmsd = 1.691 "obj and name CA" index = 77 rmsd = 1.987 "obj and name CA" index = 78 rmsd = 2.538 "obj and name CA" index = 79 rmsd = 2.465 "obj and name CA" index = 80 rmsd = 2.384 "obj and name CA" index = 81 rmsd = 2.435 "obj and name CA" index = 82 rmsd = 3.008 "obj and name CA" index = 83 rmsd = 3.053 "obj and name CA" index = 84 rmsd = 2.848 "obj and name CA" index = 85 rmsd = 2.846 "obj and name CA" index = 86 rmsd = 2.434 "obj and name CA" index = 87 rmsd = 2.546 "obj and name CA" index = 88 rmsd = 2.555 "obj and name CA" index = 89 rmsd = 2.052 "obj and name CA" index = 90 rmsd = 1.963 "obj and name CA" index = 91 rmsd = 2.234 "obj and name CA" index = 92 rmsd = 2.066 "obj and name CA" index = 93 rmsd = 1.658 "obj and name CA" index = 94 rmsd = 1.955 "obj and name CA" index = 95 rmsd = 2.226 "obj and name CA" index = 96 rmsd = 1.880 "obj and name CA" index = 97 rmsd = 1.706 "obj and name CA" index = 98 rmsd = 2.128 "obj and name CA" index = 99 rmsd = 2.371 "obj and name CA" index = 100 rmsd = 2.903 "obj and name CA" index = 101 rmsd = 2.659 "obj and name CA" index = 102 rmsd = 2.789 "obj and name CA" index = 103 rmsd = 3.309 "obj and name CA" index = 104 rmsd = 3.277 "obj and name CA" index = 105 rmsd = 3.400 "obj and name CA" index = 106 rmsd = 3.277 "obj and name CA" index = 107 rmsd = 2.711 "obj and name CA" index = 108 rmsd = 2.633 "obj and name CA" index = 109 rmsd = 2.822 "obj and name CA" index = 110 rmsd = 2.658 "obj and name CA" index = 111 rmsd = 2.216 "obj and name CA" index = 112 rmsd = 2.346 "obj and name CA" index = 113 rmsd = 2.561 "obj and name CA" index = 114 rmsd = 2.145 "obj and name CA" index = 115 rmsd = 1.944 "obj and name CA" index = 116 rmsd = 2.414 "obj and name CA" index = 117 rmsd = 2.605 "obj and name CA" index = 118 rmsd = 2.390 "obj and name CA" index = 119 rmsd = 2.136 "obj and name CA" index = 120 rmsd = 1.870 "obj and name CA" index = 121 rmsd = 1.918 "obj and name CA" index = 122 rmsd = 1.969 "obj and name CA" index = 123 rmsd = 1.653 "obj and name CA" index = 124 rmsd = 1.491 "obj and name CA" index = 125 rmsd = 1.774 "obj and name CA" index = 126 rmsd = 1.948 "obj and name CA" index = 127 rmsd = 1.762 "obj and name CA" index = 128 rmsd = 1.797 "obj and name CA" index = 129 rmsd = 2.334 "obj and name CA" index = 130 rmsd = 2.589 "obj and name CA" index = 131 rmsd = 3.031 "obj and name CA" index = 132 rmsd = 3.116 "obj and name CA" index = 133 rmsd = 2.698 "obj and name CA" index = 134 rmsd = 2.798 "obj and name CA" index = 135 rmsd = 3.196 "obj and name CA" index = 136 rmsd = 3.104 "obj and name CA" index = 137 rmsd = 2.784 "obj and name CA" index = 138 rmsd = 2.608 "obj and name CA" index = 139 rmsd = 2.531 "obj and name CA" index = 140 rmsd = 2.649 "obj and name CA" index = 141 rmsd = 2.529 "obj and name CA" index = 142 rmsd = 2.262 "obj and name CA" index = 143 rmsd = 2.266 "obj and name CA" index = 144 rmsd = 2.848 "obj and name CA" index = 145 rmsd = 3.241 "obj and name CA" index = 146 rmsd = 4.376 "obj and name CA" index = 147 rmsd = 6.126 "obj and name CA" index = 148 rmsd = 7.746 "obj and name CA" index = 149 rmsd = 9.701 "obj and name CA" index = 150 rmsd = 11.993 "obj and name CA" index = 151 rmsd = 14.319 "obj and name CA" index = 152 rmsd = 15.918 "obj and name CA" index = 153 rmsd = 17.630 "obj and name CA" index = 154 rmsd = 19.413 "obj and name CA" index = 155 rmsd = 20.171 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 246 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 4936 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: 2.07 sec. = 1741.6 frames/hour (8.61 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit