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 106 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 2354 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: 2.06 sec. = 1750.0 frames/hour (2.06 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 456 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 456 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: 7.27 sec. = 495.5 frames/hour (9.32 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, 5.4035534858703613, 3.478339672088623, 4.8993315696716309, 5.7813115119934082, 4.5496487617492676, 4.1169710159301758, 5.2264766693115234, 5.3724451065063477, 3.6047511100769043, 4.2990264892578125, 5.4464383125305176, 4.9748349189758301, 2.9507017135620117, 4.6855711936950684, 3.5692605972290039, 4.6933465003967285, 3.9899477958679199, 5.0080227851867676, 3.2679975032806396] -> atom index_map = [None, 2, 21, 35, 54, 70, 81, 103, 124, 135, 149, 164, 188, 204, 219, 241, 260, 279, 296, 308, 327, 346, 358, 374, 393, 409, 431, 446, 461, 477, 491, 505, 517, 536, 546, 565, 582, 593, 612, 619, 633, 643, 659, 673, 687, 706, 725, 735, 752, 768, 782, 797, 808, 830, 854, 870, 880, 896, 912, 924, 938, 958, 972, 994, 1004, 1023, 1045, 1062, 1073, 1089, 1108, 1123, 1140, 1157, 1174, 1191, 1208, 1226, 1245, 1259, 1278, 1294, 1305, 1327, 1348, 1359, 1373, 1388, 1412, 1428, 1443, 1465, 1484, 1503, 1520, 1532, 1551, 1570, 1582, 1598, 1617, 1633, 1655, 1670, 1685, 1701, 1715, 1729, 1741, 1760, 1770, 1789, 1806, 1817, 1836, 1843, 1857, 1867, 1883, 1897, 1911, 1930, 1949, 1959, 1976, 1992, 2006, 2021, 2032, 2054, 2078, 2094, 2104, 2120, 2136, 2148, 2162, 2182, 2196, 2218, 2228, 2247, 2269, 2286, 2297, 2313, 2332, 2347, 2364, 2381, 2398, 2415, 2432] "obj and name CA" index = 1 rmsd = 12.401 "obj and name CA" index = 2 rmsd = 10.280 "obj and name CA" index = 3 rmsd = 7.987 "obj and name CA" index = 4 rmsd = 6.362 "obj and name CA" index = 5 rmsd = 4.481 "obj and name CA" index = 6 rmsd = 3.537 "obj and name CA" index = 7 rmsd = 2.428 "obj and name CA" index = 8 rmsd = 1.870 "obj and name CA" index = 9 rmsd = 1.605 "obj and name CA" index = 10 rmsd = 1.824 "obj and name CA" index = 11 rmsd = 1.713 "obj and name CA" index = 12 rmsd = 1.203 "obj and name CA" index = 13 rmsd = 1.166 "obj and name CA" index = 14 rmsd = 1.213 "obj and name CA" index = 15 rmsd = 0.956 "obj and name CA" index = 16 rmsd = 0.865 "obj and name CA" index = 17 rmsd = 0.961 "obj and name CA" index = 18 rmsd = 0.787 "obj and name CA" index = 19 rmsd = 0.680 "obj and name CA" index = 20 rmsd = 0.843 "obj and name CA" index = 21 rmsd = 0.831 "obj and name CA" index = 22 rmsd = 0.771 "obj and name CA" index = 23 rmsd = 0.944 "obj and name CA" index = 24 rmsd = 1.291 "obj and name CA" index = 25 rmsd = 1.441 "obj and name CA" index = 26 rmsd = 1.409 "obj and name CA" index = 27 rmsd = 1.459 "obj and name CA" index = 28 rmsd = 1.340 "obj and name CA" index = 29 rmsd = 1.467 "obj and name CA" index = 30 rmsd = 1.349 "obj and name CA" index = 31 rmsd = 1.201 "obj and name CA" index = 32 rmsd = 1.164 "obj and name CA" index = 33 rmsd = 1.059 "obj and name CA" index = 34 rmsd = 1.122 "obj and name CA" index = 35 rmsd = 1.235 "obj and name CA" index = 36 rmsd = 1.069 "obj and name CA" index = 37 rmsd = 1.146 "obj and name CA" index = 38 rmsd = 1.358 "obj and name CA" index = 39 rmsd = 0.981 "obj and name CA" index = 40 rmsd = 0.994 "obj and name CA" index = 41 rmsd = 0.890 "obj and name CA" index = 42 rmsd = 0.888 "obj and name CA" index = 43 rmsd = 1.060 "obj and name CA" index = 44 rmsd = 1.128 "obj and name CA" index = 45 rmsd = 1.190 "obj and name CA" index = 46 rmsd = 1.393 "obj and name CA" index = 47 rmsd = 1.527 "obj and name CA" index = 48 rmsd = 1.685 "obj and name CA" index = 49 rmsd = 2.069 "obj and name CA" index = 50 rmsd = 2.243 "obj and name CA" index = 51 rmsd = 2.440 "obj and name CA" index = 52 rmsd = 1.918 "obj and name CA" index = 53 rmsd = 1.531 "obj and name CA" index = 54 rmsd = 1.500 "obj and name CA" index = 55 rmsd = 1.499 "obj and name CA" index = 56 rmsd = 1.112 "obj and name CA" index = 57 rmsd = 0.902 "obj and name CA" index = 58 rmsd = 0.880 "obj and name CA" index = 59 rmsd = 0.921 "obj and name CA" index = 60 rmsd = 0.773 "obj and name CA" index = 61 rmsd = 0.671 "obj and name CA" index = 62 rmsd = 0.821 "obj and name CA" index = 63 rmsd = 1.051 "obj and name CA" index = 64 rmsd = 1.212 "obj and name CA" index = 65 rmsd = 1.393 "obj and name CA" index = 66 rmsd = 1.365 "obj and name CA" index = 67 rmsd = 1.218 "obj and name CA" index = 68 rmsd = 1.383 "obj and name CA" index = 69 rmsd = 1.846 "obj and name CA" index = 70 rmsd = 2.011 "obj and name CA" index = 71 rmsd = 2.260 "obj and name CA" index = 72 rmsd = 3.668 "obj and name CA" index = 73 rmsd = 4.689 "obj and name CA" index = 74 rmsd = 6.010 "obj and name CA" index = 75 rmsd = 7.171 "obj and name CA" index = 76 rmsd = 8.844 "obj and name CA" index = 77 rmsd = 12.401 "obj and name CA" index = 78 rmsd = 10.280 "obj and name CA" index = 79 rmsd = 7.987 "obj and name CA" index = 80 rmsd = 6.362 "obj and name CA" index = 81 rmsd = 4.481 "obj and name CA" index = 82 rmsd = 3.537 "obj and name CA" index = 83 rmsd = 2.428 "obj and name CA" index = 84 rmsd = 1.870 "obj and name CA" index = 85 rmsd = 1.605 "obj and name CA" index = 86 rmsd = 1.824 "obj and name CA" index = 87 rmsd = 1.713 "obj and name CA" index = 88 rmsd = 1.203 "obj and name CA" index = 89 rmsd = 1.166 "obj and name CA" index = 90 rmsd = 1.213 "obj and name CA" index = 91 rmsd = 0.956 "obj and name CA" index = 92 rmsd = 0.865 "obj and name CA" index = 93 rmsd = 0.961 "obj and name CA" index = 94 rmsd = 0.787 "obj and name CA" index = 95 rmsd = 0.680 "obj and name CA" index = 96 rmsd = 0.843 "obj and name CA" index = 97 rmsd = 0.831 "obj and name CA" index = 98 rmsd = 0.771 "obj and name CA" index = 99 rmsd = 0.944 "obj and name CA" index = 100 rmsd = 1.291 "obj and name CA" index = 101 rmsd = 1.441 "obj and name CA" index = 102 rmsd = 1.409 "obj and name CA" index = 103 rmsd = 1.458 "obj and name CA" index = 104 rmsd = 1.340 "obj and name CA" index = 105 rmsd = 1.467 "obj and name CA" index = 106 rmsd = 1.349 "obj and name CA" index = 107 rmsd = 1.201 "obj and name CA" index = 108 rmsd = 1.164 "obj and name CA" index = 109 rmsd = 1.059 "obj and name CA" index = 110 rmsd = 1.122 "obj and name CA" index = 111 rmsd = 1.235 "obj and name CA" index = 112 rmsd = 1.069 "obj and name CA" index = 113 rmsd = 1.146 "obj and name CA" index = 114 rmsd = 1.358 "obj and name CA" index = 115 rmsd = 0.981 "obj and name CA" index = 116 rmsd = 0.993 "obj and name CA" index = 117 rmsd = 0.889 "obj and name CA" index = 118 rmsd = 0.888 "obj and name CA" index = 119 rmsd = 1.060 "obj and name CA" index = 120 rmsd = 1.128 "obj and name CA" index = 121 rmsd = 1.190 "obj and name CA" index = 122 rmsd = 1.393 "obj and name CA" index = 123 rmsd = 1.527 "obj and name CA" index = 124 rmsd = 1.685 "obj and name CA" index = 125 rmsd = 2.069 "obj and name CA" index = 126 rmsd = 2.243 "obj and name CA" index = 127 rmsd = 2.440 "obj and name CA" index = 128 rmsd = 1.918 "obj and name CA" index = 129 rmsd = 1.531 "obj and name CA" index = 130 rmsd = 1.500 "obj and name CA" index = 131 rmsd = 1.499 "obj and name CA" index = 132 rmsd = 1.112 "obj and name CA" index = 133 rmsd = 0.902 "obj and name CA" index = 134 rmsd = 0.880 "obj and name CA" index = 135 rmsd = 0.921 "obj and name CA" index = 136 rmsd = 0.773 "obj and name CA" index = 137 rmsd = 0.671 "obj and name CA" index = 138 rmsd = 0.821 "obj and name CA" index = 139 rmsd = 1.051 "obj and name CA" index = 140 rmsd = 1.211 "obj and name CA" index = 141 rmsd = 1.393 "obj and name CA" index = 142 rmsd = 1.365 "obj and name CA" index = 143 rmsd = 1.218 "obj and name CA" index = 144 rmsd = 1.383 "obj and name CA" index = 145 rmsd = 1.846 "obj and name CA" index = 146 rmsd = 2.011 "obj and name CA" index = 147 rmsd = 2.260 "obj and name CA" index = 148 rmsd = 3.668 "obj and name CA" index = 149 rmsd = 4.689 "obj and name CA" index = 150 rmsd = 6.010 "obj and name CA" index = 151 rmsd = 7.171 "obj and name CA" index = 152 rmsd = 8.844 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 318 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 4742 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: 2.25 sec. = 1601.4 frames/hour (11.57 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit