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 40 atoms. PyMOL>color cyan,ss s Executive: Colored 18 atoms. PyMOL>color gray,ss ""+l Executive: Colored 2197 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: 1.36 sec. = 2648.6 frames/hour (1.36 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: 5.66 sec. = 636.2 frames/hour (7.02 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, 4.5592250823974609, 4.5313162803649902, 8.3179702758789062, 5.3937191963195801, 5.0768952369689941, 8.0206575393676758, 6.3017044067382812, 8.5160121917724609, 7.620119571685791, 9.5262174606323242, 7.3063311576843262, 9.2278156280517578, 7.036346435546875, 7.9505281448364258, 4.8500885963439941, 8.2604598999023438, 5.309140682220459, 5.4453825950622559, 8.0093927383422852] -> atom index_map = [None, 2, 21, 31, 45, 57, 71, 85, 105, 116, 126, 145, 169, 186, 210, 229, 248, 262, 286, 293, 317, 334, 348, 364, 379, 389, 400, 414, 430, 442, 454, 478, 497, 519, 543, 559, 566, 578, 585, 601, 620, 639, 658, 669, 680, 692, 706, 730, 754, 768, 782, 797, 813, 824, 836, 850, 864, 880, 897, 916, 926, 941, 960, 979, 1003, 1018, 1038, 1052, 1069, 1089, 1101, 1125, 1142, 1158, 1168, 1184, 1194, 1206, 1225, 1240, 1257, 1268, 1283, 1293, 1312, 1319, 1331, 1355, 1375, 1389, 1405, 1429, 1453, 1473, 1487, 1497, 1511, 1530, 1546, 1566, 1580, 1592, 1599, 1621, 1640, 1664, 1671, 1681, 1700, 1711, 1718, 1737, 1754, 1768, 1792, 1802, 1817, 1836, 1855, 1869, 1888, 1905, 1929, 1940, 1959, 1975, 1987, 2001, 2015, 2025, 2035, 2052, 2067, 2081, 2097, 2114, 2133, 2148, 2165, 2182, 2199, 2216, 2233] "obj and name CA" index = 1 rmsd = 9.925 "obj and name CA" index = 2 rmsd = 9.817 "obj and name CA" index = 3 rmsd = 9.130 "obj and name CA" index = 4 rmsd = 8.021 "obj and name CA" index = 5 rmsd = 6.097 "obj and name CA" index = 6 rmsd = 5.280 "obj and name CA" index = 7 rmsd = 4.034 "obj and name CA" index = 8 rmsd = 2.692 "obj and name CA" index = 9 rmsd = 2.806 "obj and name CA" index = 10 rmsd = 2.360 "obj and name CA" index = 11 rmsd = 1.778 "obj and name CA" index = 12 rmsd = 2.192 "obj and name CA" index = 13 rmsd = 2.533 "obj and name CA" index = 14 rmsd = 2.148 "obj and name CA" index = 15 rmsd = 2.268 "obj and name CA" index = 16 rmsd = 2.847 "obj and name CA" index = 17 rmsd = 2.968 "obj and name CA" index = 18 rmsd = 3.059 "obj and name CA" index = 19 rmsd = 2.518 "obj and name CA" index = 20 rmsd = 2.543 "obj and name CA" index = 21 rmsd = 2.071 "obj and name CA" index = 22 rmsd = 2.313 "obj and name CA" index = 23 rmsd = 2.533 "obj and name CA" index = 24 rmsd = 2.968 "obj and name CA" index = 25 rmsd = 3.689 "obj and name CA" index = 26 rmsd = 3.470 "obj and name CA" index = 27 rmsd = 3.097 "obj and name CA" index = 28 rmsd = 3.744 "obj and name CA" index = 29 rmsd = 4.162 "obj and name CA" index = 30 rmsd = 3.664 "obj and name CA" index = 31 rmsd = 3.647 "obj and name CA" index = 32 rmsd = 4.483 "obj and name CA" index = 33 rmsd = 4.653 "obj and name CA" index = 34 rmsd = 4.305 "obj and name CA" index = 35 rmsd = 4.344 "obj and name CA" index = 36 rmsd = 3.774 "obj and name CA" index = 37 rmsd = 3.025 "obj and name CA" index = 38 rmsd = 2.235 "obj and name CA" index = 39 rmsd = 1.781 "obj and name CA" index = 40 rmsd = 1.239 "obj and name CA" index = 41 rmsd = 1.224 "obj and name CA" index = 42 rmsd = 1.499 "obj and name CA" index = 43 rmsd = 2.275 "obj and name CA" index = 44 rmsd = 2.598 "obj and name CA" index = 45 rmsd = 3.702 "obj and name CA" index = 46 rmsd = 5.128 "obj and name CA" index = 47 rmsd = 5.523 "obj and name CA" index = 48 rmsd = 5.458 "obj and name CA" index = 49 rmsd = 5.922 "obj and name CA" index = 50 rmsd = 6.134 "obj and name CA" index = 51 rmsd = 5.323 "obj and name CA" index = 52 rmsd = 4.476 "obj and name CA" index = 53 rmsd = 3.088 "obj and name CA" index = 54 rmsd = 2.616 "obj and name CA" index = 55 rmsd = 1.822 "obj and name CA" index = 56 rmsd = 2.276 "obj and name CA" index = 57 rmsd = 2.788 "obj and name CA" index = 58 rmsd = 2.248 "obj and name CA" index = 59 rmsd = 2.994 "obj and name CA" index = 60 rmsd = 3.343 "obj and name CA" index = 61 rmsd = 2.756 "obj and name CA" index = 62 rmsd = 3.097 "obj and name CA" index = 63 rmsd = 3.885 "obj and name CA" index = 64 rmsd = 3.720 "obj and name CA" index = 65 rmsd = 3.791 "obj and name CA" index = 66 rmsd = 4.583 "obj and name CA" index = 67 rmsd = 4.690 "obj and name CA" index = 68 rmsd = 4.459 "obj and name CA" index = 69 rmsd = 4.569 "obj and name CA" index = 70 rmsd = 3.619 "obj and name CA" index = 71 rmsd = 3.301 "obj and name CA" index = 72 rmsd = 2.523 "obj and name CA" index = 73 rmsd = 2.183 "obj and name CA" index = 74 rmsd = 1.593 "obj and name CA" index = 75 rmsd = 1.617 "obj and name CA" index = 76 rmsd = 1.909 "obj and name CA" index = 77 rmsd = 2.197 "obj and name CA" index = 78 rmsd = 2.535 "obj and name CA" index = 79 rmsd = 2.235 "obj and name CA" index = 80 rmsd = 1.868 "obj and name CA" index = 81 rmsd = 2.498 "obj and name CA" index = 82 rmsd = 2.897 "obj and name CA" index = 83 rmsd = 2.592 "obj and name CA" index = 84 rmsd = 2.514 "obj and name CA" index = 85 rmsd = 3.223 "obj and name CA" index = 86 rmsd = 3.434 "obj and name CA" index = 87 rmsd = 3.107 "obj and name CA" index = 88 rmsd = 3.298 "obj and name CA" index = 89 rmsd = 2.503 "obj and name CA" index = 90 rmsd = 3.254 "obj and name CA" index = 91 rmsd = 3.603 "obj and name CA" index = 92 rmsd = 2.698 "obj and name CA" index = 93 rmsd = 2.095 "obj and name CA" index = 94 rmsd = 1.327 "obj and name CA" index = 95 rmsd = 1.217 "obj and name CA" index = 96 rmsd = 1.690 "obj and name CA" index = 97 rmsd = 2.215 "obj and name CA" index = 98 rmsd = 2.937 "obj and name CA" index = 99 rmsd = 3.664 "obj and name CA" index = 100 rmsd = 4.481 "obj and name CA" index = 101 rmsd = 4.227 "obj and name CA" index = 102 rmsd = 3.842 "obj and name CA" index = 103 rmsd = 3.133 "obj and name CA" index = 104 rmsd = 2.883 "obj and name CA" index = 105 rmsd = 2.343 "obj and name CA" index = 106 rmsd = 1.755 "obj and name CA" index = 107 rmsd = 1.517 "obj and name CA" index = 108 rmsd = 2.431 "obj and name CA" index = 109 rmsd = 3.583 "obj and name CA" index = 110 rmsd = 4.051 "obj and name CA" index = 111 rmsd = 3.850 "obj and name CA" index = 112 rmsd = 3.518 "obj and name CA" index = 113 rmsd = 3.038 "obj and name CA" index = 114 rmsd = 3.141 "obj and name CA" index = 115 rmsd = 2.724 "obj and name CA" index = 116 rmsd = 2.218 "obj and name CA" index = 117 rmsd = 2.551 "obj and name CA" index = 118 rmsd = 2.484 "obj and name CA" index = 119 rmsd = 2.071 "obj and name CA" index = 120 rmsd = 2.039 "obj and name CA" index = 121 rmsd = 2.542 "obj and name CA" index = 122 rmsd = 2.450 "obj and name CA" index = 123 rmsd = 2.410 "obj and name CA" index = 124 rmsd = 2.949 "obj and name CA" index = 125 rmsd = 3.241 "obj and name CA" index = 126 rmsd = 3.754 "obj and name CA" index = 127 rmsd = 4.401 "obj and name CA" index = 128 rmsd = 5.127 "obj and name CA" index = 129 rmsd = 5.853 "obj and name CA" index = 130 rmsd = 6.506 "obj and name CA" index = 131 rmsd = 6.526 "obj and name CA" index = 132 rmsd = 7.079 "obj and name CA" index = 133 rmsd = 8.509 "obj and name CA" index = 134 rmsd = 9.568 "obj and name CA" index = 135 rmsd = 11.326 "obj and name CA" index = 136 rmsd = 12.898 "obj and name CA" index = 137 rmsd = 14.542 "obj and name CA" index = 138 rmsd = 16.229 "obj and name CA" index = 139 rmsd = 17.686 "obj and name CA" index = 140 rmsd = 19.475 "obj and name CA" index = 141 rmsd = 21.320 "obj and name CA" index = 142 rmsd = 22.928 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 120 atoms. PyMOL>color cyan,ss s Executive: Colored 54 atoms. PyMOL>color gray,ss ""+l Executive: Colored 4472 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: 1.85 sec. = 1944.2 frames/hour (8.87 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit