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 PyMOL>color cyan,ss s Executive: Colored 62 atoms. PyMOL>color gray,ss ""+l Executive: Colored 2228 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: 1.30 sec. = 2761.2 frames/hour (1.30 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 426 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 426 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: 6.57 sec. = 547.9 frames/hour (7.87 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, 3.5527076721191406, 5.1295886039733887, 2.6161220073699951, 2.8716309070587158, 5.5403790473937988, 5.4703917503356934, 6.1944160461425781, 3.4268207550048828, 2.5303030014038086, 6.7286081314086914, 4.2536158561706543, 4.2786836624145508, 2.9466850757598877, 3.5285680294036865, 3.5162017345428467, 2.3868298530578613, 6.2576508522033691, 3.6405487060546875, 4.2266454696655273] -> atom index_map = [None, 2, 21, 33, 47, 71, 88, 108, 127, 138, 157, 171, 178, 194, 205, 227, 243, 260, 271, 291, 303, 317, 339, 354, 373, 392, 411, 426, 440, 459, 476, 483, 499, 518, 529, 548, 570, 577, 592, 614, 633, 640, 659, 681, 698, 717, 729, 748, 770, 780, 787, 804, 820, 835, 851, 866, 873, 892, 911, 923, 933, 952, 968, 989, 1003, 1022, 1037, 1054, 1071, 1088, 1105, 1122, 1140, 1159, 1171, 1185, 1209, 1226, 1246, 1265, 1276, 1295, 1309, 1316, 1332, 1343, 1365, 1381, 1398, 1409, 1429, 1441, 1455, 1477, 1492, 1511, 1530, 1549, 1564, 1578, 1597, 1614, 1621, 1637, 1656, 1667, 1686, 1708, 1715, 1730, 1752, 1771, 1778, 1797, 1819, 1836, 1855, 1867, 1886, 1908, 1918, 1925, 1942, 1958, 1973, 1989, 2004, 2011, 2030, 2049, 2061, 2071, 2090, 2106, 2127, 2141, 2160, 2175, 2192, 2209, 2226, 2243, 2260] "obj and name CA" index = 1 rmsd = 5.078 "obj and name CA" index = 2 rmsd = 2.785 "obj and name CA" index = 3 rmsd = 1.620 "obj and name CA" index = 4 rmsd = 1.152 "obj and name CA" index = 5 rmsd = 0.939 "obj and name CA" index = 6 rmsd = 0.806 "obj and name CA" index = 7 rmsd = 0.783 "obj and name CA" index = 8 rmsd = 0.851 "obj and name CA" index = 9 rmsd = 0.732 "obj and name CA" index = 10 rmsd = 0.817 "obj and name CA" index = 11 rmsd = 0.944 "obj and name CA" index = 12 rmsd = 0.909 "obj and name CA" index = 13 rmsd = 1.202 "obj and name CA" index = 14 rmsd = 1.251 "obj and name CA" index = 15 rmsd = 1.076 "obj and name CA" index = 16 rmsd = 1.022 "obj and name CA" index = 17 rmsd = 1.003 "obj and name CA" index = 18 rmsd = 1.079 "obj and name CA" index = 19 rmsd = 1.013 "obj and name CA" index = 20 rmsd = 1.088 "obj and name CA" index = 21 rmsd = 0.972 "obj and name CA" index = 22 rmsd = 0.844 "obj and name CA" index = 23 rmsd = 0.782 "obj and name CA" index = 24 rmsd = 0.823 "obj and name CA" index = 25 rmsd = 0.843 "obj and name CA" index = 26 rmsd = 0.989 "obj and name CA" index = 27 rmsd = 0.984 "obj and name CA" index = 28 rmsd = 1.439 "obj and name CA" index = 29 rmsd = 1.838 "obj and name CA" index = 30 rmsd = 1.509 "obj and name CA" index = 31 rmsd = 1.072 "obj and name CA" index = 32 rmsd = 0.780 "obj and name CA" index = 33 rmsd = 0.729 "obj and name CA" index = 34 rmsd = 0.722 "obj and name CA" index = 35 rmsd = 0.807 "obj and name CA" index = 36 rmsd = 0.945 "obj and name CA" index = 37 rmsd = 1.094 "obj and name CA" index = 38 rmsd = 1.021 "obj and name CA" index = 39 rmsd = 0.905 "obj and name CA" index = 40 rmsd = 1.076 "obj and name CA" index = 41 rmsd = 1.692 "obj and name CA" index = 42 rmsd = 2.559 "obj and name CA" index = 43 rmsd = 2.752 "obj and name CA" index = 44 rmsd = 3.414 "obj and name CA" index = 45 rmsd = 2.665 "obj and name CA" index = 46 rmsd = 1.727 "obj and name CA" index = 47 rmsd = 2.193 "obj and name CA" index = 48 rmsd = 1.548 "obj and name CA" index = 49 rmsd = 0.902 "obj and name CA" index = 50 rmsd = 0.875 "obj and name CA" index = 51 rmsd = 0.764 "obj and name CA" index = 52 rmsd = 0.806 "obj and name CA" index = 53 rmsd = 0.848 "obj and name CA" index = 54 rmsd = 0.900 "obj and name CA" index = 55 rmsd = 0.974 "obj and name CA" index = 56 rmsd = 1.058 "obj and name CA" index = 57 rmsd = 0.985 "obj and name CA" index = 58 rmsd = 1.082 "obj and name CA" index = 59 rmsd = 1.010 "obj and name CA" index = 60 rmsd = 0.979 "obj and name CA" index = 61 rmsd = 0.897 "obj and name CA" index = 62 rmsd = 0.658 "obj and name CA" index = 63 rmsd = 1.377 "obj and name CA" index = 64 rmsd = 2.376 "obj and name CA" index = 65 rmsd = 3.692 "obj and name CA" index = 66 rmsd = 5.061 "obj and name CA" index = 67 rmsd = 6.602 "obj and name CA" index = 68 rmsd = 8.294 "obj and name CA" index = 69 rmsd = 10.483 "obj and name CA" index = 70 rmsd = 11.954 "obj and name CA" index = 71 rmsd = 13.308 "obj and name CA" index = 72 rmsd = 5.078 "obj and name CA" index = 73 rmsd = 2.785 "obj and name CA" index = 74 rmsd = 1.620 "obj and name CA" index = 75 rmsd = 1.152 "obj and name CA" index = 76 rmsd = 0.939 "obj and name CA" index = 77 rmsd = 0.806 "obj and name CA" index = 78 rmsd = 0.783 "obj and name CA" index = 79 rmsd = 0.851 "obj and name CA" index = 80 rmsd = 0.731 "obj and name CA" index = 81 rmsd = 0.817 "obj and name CA" index = 82 rmsd = 0.943 "obj and name CA" index = 83 rmsd = 0.909 "obj and name CA" index = 84 rmsd = 1.202 "obj and name CA" index = 85 rmsd = 1.251 "obj and name CA" index = 86 rmsd = 1.076 "obj and name CA" index = 87 rmsd = 1.022 "obj and name CA" index = 88 rmsd = 1.003 "obj and name CA" index = 89 rmsd = 1.079 "obj and name CA" index = 90 rmsd = 1.013 "obj and name CA" index = 91 rmsd = 1.088 "obj and name CA" index = 92 rmsd = 0.972 "obj and name CA" index = 93 rmsd = 0.844 "obj and name CA" index = 94 rmsd = 0.782 "obj and name CA" index = 95 rmsd = 0.823 "obj and name CA" index = 96 rmsd = 0.843 "obj and name CA" index = 97 rmsd = 0.989 "obj and name CA" index = 98 rmsd = 0.984 "obj and name CA" index = 99 rmsd = 1.439 "obj and name CA" index = 100 rmsd = 1.838 "obj and name CA" index = 101 rmsd = 1.509 "obj and name CA" index = 102 rmsd = 1.071 "obj and name CA" index = 103 rmsd = 0.780 "obj and name CA" index = 104 rmsd = 0.729 "obj and name CA" index = 105 rmsd = 0.722 "obj and name CA" index = 106 rmsd = 0.807 "obj and name CA" index = 107 rmsd = 0.945 "obj and name CA" index = 108 rmsd = 1.094 "obj and name CA" index = 109 rmsd = 1.021 "obj and name CA" index = 110 rmsd = 0.905 "obj and name CA" index = 111 rmsd = 1.076 "obj and name CA" index = 112 rmsd = 1.692 "obj and name CA" index = 113 rmsd = 2.559 "obj and name CA" index = 114 rmsd = 2.752 "obj and name CA" index = 115 rmsd = 3.414 "obj and name CA" index = 116 rmsd = 2.665 "obj and name CA" index = 117 rmsd = 1.727 "obj and name CA" index = 118 rmsd = 2.194 "obj and name CA" index = 119 rmsd = 1.548 "obj and name CA" index = 120 rmsd = 0.902 "obj and name CA" index = 121 rmsd = 0.875 "obj and name CA" index = 122 rmsd = 0.764 "obj and name CA" index = 123 rmsd = 0.805 "obj and name CA" index = 124 rmsd = 0.849 "obj and name CA" index = 125 rmsd = 0.900 "obj and name CA" index = 126 rmsd = 0.974 "obj and name CA" index = 127 rmsd = 1.058 "obj and name CA" index = 128 rmsd = 0.985 "obj and name CA" index = 129 rmsd = 1.082 "obj and name CA" index = 130 rmsd = 1.009 "obj and name CA" index = 131 rmsd = 0.979 "obj and name CA" index = 132 rmsd = 0.897 "obj and name CA" index = 133 rmsd = 0.658 "obj and name CA" index = 134 rmsd = 1.377 "obj and name CA" index = 135 rmsd = 2.376 "obj and name CA" index = 136 rmsd = 3.691 "obj and name CA" index = 137 rmsd = 5.061 "obj and name CA" index = 138 rmsd = 6.602 "obj and name CA" index = 139 rmsd = 8.294 "obj and name CA" index = 140 rmsd = 10.483 "obj and name CA" index = 141 rmsd = 11.953 "obj and name CA" index = 142 rmsd = 13.308 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h PyMOL>color cyan,ss s Executive: Colored 186 atoms. PyMOL>color gray,ss ""+l Executive: Colored 4522 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: 2.35 sec. = 1531.1 frames/hour (10.23 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit