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 38 atoms. PyMOL>color cyan,ss s Executive: Colored 23 atoms. PyMOL>color gray,ss ""+l Executive: Colored 2016 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: 1.33 sec. = 2711.6 frames/hour (1.33 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 375 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 375 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: 4.73 sec. = 761.5 frames/hour (6.05 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, 2.9580421447753906, 3.0994935035705566, 1.852256178855896, 2.7535305023193359, 2.8848576545715332, 3.84529709815979, 2.9035487174987793, 3.1324148178100586, 2.061143159866333, 4.1940011978149414, 2.968104362487793, 2.2075788974761963, 3.500713586807251, 2.9027459621429443, 3.6104195117950439, 2.6993186473846436, 2.2754485607147217, 2.1190135478973389, 2.8732562065124512] -> atom index_map = [None, 2, 21, 35, 59, 76, 93, 113, 132, 144, 165, 175, 192, 214, 236, 257, 269, 283, 305, 319, 331, 348, 362, 386, 401, 423, 443, 457, 469, 490, 500, 516, 536, 560, 577, 588, 600, 614, 626, 648, 672, 693, 703, 722, 741, 758, 770, 789, 803, 813, 828, 850, 869, 876, 895, 909, 916, 928, 950, 974, 990, 1002, 1018, 1037, 1049, 1068, 1090, 1106, 1123, 1137, 1152, 1171, 1187, 1194, 1205, 1224, 1248, 1270, 1292, 1306, 1313, 1332, 1353, 1367, 1377, 1398, 1415, 1432, 1446, 1468, 1483, 1500, 1524, 1543, 1557, 1573, 1592, 1611, 1625, 1632, 1646, 1665, 1672, 1682, 1704, 1719, 1738, 1755, 1766, 1785, 1804, 1819, 1831, 1842, 1862, 1879, 1898, 1912, 1936, 1955, 1970, 1987, 2004, 2021, 2038, 2055] "obj and name CA" index = 1 rmsd = 1.592 "obj and name CA" index = 2 rmsd = 1.428 "obj and name CA" index = 3 rmsd = 1.319 "obj and name CA" index = 4 rmsd = 1.583 "obj and name CA" index = 5 rmsd = 1.259 "obj and name CA" index = 6 rmsd = 0.871 "obj and name CA" index = 7 rmsd = 1.178 "obj and name CA" index = 8 rmsd = 1.518 "obj and name CA" index = 9 rmsd = 1.310 "obj and name CA" index = 10 rmsd = 1.335 "obj and name CA" index = 11 rmsd = 1.687 "obj and name CA" index = 12 rmsd = 2.103 "obj and name CA" index = 13 rmsd = 2.102 "obj and name CA" index = 14 rmsd = 1.920 "obj and name CA" index = 15 rmsd = 1.846 "obj and name CA" index = 16 rmsd = 1.502 "obj and name CA" index = 17 rmsd = 1.378 "obj and name CA" index = 18 rmsd = 1.175 "obj and name CA" index = 19 rmsd = 1.097 "obj and name CA" index = 20 rmsd = 1.169 "obj and name CA" index = 21 rmsd = 1.456 "obj and name CA" index = 22 rmsd = 1.804 "obj and name CA" index = 23 rmsd = 2.311 "obj and name CA" index = 24 rmsd = 2.540 "obj and name CA" index = 25 rmsd = 1.830 "obj and name CA" index = 26 rmsd = 1.855 "obj and name CA" index = 27 rmsd = 1.532 "obj and name CA" index = 28 rmsd = 1.003 "obj and name CA" index = 29 rmsd = 0.872 "obj and name CA" index = 30 rmsd = 0.912 "obj and name CA" index = 31 rmsd = 1.059 "obj and name CA" index = 32 rmsd = 1.361 "obj and name CA" index = 33 rmsd = 1.675 "obj and name CA" index = 34 rmsd = 2.317 "obj and name CA" index = 35 rmsd = 2.475 "obj and name CA" index = 36 rmsd = 2.214 "obj and name CA" index = 37 rmsd = 2.400 "obj and name CA" index = 38 rmsd = 2.608 "obj and name CA" index = 39 rmsd = 2.181 "obj and name CA" index = 40 rmsd = 1.481 "obj and name CA" index = 41 rmsd = 0.965 "obj and name CA" index = 42 rmsd = 0.806 "obj and name CA" index = 43 rmsd = 0.540 "obj and name CA" index = 44 rmsd = 0.487 "obj and name CA" index = 45 rmsd = 0.624 "obj and name CA" index = 46 rmsd = 0.681 "obj and name CA" index = 47 rmsd = 0.874 "obj and name CA" index = 48 rmsd = 0.929 "obj and name CA" index = 49 rmsd = 1.120 "obj and name CA" index = 50 rmsd = 1.047 "obj and name CA" index = 51 rmsd = 1.070 "obj and name CA" index = 52 rmsd = 1.333 "obj and name CA" index = 53 rmsd = 1.343 "obj and name CA" index = 54 rmsd = 1.746 "obj and name CA" index = 55 rmsd = 1.862 "obj and name CA" index = 56 rmsd = 1.513 "obj and name CA" index = 57 rmsd = 1.345 "obj and name CA" index = 58 rmsd = 1.014 "obj and name CA" index = 59 rmsd = 0.755 "obj and name CA" index = 60 rmsd = 0.546 "obj and name CA" index = 61 rmsd = 0.345 "obj and name CA" index = 62 rmsd = 0.351 "obj and name CA" index = 63 rmsd = 0.553 "obj and name CA" index = 64 rmsd = 0.925 "obj and name CA" index = 65 rmsd = 1.007 "obj and name CA" index = 66 rmsd = 1.065 "obj and name CA" index = 67 rmsd = 1.287 "obj and name CA" index = 68 rmsd = 1.405 "obj and name CA" index = 69 rmsd = 1.511 "obj and name CA" index = 70 rmsd = 1.260 "obj and name CA" index = 71 rmsd = 1.093 "obj and name CA" index = 72 rmsd = 1.248 "obj and name CA" index = 73 rmsd = 1.193 "obj and name CA" index = 74 rmsd = 0.994 "obj and name CA" index = 75 rmsd = 0.904 "obj and name CA" index = 76 rmsd = 1.180 "obj and name CA" index = 77 rmsd = 1.023 "obj and name CA" index = 78 rmsd = 0.968 "obj and name CA" index = 79 rmsd = 0.821 "obj and name CA" index = 80 rmsd = 0.647 "obj and name CA" index = 81 rmsd = 0.639 "obj and name CA" index = 82 rmsd = 0.776 "obj and name CA" index = 83 rmsd = 0.727 "obj and name CA" index = 84 rmsd = 1.429 "obj and name CA" index = 85 rmsd = 2.216 "obj and name CA" index = 86 rmsd = 2.327 "obj and name CA" index = 87 rmsd = 1.690 "obj and name CA" index = 88 rmsd = 1.268 "obj and name CA" index = 89 rmsd = 1.479 "obj and name CA" index = 90 rmsd = 1.205 "obj and name CA" index = 91 rmsd = 0.862 "obj and name CA" index = 92 rmsd = 0.647 "obj and name CA" index = 93 rmsd = 0.467 "obj and name CA" index = 94 rmsd = 0.442 "obj and name CA" index = 95 rmsd = 0.477 "obj and name CA" index = 96 rmsd = 0.535 "obj and name CA" index = 97 rmsd = 0.741 "obj and name CA" index = 98 rmsd = 0.758 "obj and name CA" index = 99 rmsd = 0.914 "obj and name CA" index = 100 rmsd = 1.085 "obj and name CA" index = 101 rmsd = 0.788 "obj and name CA" index = 102 rmsd = 0.884 "obj and name CA" index = 103 rmsd = 0.926 "obj and name CA" index = 104 rmsd = 0.768 "obj and name CA" index = 105 rmsd = 0.661 "obj and name CA" index = 106 rmsd = 0.860 "obj and name CA" index = 107 rmsd = 0.980 "obj and name CA" index = 108 rmsd = 0.926 "obj and name CA" index = 109 rmsd = 0.970 "obj and name CA" index = 110 rmsd = 1.282 "obj and name CA" index = 111 rmsd = 1.369 "obj and name CA" index = 112 rmsd = 1.211 "obj and name CA" index = 113 rmsd = 1.504 "obj and name CA" index = 114 rmsd = 1.733 "obj and name CA" index = 115 rmsd = 1.540 "obj and name CA" index = 116 rmsd = 1.605 "obj and name CA" index = 117 rmsd = 1.774 "obj and name CA" index = 118 rmsd = 1.838 "obj and name CA" index = 119 rmsd = 2.713 "obj and name CA" index = 120 rmsd = 3.616 "obj and name CA" index = 121 rmsd = 4.877 "obj and name CA" index = 122 rmsd = 6.529 "obj and name CA" index = 123 rmsd = 8.384 "obj and name CA" index = 124 rmsd = 9.959 "obj and name CA" index = 125 rmsd = 11.421 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 114 atoms. PyMOL>color cyan,ss s Executive: Colored 69 atoms. PyMOL>color gray,ss ""+l Executive: Colored 4090 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: 1.83 sec. = 1964.8 frames/hour (7.89 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit