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 25 atoms. PyMOL>color cyan,ss s Executive: Colored 37 atoms. PyMOL>color gray,ss ""+l Executive: Colored 1950 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: 1.06 sec. = 3397.1 frames/hour (1.06 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: 4.10 sec. = 878.2 frames/hour (5.16 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, 3.225541353225708, 3.9576337337493896, 2.3698792457580566, 5.5931234359741211, 3.7907571792602539, 2.9795684814453125, 3.2163963317871094, 3.3628377914428711, 2.4731888771057129, 3.0882551670074463, 3.4630517959594727, 3.830958366394043, 3.3868236541748047, 2.3278565406799316, 3.0192928314208984, 3.8457396030426025, 4.3800487518310547, 3.5574467182159424, 2.9344081878662109] -> 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 = 8.438 "obj and name CA" index = 2 rmsd = 7.139 "obj and name CA" index = 3 rmsd = 5.547 "obj and name CA" index = 4 rmsd = 4.130 "obj and name CA" index = 5 rmsd = 2.696 "obj and name CA" index = 6 rmsd = 2.355 "obj and name CA" index = 7 rmsd = 1.712 "obj and name CA" index = 8 rmsd = 1.524 "obj and name CA" index = 9 rmsd = 1.313 "obj and name CA" index = 10 rmsd = 1.372 "obj and name CA" index = 11 rmsd = 1.278 "obj and name CA" index = 12 rmsd = 1.004 "obj and name CA" index = 13 rmsd = 0.950 "obj and name CA" index = 14 rmsd = 1.094 "obj and name CA" index = 15 rmsd = 0.986 "obj and name CA" index = 16 rmsd = 0.843 "obj and name CA" index = 17 rmsd = 0.822 "obj and name CA" index = 18 rmsd = 0.721 "obj and name CA" index = 19 rmsd = 0.962 "obj and name CA" index = 20 rmsd = 1.019 "obj and name CA" index = 21 rmsd = 0.844 "obj and name CA" index = 22 rmsd = 0.661 "obj and name CA" index = 23 rmsd = 0.617 "obj and name CA" index = 24 rmsd = 0.579 "obj and name CA" index = 25 rmsd = 0.777 "obj and name CA" index = 26 rmsd = 0.901 "obj and name CA" index = 27 rmsd = 1.127 "obj and name CA" index = 28 rmsd = 1.262 "obj and name CA" index = 29 rmsd = 1.237 "obj and name CA" index = 30 rmsd = 1.280 "obj and name CA" index = 31 rmsd = 1.465 "obj and name CA" index = 32 rmsd = 1.347 "obj and name CA" index = 33 rmsd = 1.102 "obj and name CA" index = 34 rmsd = 1.010 "obj and name CA" index = 35 rmsd = 1.324 "obj and name CA" index = 36 rmsd = 1.515 "obj and name CA" index = 37 rmsd = 1.232 "obj and name CA" index = 38 rmsd = 1.239 "obj and name CA" index = 39 rmsd = 1.155 "obj and name CA" index = 40 rmsd = 1.226 "obj and name CA" index = 41 rmsd = 1.030 "obj and name CA" index = 42 rmsd = 0.792 "obj and name CA" index = 43 rmsd = 1.111 "obj and name CA" index = 44 rmsd = 1.255 "obj and name CA" index = 45 rmsd = 1.199 "obj and name CA" index = 46 rmsd = 1.141 "obj and name CA" index = 47 rmsd = 1.125 "obj and name CA" index = 48 rmsd = 1.052 "obj and name CA" index = 49 rmsd = 0.997 "obj and name CA" index = 50 rmsd = 0.872 "obj and name CA" index = 51 rmsd = 0.836 "obj and name CA" index = 52 rmsd = 0.653 "obj and name CA" index = 53 rmsd = 0.707 "obj and name CA" index = 54 rmsd = 0.888 "obj and name CA" index = 55 rmsd = 1.010 "obj and name CA" index = 56 rmsd = 1.028 "obj and name CA" index = 57 rmsd = 1.298 "obj and name CA" index = 58 rmsd = 1.029 "obj and name CA" index = 59 rmsd = 1.365 "obj and name CA" index = 60 rmsd = 1.291 "obj and name CA" index = 61 rmsd = 0.982 "obj and name CA" index = 62 rmsd = 0.933 "obj and name CA" index = 63 rmsd = 0.774 "obj and name CA" index = 64 rmsd = 0.743 "obj and name CA" index = 65 rmsd = 0.636 "obj and name CA" index = 66 rmsd = 0.745 "obj and name CA" index = 67 rmsd = 0.743 "obj and name CA" index = 68 rmsd = 0.739 "obj and name CA" index = 69 rmsd = 0.930 "obj and name CA" index = 70 rmsd = 1.124 "obj and name CA" index = 71 rmsd = 1.443 "obj and name CA" index = 72 rmsd = 2.319 "obj and name CA" index = 73 rmsd = 1.980 "obj and name CA" index = 74 rmsd = 1.799 "obj and name CA" index = 75 rmsd = 1.574 "obj and name CA" index = 76 rmsd = 1.910 "obj and name CA" index = 77 rmsd = 1.770 "obj and name CA" index = 78 rmsd = 1.377 "obj and name CA" index = 79 rmsd = 1.645 "obj and name CA" index = 80 rmsd = 1.891 "obj and name CA" index = 81 rmsd = 1.708 "obj and name CA" index = 82 rmsd = 1.462 "obj and name CA" index = 83 rmsd = 1.171 "obj and name CA" index = 84 rmsd = 0.970 "obj and name CA" index = 85 rmsd = 0.891 "obj and name CA" index = 86 rmsd = 0.704 "obj and name CA" index = 87 rmsd = 0.752 "obj and name CA" index = 88 rmsd = 0.726 "obj and name CA" index = 89 rmsd = 0.844 "obj and name CA" index = 90 rmsd = 0.891 "obj and name CA" index = 91 rmsd = 1.052 "obj and name CA" index = 92 rmsd = 1.223 "obj and name CA" index = 93 rmsd = 1.530 "obj and name CA" index = 94 rmsd = 1.713 "obj and name CA" index = 95 rmsd = 1.682 "obj and name CA" index = 96 rmsd = 1.593 "obj and name CA" index = 97 rmsd = 1.416 "obj and name CA" index = 98 rmsd = 1.239 "obj and name CA" index = 99 rmsd = 1.203 "obj and name CA" index = 100 rmsd = 1.122 "obj and name CA" index = 101 rmsd = 0.999 "obj and name CA" index = 102 rmsd = 0.948 "obj and name CA" index = 103 rmsd = 0.903 "obj and name CA" index = 104 rmsd = 0.983 "obj and name CA" index = 105 rmsd = 0.995 "obj and name CA" index = 106 rmsd = 1.211 "obj and name CA" index = 107 rmsd = 1.365 "obj and name CA" index = 108 rmsd = 1.181 "obj and name CA" index = 109 rmsd = 1.471 "obj and name CA" index = 110 rmsd = 1.904 "obj and name CA" index = 111 rmsd = 1.755 "obj and name CA" index = 112 rmsd = 2.072 "obj and name CA" index = 113 rmsd = 2.083 "obj and name CA" index = 114 rmsd = 1.770 "obj and name CA" index = 115 rmsd = 1.905 "obj and name CA" index = 116 rmsd = 2.571 "obj and name CA" index = 117 rmsd = 4.099 "obj and name CA" index = 118 rmsd = 5.883 "obj and name CA" index = 119 rmsd = 7.512 "obj and name CA" index = 120 rmsd = 8.847 "obj and name CA" index = 121 rmsd = 10.141 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 75 atoms. PyMOL>color cyan,ss s Executive: Colored 111 atoms. PyMOL>color gray,ss ""+l Executive: Colored 3953 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: 1.42 sec. = 2534.2 frames/hour (6.58 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit