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 82 atoms. PyMOL>color cyan,ss s 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: 1.69 sec. = 2124.5 frames/hour (1.69 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 369 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 369 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: 5.25 sec. = 685.1 frames/hour (6.95 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, 2.3286232948303223, 2.5871484279632568, 3.6938364505767822, 3.0014100074768066, 2.9725015163421631, 2.5394368171691895, 2.8294816017150879, 2.6928689479827881, 2.21134352684021, 2.9950206279754639, 2.62935471534729, 2.4066851139068604, 3.1685171127319336, 2.5956864356994629, 2.900521993637085, 3.0360276699066162, 3.0751652717590332, 3.1414141654968262, 2.8496372699737549] -> atom index_map = [None, 2, 21, 40, 51, 68, 82, 101, 120, 135, 152, 166, 181, 198, 215, 234, 249, 265, 275, 290, 312, 319, 329, 341, 365, 386, 403, 418, 425, 447, 461, 472, 486, 503, 514, 535, 547, 567, 587, 602, 616, 635, 657, 671, 681, 697, 712, 727, 741, 753, 768, 787, 797, 807, 831, 855, 865, 880, 887, 897, 916, 931, 950, 969, 991, 1007, 1031, 1055, 1069, 1091, 1112, 1128, 1145, 1167, 1182, 1199, 1218, 1233, 1243, 1259, 1281, 1293, 1307, 1327, 1346, 1361, 1380, 1396, 1415, 1432, 1443, 1464, 1480, 1497, 1514, 1533, 1550, 1572, 1594, 1618, 1638, 1660, 1672, 1691, 1705, 1720, 1731, 1747, 1766, 1787, 1801, 1820, 1837, 1847, 1863, 1885, 1897, 1912, 1931, 1941, 1965, 1980, 1992, 2003] "obj and name CA" index = 1 rmsd = 8.245 "obj and name CA" index = 2 rmsd = 6.260 "obj and name CA" index = 3 rmsd = 4.721 "obj and name CA" index = 4 rmsd = 3.075 "obj and name CA" index = 5 rmsd = 1.705 "obj and name CA" index = 6 rmsd = 0.877 "obj and name CA" index = 7 rmsd = 0.815 "obj and name CA" index = 8 rmsd = 0.856 "obj and name CA" index = 9 rmsd = 0.662 "obj and name CA" index = 10 rmsd = 0.559 "obj and name CA" index = 11 rmsd = 0.699 "obj and name CA" index = 12 rmsd = 0.754 "obj and name CA" index = 13 rmsd = 0.598 "obj and name CA" index = 14 rmsd = 0.663 "obj and name CA" index = 15 rmsd = 0.831 "obj and name CA" index = 16 rmsd = 0.799 "obj and name CA" index = 17 rmsd = 0.747 "obj and name CA" index = 18 rmsd = 0.930 "obj and name CA" index = 19 rmsd = 1.063 "obj and name CA" index = 20 rmsd = 0.865 "obj and name CA" index = 21 rmsd = 0.960 "obj and name CA" index = 22 rmsd = 1.124 "obj and name CA" index = 23 rmsd = 1.064 "obj and name CA" index = 24 rmsd = 1.032 "obj and name CA" index = 25 rmsd = 1.359 "obj and name CA" index = 26 rmsd = 1.539 "obj and name CA" index = 27 rmsd = 1.511 "obj and name CA" index = 28 rmsd = 2.970 "obj and name CA" index = 29 rmsd = 3.898 "obj and name CA" index = 30 rmsd = 5.125 "obj and name CA" index = 31 rmsd = 5.214 "obj and name CA" index = 32 rmsd = 5.017 "obj and name CA" index = 33 rmsd = 4.549 "obj and name CA" index = 34 rmsd = 3.035 "obj and name CA" index = 35 rmsd = 2.791 "obj and name CA" index = 36 rmsd = 2.333 "obj and name CA" index = 37 rmsd = 2.212 "obj and name CA" index = 38 rmsd = 2.271 "obj and name CA" index = 39 rmsd = 1.934 "obj and name CA" index = 40 rmsd = 1.367 "obj and name CA" index = 41 rmsd = 1.550 "obj and name CA" index = 42 rmsd = 1.673 "obj and name CA" index = 43 rmsd = 1.308 "obj and name CA" index = 44 rmsd = 1.011 "obj and name CA" index = 45 rmsd = 1.018 "obj and name CA" index = 46 rmsd = 1.081 "obj and name CA" index = 47 rmsd = 0.754 "obj and name CA" index = 48 rmsd = 0.679 "obj and name CA" index = 49 rmsd = 0.811 "obj and name CA" index = 50 rmsd = 0.691 "obj and name CA" index = 51 rmsd = 0.515 "obj and name CA" index = 52 rmsd = 0.673 "obj and name CA" index = 53 rmsd = 0.815 "obj and name CA" index = 54 rmsd = 0.603 "obj and name CA" index = 55 rmsd = 0.586 "obj and name CA" index = 56 rmsd = 0.759 "obj and name CA" index = 57 rmsd = 0.690 "obj and name CA" index = 58 rmsd = 0.604 "obj and name CA" index = 59 rmsd = 0.718 "obj and name CA" index = 60 rmsd = 0.845 "obj and name CA" index = 61 rmsd = 0.838 "obj and name CA" index = 62 rmsd = 0.805 "obj and name CA" index = 63 rmsd = 1.107 "obj and name CA" index = 64 rmsd = 1.523 "obj and name CA" index = 65 rmsd = 1.640 "obj and name CA" index = 66 rmsd = 1.467 "obj and name CA" index = 67 rmsd = 1.279 "obj and name CA" index = 68 rmsd = 1.480 "obj and name CA" index = 69 rmsd = 1.427 "obj and name CA" index = 70 rmsd = 1.134 "obj and name CA" index = 71 rmsd = 1.034 "obj and name CA" index = 72 rmsd = 0.935 "obj and name CA" index = 73 rmsd = 0.828 "obj and name CA" index = 74 rmsd = 0.714 "obj and name CA" index = 75 rmsd = 0.615 "obj and name CA" index = 76 rmsd = 0.751 "obj and name CA" index = 77 rmsd = 0.741 "obj and name CA" index = 78 rmsd = 0.590 "obj and name CA" index = 79 rmsd = 0.652 "obj and name CA" index = 80 rmsd = 0.756 "obj and name CA" index = 81 rmsd = 0.703 "obj and name CA" index = 82 rmsd = 0.534 "obj and name CA" index = 83 rmsd = 0.603 "obj and name CA" index = 84 rmsd = 0.685 "obj and name CA" index = 85 rmsd = 0.735 "obj and name CA" index = 86 rmsd = 0.834 "obj and name CA" index = 87 rmsd = 0.836 "obj and name CA" index = 88 rmsd = 0.970 "obj and name CA" index = 89 rmsd = 1.236 "obj and name CA" index = 90 rmsd = 1.181 "obj and name CA" index = 91 rmsd = 1.158 "obj and name CA" index = 92 rmsd = 1.210 "obj and name CA" index = 93 rmsd = 1.218 "obj and name CA" index = 94 rmsd = 1.349 "obj and name CA" index = 95 rmsd = 1.994 "obj and name CA" index = 96 rmsd = 1.771 "obj and name CA" index = 97 rmsd = 1.343 "obj and name CA" index = 98 rmsd = 1.152 "obj and name CA" index = 99 rmsd = 0.911 "obj and name CA" index = 100 rmsd = 1.095 "obj and name CA" index = 101 rmsd = 1.065 "obj and name CA" index = 102 rmsd = 0.838 "obj and name CA" index = 103 rmsd = 0.863 "obj and name CA" index = 104 rmsd = 1.005 "obj and name CA" index = 105 rmsd = 0.885 "obj and name CA" index = 106 rmsd = 0.605 "obj and name CA" index = 107 rmsd = 0.716 "obj and name CA" index = 108 rmsd = 0.962 "obj and name CA" index = 109 rmsd = 0.855 "obj and name CA" index = 110 rmsd = 0.575 "obj and name CA" index = 111 rmsd = 0.731 "obj and name CA" index = 112 rmsd = 0.823 "obj and name CA" index = 113 rmsd = 0.773 "obj and name CA" index = 114 rmsd = 0.726 "obj and name CA" index = 115 rmsd = 0.864 "obj and name CA" index = 116 rmsd = 0.913 "obj and name CA" index = 117 rmsd = 1.021 "obj and name CA" index = 118 rmsd = 1.228 "obj and name CA" index = 119 rmsd = 1.376 "obj and name CA" index = 120 rmsd = 1.663 "obj and name CA" index = 121 rmsd = 2.286 "obj and name CA" index = 122 rmsd = 4.172 "obj and name CA" index = 123 rmsd = 5.885 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 246 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 3935 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: 1.93 sec. = 1865.2 frames/hour (8.88 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit