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 85 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 2431 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: 1.71 sec. = 2107.7 frames/hour (1.71 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: 6.75 sec. = 533.4 frames/hour (8.46 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, 8.6739597320556641, 5.5367264747619629, 5.7019548416137695, 8.1065864562988281, 6.4782085418701172, 6.8810873031616211, 5.0595035552978516, 6.4693708419799805, 10.067280769348145, 6.1443595886230469, 6.8020758628845215, 6.633364200592041, 6.1258749961853027, 6.5014667510986328, 7.1379470825195312, 6.4013705253601074, 4.8869023323059082, 6.4817066192626953, 5.9317212104797363] -> 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 = 12.836 "obj and name CA" index = 2 rmsd = 12.072 "obj and name CA" index = 3 rmsd = 10.850 "obj and name CA" index = 4 rmsd = 10.389 "obj and name CA" index = 5 rmsd = 9.754 "obj and name CA" index = 6 rmsd = 9.448 "obj and name CA" index = 7 rmsd = 8.555 "obj and name CA" index = 8 rmsd = 7.908 "obj and name CA" index = 9 rmsd = 6.996 "obj and name CA" index = 10 rmsd = 6.083 "obj and name CA" index = 11 rmsd = 5.148 "obj and name CA" index = 12 rmsd = 3.865 "obj and name CA" index = 13 rmsd = 2.555 "obj and name CA" index = 14 rmsd = 2.342 "obj and name CA" index = 15 rmsd = 2.271 "obj and name CA" index = 16 rmsd = 2.219 "obj and name CA" index = 17 rmsd = 2.491 "obj and name CA" index = 18 rmsd = 2.841 "obj and name CA" index = 19 rmsd = 3.387 "obj and name CA" index = 20 rmsd = 3.074 "obj and name CA" index = 21 rmsd = 3.278 "obj and name CA" index = 22 rmsd = 3.031 "obj and name CA" index = 23 rmsd = 3.150 "obj and name CA" index = 24 rmsd = 2.936 "obj and name CA" index = 25 rmsd = 2.465 "obj and name CA" index = 26 rmsd = 2.467 "obj and name CA" index = 27 rmsd = 2.562 "obj and name CA" index = 28 rmsd = 2.164 "obj and name CA" index = 29 rmsd = 1.841 "obj and name CA" index = 30 rmsd = 2.052 "obj and name CA" index = 31 rmsd = 1.999 "obj and name CA" index = 32 rmsd = 1.538 "obj and name CA" index = 33 rmsd = 1.537 "obj and name CA" index = 34 rmsd = 1.898 "obj and name CA" index = 35 rmsd = 1.691 "obj and name CA" index = 36 rmsd = 1.313 "obj and name CA" index = 37 rmsd = 1.514 "obj and name CA" index = 38 rmsd = 2.136 "obj and name CA" index = 39 rmsd = 2.790 "obj and name CA" index = 40 rmsd = 3.097 "obj and name CA" index = 41 rmsd = 2.512 "obj and name CA" index = 42 rmsd = 3.162 "obj and name CA" index = 43 rmsd = 3.627 "obj and name CA" index = 44 rmsd = 3.474 "obj and name CA" index = 45 rmsd = 2.086 "obj and name CA" index = 46 rmsd = 2.809 "obj and name CA" index = 47 rmsd = 2.039 "obj and name CA" index = 48 rmsd = 1.844 "obj and name CA" index = 49 rmsd = 1.771 "obj and name CA" index = 50 rmsd = 1.871 "obj and name CA" index = 51 rmsd = 1.671 "obj and name CA" index = 52 rmsd = 1.463 "obj and name CA" index = 53 rmsd = 1.705 "obj and name CA" index = 54 rmsd = 1.979 "obj and name CA" index = 55 rmsd = 1.772 "obj and name CA" index = 56 rmsd = 1.779 "obj and name CA" index = 57 rmsd = 2.202 "obj and name CA" index = 58 rmsd = 2.362 "obj and name CA" index = 59 rmsd = 2.283 "obj and name CA" index = 60 rmsd = 2.102 "obj and name CA" index = 61 rmsd = 1.733 "obj and name CA" index = 62 rmsd = 1.707 "obj and name CA" index = 63 rmsd = 1.517 "obj and name CA" index = 64 rmsd = 1.483 "obj and name CA" index = 65 rmsd = 1.267 "obj and name CA" index = 66 rmsd = 1.138 "obj and name CA" index = 67 rmsd = 1.008 "obj and name CA" index = 68 rmsd = 0.951 "obj and name CA" index = 69 rmsd = 0.862 "obj and name CA" index = 70 rmsd = 0.779 "obj and name CA" index = 71 rmsd = 0.760 "obj and name CA" index = 72 rmsd = 1.034 "obj and name CA" index = 73 rmsd = 1.207 "obj and name CA" index = 74 rmsd = 1.705 "obj and name CA" index = 75 rmsd = 1.723 "obj and name CA" index = 76 rmsd = 1.299 "obj and name CA" index = 77 rmsd = 1.549 "obj and name CA" index = 78 rmsd = 2.074 "obj and name CA" index = 79 rmsd = 2.132 "obj and name CA" index = 80 rmsd = 1.862 "obj and name CA" index = 81 rmsd = 1.627 "obj and name CA" index = 82 rmsd = 2.047 "obj and name CA" index = 83 rmsd = 2.302 "obj and name CA" index = 84 rmsd = 2.130 "obj and name CA" index = 85 rmsd = 1.969 "obj and name CA" index = 86 rmsd = 1.646 "obj and name CA" index = 87 rmsd = 1.667 "obj and name CA" index = 88 rmsd = 1.732 "obj and name CA" index = 89 rmsd = 1.422 "obj and name CA" index = 90 rmsd = 1.277 "obj and name CA" index = 91 rmsd = 1.571 "obj and name CA" index = 92 rmsd = 1.493 "obj and name CA" index = 93 rmsd = 1.108 "obj and name CA" index = 94 rmsd = 1.493 "obj and name CA" index = 95 rmsd = 1.818 "obj and name CA" index = 96 rmsd = 1.517 "obj and name CA" index = 97 rmsd = 1.228 "obj and name CA" index = 98 rmsd = 1.740 "obj and name CA" index = 99 rmsd = 2.135 "obj and name CA" index = 100 rmsd = 2.472 "obj and name CA" index = 101 rmsd = 2.141 "obj and name CA" index = 102 rmsd = 2.083 "obj and name CA" index = 103 rmsd = 2.635 "obj and name CA" index = 104 rmsd = 2.467 "obj and name CA" index = 105 rmsd = 2.444 "obj and name CA" index = 106 rmsd = 2.466 "obj and name CA" index = 107 rmsd = 2.000 "obj and name CA" index = 108 rmsd = 1.783 "obj and name CA" index = 109 rmsd = 2.004 "obj and name CA" index = 110 rmsd = 1.965 "obj and name CA" index = 111 rmsd = 1.548 "obj and name CA" index = 112 rmsd = 1.599 "obj and name CA" index = 113 rmsd = 1.954 "obj and name CA" index = 114 rmsd = 1.735 "obj and name CA" index = 115 rmsd = 1.460 "obj and name CA" index = 116 rmsd = 1.907 "obj and name CA" index = 117 rmsd = 2.228 "obj and name CA" index = 118 rmsd = 2.071 "obj and name CA" index = 119 rmsd = 1.757 "obj and name CA" index = 120 rmsd = 1.231 "obj and name CA" index = 121 rmsd = 1.358 "obj and name CA" index = 122 rmsd = 1.537 "obj and name CA" index = 123 rmsd = 1.129 "obj and name CA" index = 124 rmsd = 0.951 "obj and name CA" index = 125 rmsd = 1.413 "obj and name CA" index = 126 rmsd = 1.585 "obj and name CA" index = 127 rmsd = 1.369 "obj and name CA" index = 128 rmsd = 1.456 "obj and name CA" index = 129 rmsd = 2.019 "obj and name CA" index = 130 rmsd = 2.390 "obj and name CA" index = 131 rmsd = 2.622 "obj and name CA" index = 132 rmsd = 2.819 "obj and name CA" index = 133 rmsd = 2.452 "obj and name CA" index = 134 rmsd = 2.272 "obj and name CA" index = 135 rmsd = 2.751 "obj and name CA" index = 136 rmsd = 3.087 "obj and name CA" index = 137 rmsd = 2.655 "obj and name CA" index = 138 rmsd = 2.117 "obj and name CA" index = 139 rmsd = 1.955 "obj and name CA" index = 140 rmsd = 2.019 "obj and name CA" index = 141 rmsd = 2.012 "obj and name CA" index = 142 rmsd = 1.666 "obj and name CA" index = 143 rmsd = 1.696 "obj and name CA" index = 144 rmsd = 2.318 "obj and name CA" index = 145 rmsd = 2.413 "obj and name CA" index = 146 rmsd = 3.749 "obj and name CA" index = 147 rmsd = 5.855 "obj and name CA" index = 148 rmsd = 7.759 "obj and name CA" index = 149 rmsd = 9.908 "obj and name CA" index = 150 rmsd = 11.795 "obj and name CA" index = 151 rmsd = 14.120 "obj and name CA" index = 152 rmsd = 16.365 "obj and name CA" index = 153 rmsd = 17.756 "obj and name CA" index = 154 rmsd = 19.737 "obj and name CA" index = 155 rmsd = 20.586 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 255 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 4926 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: 2.48 sec. = 1453.0 frames/hour (10.93 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit