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 29 atoms. PyMOL>color gray,ss ""+l Executive: Colored 1965 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: 1.09 sec. = 3298.0 frames/hour (1.09 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 363 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 363 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: 4.80 sec. = 750.6 frames/hour (5.89 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, 3.4540424346923828, 3.5855739116668701, 4.3351607322692871, 3.8473114967346191, 3.7093336582183838, 4.079472541809082, 2.7581703662872314, 3.2046868801116943, 2.5268959999084473, 3.4253451824188232, 1.9878888130187988, 2.948986291885376, 3.5570077896118164, 3.4399328231811523, 2.9656305313110352, 3.2833340167999268, 3.3907909393310547, 3.6007182598114014, 4.0094566345214844] -> atom index_map = [None, 2, 21, 40, 51, 68, 78, 92, 107, 119, 139, 161, 183, 202, 218, 232, 246, 265, 289, 308, 330, 342, 356, 376, 388, 408, 430, 449, 459, 469, 489, 503, 517, 534, 548, 569, 581, 598, 617, 636, 650, 661, 678, 697, 718, 740, 754, 775, 796, 813, 820, 839, 854, 873, 890, 907, 924, 946, 967, 984, 998, 1013, 1032, 1044, 1063, 1085, 1104, 1123, 1137, 1157, 1176, 1197, 1211, 1223, 1230, 1242, 1262, 1269, 1280, 1290, 1304, 1326, 1340, 1347, 1361, 1380, 1402, 1421, 1432, 1451, 1468, 1487, 1501, 1513, 1535, 1557, 1571, 1585, 1602, 1618, 1639, 1660, 1682, 1701, 1720, 1735, 1751, 1762, 1769, 1789, 1811, 1822, 1836, 1850, 1871, 1890, 1905, 1922, 1939, 1956, 1973, 1990] "obj and name CA" index = 1 rmsd = 4.954 "obj and name CA" index = 2 rmsd = 3.427 "obj and name CA" index = 3 rmsd = 3.032 "obj and name CA" index = 4 rmsd = 2.561 "obj and name CA" index = 5 rmsd = 2.615 "obj and name CA" index = 6 rmsd = 2.632 "obj and name CA" index = 7 rmsd = 2.402 "obj and name CA" index = 8 rmsd = 1.997 "obj and name CA" index = 9 rmsd = 1.701 "obj and name CA" index = 10 rmsd = 1.692 "obj and name CA" index = 11 rmsd = 1.657 "obj and name CA" index = 12 rmsd = 1.404 "obj and name CA" index = 13 rmsd = 1.362 "obj and name CA" index = 14 rmsd = 1.578 "obj and name CA" index = 15 rmsd = 1.565 "obj and name CA" index = 16 rmsd = 1.153 "obj and name CA" index = 17 rmsd = 1.257 "obj and name CA" index = 18 rmsd = 1.369 "obj and name CA" index = 19 rmsd = 1.571 "obj and name CA" index = 20 rmsd = 1.421 "obj and name CA" index = 21 rmsd = 0.997 "obj and name CA" index = 22 rmsd = 0.812 "obj and name CA" index = 23 rmsd = 0.891 "obj and name CA" index = 24 rmsd = 0.868 "obj and name CA" index = 25 rmsd = 1.046 "obj and name CA" index = 26 rmsd = 1.194 "obj and name CA" index = 27 rmsd = 1.387 "obj and name CA" index = 28 rmsd = 1.443 "obj and name CA" index = 29 rmsd = 1.394 "obj and name CA" index = 30 rmsd = 1.677 "obj and name CA" index = 31 rmsd = 2.019 "obj and name CA" index = 32 rmsd = 1.715 "obj and name CA" index = 33 rmsd = 1.316 "obj and name CA" index = 34 rmsd = 1.279 "obj and name CA" index = 35 rmsd = 1.270 "obj and name CA" index = 36 rmsd = 1.428 "obj and name CA" index = 37 rmsd = 1.217 "obj and name CA" index = 38 rmsd = 1.181 "obj and name CA" index = 39 rmsd = 1.263 "obj and name CA" index = 40 rmsd = 1.524 "obj and name CA" index = 41 rmsd = 1.368 "obj and name CA" index = 42 rmsd = 1.172 "obj and name CA" index = 43 rmsd = 1.388 "obj and name CA" index = 44 rmsd = 1.523 "obj and name CA" index = 45 rmsd = 1.632 "obj and name CA" index = 46 rmsd = 1.612 "obj and name CA" index = 47 rmsd = 1.509 "obj and name CA" index = 48 rmsd = 1.483 "obj and name CA" index = 49 rmsd = 1.388 "obj and name CA" index = 50 rmsd = 1.105 "obj and name CA" index = 51 rmsd = 0.974 "obj and name CA" index = 52 rmsd = 0.891 "obj and name CA" index = 53 rmsd = 1.005 "obj and name CA" index = 54 rmsd = 1.077 "obj and name CA" index = 55 rmsd = 1.124 "obj and name CA" index = 56 rmsd = 1.216 "obj and name CA" index = 57 rmsd = 1.516 "obj and name CA" index = 58 rmsd = 1.563 "obj and name CA" index = 59 rmsd = 1.790 "obj and name CA" index = 60 rmsd = 1.711 "obj and name CA" index = 61 rmsd = 1.306 "obj and name CA" index = 62 rmsd = 0.922 "obj and name CA" index = 63 rmsd = 0.862 "obj and name CA" index = 64 rmsd = 0.945 "obj and name CA" index = 65 rmsd = 0.924 "obj and name CA" index = 66 rmsd = 1.076 "obj and name CA" index = 67 rmsd = 1.179 "obj and name CA" index = 68 rmsd = 1.102 "obj and name CA" index = 69 rmsd = 1.192 "obj and name CA" index = 70 rmsd = 1.156 "obj and name CA" index = 71 rmsd = 1.316 "obj and name CA" index = 72 rmsd = 1.792 "obj and name CA" index = 73 rmsd = 2.258 "obj and name CA" index = 74 rmsd = 1.666 "obj and name CA" index = 75 rmsd = 1.441 "obj and name CA" index = 76 rmsd = 1.416 "obj and name CA" index = 77 rmsd = 1.450 "obj and name CA" index = 78 rmsd = 1.205 "obj and name CA" index = 79 rmsd = 1.209 "obj and name CA" index = 80 rmsd = 1.269 "obj and name CA" index = 81 rmsd = 1.357 "obj and name CA" index = 82 rmsd = 1.224 "obj and name CA" index = 83 rmsd = 1.085 "obj and name CA" index = 84 rmsd = 0.983 "obj and name CA" index = 85 rmsd = 1.084 "obj and name CA" index = 86 rmsd = 1.017 "obj and name CA" index = 87 rmsd = 0.999 "obj and name CA" index = 88 rmsd = 0.947 "obj and name CA" index = 89 rmsd = 1.032 "obj and name CA" index = 90 rmsd = 0.886 "obj and name CA" index = 91 rmsd = 0.954 "obj and name CA" index = 92 rmsd = 1.093 "obj and name CA" index = 93 rmsd = 1.567 "obj and name CA" index = 94 rmsd = 1.753 "obj and name CA" index = 95 rmsd = 1.487 "obj and name CA" index = 96 rmsd = 1.547 "obj and name CA" index = 97 rmsd = 1.380 "obj and name CA" index = 98 rmsd = 1.338 "obj and name CA" index = 99 rmsd = 1.344 "obj and name CA" index = 100 rmsd = 1.301 "obj and name CA" index = 101 rmsd = 1.184 "obj and name CA" index = 102 rmsd = 1.161 "obj and name CA" index = 103 rmsd = 1.212 "obj and name CA" index = 104 rmsd = 1.184 "obj and name CA" index = 105 rmsd = 1.160 "obj and name CA" index = 106 rmsd = 1.266 "obj and name CA" index = 107 rmsd = 1.218 "obj and name CA" index = 108 rmsd = 1.252 "obj and name CA" index = 109 rmsd = 1.232 "obj and name CA" index = 110 rmsd = 1.299 "obj and name CA" index = 111 rmsd = 1.353 "obj and name CA" index = 112 rmsd = 1.501 "obj and name CA" index = 113 rmsd = 1.975 "obj and name CA" index = 114 rmsd = 2.296 "obj and name CA" index = 115 rmsd = 2.369 "obj and name CA" index = 116 rmsd = 2.605 "obj and name CA" index = 117 rmsd = 4.140 "obj and name CA" index = 118 rmsd = 5.543 "obj and name CA" index = 119 rmsd = 7.604 "obj and name CA" index = 120 rmsd = 9.054 "obj and name CA" index = 121 rmsd = 10.522 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 87 atoms. PyMOL>color gray,ss ""+l Executive: Colored 3996 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: 1.70 sec. = 2120.6 frames/hour (7.59 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit