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 30 atoms. PyMOL>color cyan,ss s Executive: Colored 48 atoms. PyMOL>color gray,ss ""+l Executive: Colored 2060 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: 1.16 sec. = 3101.9 frames/hour (1.16 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 402 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 402 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: 5.00 sec. = 719.4 frames/hour (6.16 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, 6.7238907814025879, 8.7932920455932617, 5.4042534828186035, 6.5043668746948242, 9.4416112899780273, 6.0249533653259277, 9.0796842575073242, 7.3839249610900879, 6.4527955055236816, 8.9279518127441406, 6.8285655975341797, 8.0304975509643555, 8.9909534454345703, 5.3072733879089355, 6.2449245452880859, 4.6687140464782715, 4.858980655670166, 4.1778702735900879, 7.0075826644897461] -> atom index_map = [None, 2, 21, 35, 45, 56, 80, 101, 120, 134, 146, 163, 177, 196, 211, 226, 245, 256, 280, 292, 316, 336, 353, 372, 389, 403, 425, 442, 464, 480, 495, 502, 516, 535, 546, 565, 589, 608, 620, 637, 647, 666, 683, 695, 717, 731, 750, 767, 786, 808, 818, 832, 852, 863, 879, 898, 918, 930, 954, 973, 988, 1002, 1021, 1040, 1059, 1078, 1102, 1112, 1132, 1146, 1161, 1176, 1183, 1193, 1212, 1228, 1235, 1250, 1269, 1280, 1294, 1313, 1327, 1338, 1358, 1372, 1379, 1396, 1410, 1429, 1444, 1456, 1472, 1494, 1508, 1518, 1537, 1544, 1560, 1579, 1598, 1605, 1612, 1631, 1646, 1670, 1684, 1696, 1710, 1724, 1740, 1764, 1780, 1791, 1813, 1827, 1846, 1863, 1887, 1907, 1917, 1941, 1948, 1959, 1970, 1984, 1999, 2013, 2020, 2044, 2058, 2072, 2091, 2105, 2124] "obj and name CA" index = 1 rmsd = 7.771 "obj and name CA" index = 2 rmsd = 5.773 "obj and name CA" index = 3 rmsd = 5.090 "obj and name CA" index = 4 rmsd = 3.799 "obj and name CA" index = 5 rmsd = 3.443 "obj and name CA" index = 6 rmsd = 3.052 "obj and name CA" index = 7 rmsd = 2.834 "obj and name CA" index = 8 rmsd = 2.962 "obj and name CA" index = 9 rmsd = 2.851 "obj and name CA" index = 10 rmsd = 2.829 "obj and name CA" index = 11 rmsd = 3.663 "obj and name CA" index = 12 rmsd = 3.961 "obj and name CA" index = 13 rmsd = 4.370 "obj and name CA" index = 14 rmsd = 3.429 "obj and name CA" index = 15 rmsd = 2.967 "obj and name CA" index = 16 rmsd = 3.858 "obj and name CA" index = 17 rmsd = 3.737 "obj and name CA" index = 18 rmsd = 3.917 "obj and name CA" index = 19 rmsd = 3.228 "obj and name CA" index = 20 rmsd = 3.160 "obj and name CA" index = 21 rmsd = 2.755 "obj and name CA" index = 22 rmsd = 3.231 "obj and name CA" index = 23 rmsd = 3.150 "obj and name CA" index = 24 rmsd = 2.848 "obj and name CA" index = 25 rmsd = 2.989 "obj and name CA" index = 26 rmsd = 3.160 "obj and name CA" index = 27 rmsd = 3.537 "obj and name CA" index = 28 rmsd = 3.702 "obj and name CA" index = 29 rmsd = 3.940 "obj and name CA" index = 30 rmsd = 4.416 "obj and name CA" index = 31 rmsd = 3.867 "obj and name CA" index = 32 rmsd = 2.883 "obj and name CA" index = 33 rmsd = 2.669 "obj and name CA" index = 34 rmsd = 2.250 "obj and name CA" index = 35 rmsd = 1.899 "obj and name CA" index = 36 rmsd = 2.116 "obj and name CA" index = 37 rmsd = 2.412 "obj and name CA" index = 38 rmsd = 3.164 "obj and name CA" index = 39 rmsd = 3.316 "obj and name CA" index = 40 rmsd = 3.295 "obj and name CA" index = 41 rmsd = 4.167 "obj and name CA" index = 42 rmsd = 4.964 "obj and name CA" index = 43 rmsd = 4.372 "obj and name CA" index = 44 rmsd = 4.420 "obj and name CA" index = 45 rmsd = 3.407 "obj and name CA" index = 46 rmsd = 3.189 "obj and name CA" index = 47 rmsd = 2.369 "obj and name CA" index = 48 rmsd = 2.026 "obj and name CA" index = 49 rmsd = 1.431 "obj and name CA" index = 50 rmsd = 1.779 "obj and name CA" index = 51 rmsd = 1.886 "obj and name CA" index = 52 rmsd = 2.495 "obj and name CA" index = 53 rmsd = 2.940 "obj and name CA" index = 54 rmsd = 3.520 "obj and name CA" index = 55 rmsd = 4.280 "obj and name CA" index = 56 rmsd = 4.185 "obj and name CA" index = 57 rmsd = 3.757 "obj and name CA" index = 58 rmsd = 2.888 "obj and name CA" index = 59 rmsd = 2.948 "obj and name CA" index = 60 rmsd = 2.543 "obj and name CA" index = 61 rmsd = 1.793 "obj and name CA" index = 62 rmsd = 1.906 "obj and name CA" index = 63 rmsd = 1.293 "obj and name CA" index = 64 rmsd = 0.770 "obj and name CA" index = 65 rmsd = 1.060 "obj and name CA" index = 66 rmsd = 1.688 "obj and name CA" index = 67 rmsd = 2.475 "obj and name CA" index = 68 rmsd = 3.298 "obj and name CA" index = 69 rmsd = 4.254 "obj and name CA" index = 70 rmsd = 4.260 "obj and name CA" index = 71 rmsd = 3.691 "obj and name CA" index = 72 rmsd = 3.137 "obj and name CA" index = 73 rmsd = 2.233 "obj and name CA" index = 74 rmsd = 2.044 "obj and name CA" index = 75 rmsd = 1.458 "obj and name CA" index = 76 rmsd = 0.979 "obj and name CA" index = 77 rmsd = 1.239 "obj and name CA" index = 78 rmsd = 1.796 "obj and name CA" index = 79 rmsd = 2.617 "obj and name CA" index = 80 rmsd = 3.594 "obj and name CA" index = 81 rmsd = 4.582 "obj and name CA" index = 82 rmsd = 5.399 "obj and name CA" index = 83 rmsd = 4.740 "obj and name CA" index = 84 rmsd = 4.982 "obj and name CA" index = 85 rmsd = 4.261 "obj and name CA" index = 86 rmsd = 3.599 "obj and name CA" index = 87 rmsd = 3.786 "obj and name CA" index = 88 rmsd = 3.526 "obj and name CA" index = 89 rmsd = 4.335 "obj and name CA" index = 90 rmsd = 3.727 "obj and name CA" index = 91 rmsd = 2.772 "obj and name CA" index = 92 rmsd = 3.680 "obj and name CA" index = 93 rmsd = 4.137 "obj and name CA" index = 94 rmsd = 3.049 "obj and name CA" index = 95 rmsd = 2.897 "obj and name CA" index = 96 rmsd = 4.072 "obj and name CA" index = 97 rmsd = 3.836 "obj and name CA" index = 98 rmsd = 2.884 "obj and name CA" index = 99 rmsd = 3.771 "obj and name CA" index = 100 rmsd = 4.562 "obj and name CA" index = 101 rmsd = 3.907 "obj and name CA" index = 102 rmsd = 3.717 "obj and name CA" index = 103 rmsd = 4.862 "obj and name CA" index = 104 rmsd = 5.026 "obj and name CA" index = 105 rmsd = 4.443 "obj and name CA" index = 106 rmsd = 5.181 "obj and name CA" index = 107 rmsd = 4.600 "obj and name CA" index = 108 rmsd = 4.885 "obj and name CA" index = 109 rmsd = 4.197 "obj and name CA" index = 110 rmsd = 4.248 "obj and name CA" index = 111 rmsd = 3.628 "obj and name CA" index = 112 rmsd = 3.406 "obj and name CA" index = 113 rmsd = 4.300 "obj and name CA" index = 114 rmsd = 3.573 "obj and name CA" index = 115 rmsd = 3.169 "obj and name CA" index = 116 rmsd = 4.349 "obj and name CA" index = 117 rmsd = 4.602 "obj and name CA" index = 118 rmsd = 3.836 "obj and name CA" index = 119 rmsd = 3.698 "obj and name CA" index = 120 rmsd = 4.356 "obj and name CA" index = 121 rmsd = 5.420 "obj and name CA" index = 122 rmsd = 4.783 "obj and name CA" index = 123 rmsd = 4.203 "obj and name CA" index = 124 rmsd = 4.499 "obj and name CA" index = 125 rmsd = 5.621 "obj and name CA" index = 126 rmsd = 7.089 "obj and name CA" index = 127 rmsd = 9.586 "obj and name CA" index = 128 rmsd = 11.534 "obj and name CA" index = 129 rmsd = 13.427 "obj and name CA" index = 130 rmsd = 15.656 "obj and name CA" index = 131 rmsd = 17.803 "obj and name CA" index = 132 rmsd = 20.291 "obj and name CA" index = 133 rmsd = 23.010 "obj and name CA" index = 134 rmsd = 25.065 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 90 atoms. PyMOL>color cyan,ss s Executive: Colored 144 atoms. PyMOL>color gray,ss ""+l Executive: Colored 4176 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: 1.94 sec. = 1851.1 frames/hour (8.11 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit