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 17 atoms. PyMOL>color gray,ss ""+l Executive: Colored 2201 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: 1.34 sec. = 2692.4 frames/hour (1.34 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: 5.24 sec. = 687.4 frames/hour (6.57 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, 7.9909963607788086, 7.0349154472351074, 7.7803468704223633, 4.8712010383605957, 9.7577581405639648, 7.057070255279541, 9.5212745666503906, 8.6945924758911133, 9.1727142333984375, 7.6976938247680664, 9.9629373550415039, 10.431814193725586, 7.7435250282287598, 5.4825053215026855, 5.3101277351379395, 10.138916015625, 8.9252405166625977, 8.3140163421630859, 9.7770843505859375] -> 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 = 12.851 "obj and name CA" index = 2 rmsd = 10.997 "obj and name CA" index = 3 rmsd = 9.902 "obj and name CA" index = 4 rmsd = 8.592 "obj and name CA" index = 5 rmsd = 6.466 "obj and name CA" index = 6 rmsd = 5.259 "obj and name CA" index = 7 rmsd = 3.933 "obj and name CA" index = 8 rmsd = 3.152 "obj and name CA" index = 9 rmsd = 3.284 "obj and name CA" index = 10 rmsd = 2.487 "obj and name CA" index = 11 rmsd = 1.937 "obj and name CA" index = 12 rmsd = 2.277 "obj and name CA" index = 13 rmsd = 2.568 "obj and name CA" index = 14 rmsd = 1.973 "obj and name CA" index = 15 rmsd = 1.986 "obj and name CA" index = 16 rmsd = 2.730 "obj and name CA" index = 17 rmsd = 2.574 "obj and name CA" index = 18 rmsd = 2.346 "obj and name CA" index = 19 rmsd = 1.673 "obj and name CA" index = 20 rmsd = 1.525 "obj and name CA" index = 21 rmsd = 1.680 "obj and name CA" index = 22 rmsd = 1.808 "obj and name CA" index = 23 rmsd = 2.176 "obj and name CA" index = 24 rmsd = 2.551 "obj and name CA" index = 25 rmsd = 2.998 "obj and name CA" index = 26 rmsd = 2.414 "obj and name CA" index = 27 rmsd = 2.109 "obj and name CA" index = 28 rmsd = 2.434 "obj and name CA" index = 29 rmsd = 2.406 "obj and name CA" index = 30 rmsd = 1.895 "obj and name CA" index = 31 rmsd = 1.939 "obj and name CA" index = 32 rmsd = 2.274 "obj and name CA" index = 33 rmsd = 2.090 "obj and name CA" index = 34 rmsd = 1.955 "obj and name CA" index = 35 rmsd = 2.213 "obj and name CA" index = 36 rmsd = 2.142 "obj and name CA" index = 37 rmsd = 1.819 "obj and name CA" index = 38 rmsd = 1.679 "obj and name CA" index = 39 rmsd = 1.559 "obj and name CA" index = 40 rmsd = 1.486 "obj and name CA" index = 41 rmsd = 1.759 "obj and name CA" index = 42 rmsd = 1.848 "obj and name CA" index = 43 rmsd = 2.730 "obj and name CA" index = 44 rmsd = 2.741 "obj and name CA" index = 45 rmsd = 3.780 "obj and name CA" index = 46 rmsd = 4.829 "obj and name CA" index = 47 rmsd = 5.629 "obj and name CA" index = 48 rmsd = 5.420 "obj and name CA" index = 49 rmsd = 5.568 "obj and name CA" index = 50 rmsd = 5.937 "obj and name CA" index = 51 rmsd = 5.331 "obj and name CA" index = 52 rmsd = 5.007 "obj and name CA" index = 53 rmsd = 3.893 "obj and name CA" index = 54 rmsd = 3.053 "obj and name CA" index = 55 rmsd = 2.602 "obj and name CA" index = 56 rmsd = 2.882 "obj and name CA" index = 57 rmsd = 2.665 "obj and name CA" index = 58 rmsd = 2.117 "obj and name CA" index = 59 rmsd = 2.417 "obj and name CA" index = 60 rmsd = 2.787 "obj and name CA" index = 61 rmsd = 2.694 "obj and name CA" index = 62 rmsd = 2.558 "obj and name CA" index = 63 rmsd = 2.989 "obj and name CA" index = 64 rmsd = 3.464 "obj and name CA" index = 65 rmsd = 3.424 "obj and name CA" index = 66 rmsd = 3.391 "obj and name CA" index = 67 rmsd = 3.553 "obj and name CA" index = 68 rmsd = 2.925 "obj and name CA" index = 69 rmsd = 2.508 "obj and name CA" index = 70 rmsd = 2.073 "obj and name CA" index = 71 rmsd = 1.685 "obj and name CA" index = 72 rmsd = 1.455 "obj and name CA" index = 73 rmsd = 1.353 "obj and name CA" index = 74 rmsd = 1.335 "obj and name CA" index = 75 rmsd = 1.895 "obj and name CA" index = 76 rmsd = 2.274 "obj and name CA" index = 77 rmsd = 2.438 "obj and name CA" index = 78 rmsd = 2.782 "obj and name CA" index = 79 rmsd = 2.434 "obj and name CA" index = 80 rmsd = 2.221 "obj and name CA" index = 81 rmsd = 2.855 "obj and name CA" index = 82 rmsd = 3.120 "obj and name CA" index = 83 rmsd = 2.544 "obj and name CA" index = 84 rmsd = 2.810 "obj and name CA" index = 85 rmsd = 3.500 "obj and name CA" index = 86 rmsd = 3.421 "obj and name CA" index = 87 rmsd = 3.300 "obj and name CA" index = 88 rmsd = 3.807 "obj and name CA" index = 89 rmsd = 3.333 "obj and name CA" index = 90 rmsd = 3.909 "obj and name CA" index = 91 rmsd = 4.221 "obj and name CA" index = 92 rmsd = 3.355 "obj and name CA" index = 93 rmsd = 2.525 "obj and name CA" index = 94 rmsd = 2.311 "obj and name CA" index = 95 rmsd = 2.028 "obj and name CA" index = 96 rmsd = 2.215 "obj and name CA" index = 97 rmsd = 2.348 "obj and name CA" index = 98 rmsd = 2.378 "obj and name CA" index = 99 rmsd = 2.667 "obj and name CA" index = 100 rmsd = 2.893 "obj and name CA" index = 101 rmsd = 2.742 "obj and name CA" index = 102 rmsd = 3.088 "obj and name CA" index = 103 rmsd = 3.051 "obj and name CA" index = 104 rmsd = 3.356 "obj and name CA" index = 105 rmsd = 3.338 "obj and name CA" index = 106 rmsd = 2.971 "obj and name CA" index = 107 rmsd = 2.811 "obj and name CA" index = 108 rmsd = 2.993 "obj and name CA" index = 109 rmsd = 3.743 "obj and name CA" index = 110 rmsd = 3.553 "obj and name CA" index = 111 rmsd = 3.388 "obj and name CA" index = 112 rmsd = 3.636 "obj and name CA" index = 113 rmsd = 3.212 "obj and name CA" index = 114 rmsd = 3.821 "obj and name CA" index = 115 rmsd = 3.759 "obj and name CA" index = 116 rmsd = 3.313 "obj and name CA" index = 117 rmsd = 3.533 "obj and name CA" index = 118 rmsd = 4.027 "obj and name CA" index = 119 rmsd = 3.759 "obj and name CA" index = 120 rmsd = 3.334 "obj and name CA" index = 121 rmsd = 3.956 "obj and name CA" index = 122 rmsd = 4.313 "obj and name CA" index = 123 rmsd = 3.669 "obj and name CA" index = 124 rmsd = 3.587 "obj and name CA" index = 125 rmsd = 4.281 "obj and name CA" index = 126 rmsd = 3.930 "obj and name CA" index = 127 rmsd = 4.571 "obj and name CA" index = 128 rmsd = 5.128 "obj and name CA" index = 129 rmsd = 6.285 "obj and name CA" index = 130 rmsd = 7.788 "obj and name CA" index = 131 rmsd = 8.534 "obj and name CA" index = 132 rmsd = 9.190 "obj and name CA" index = 133 rmsd = 10.418 "obj and name CA" index = 134 rmsd = 11.492 "obj and name CA" index = 135 rmsd = 12.783 "obj and name CA" index = 136 rmsd = 14.050 "obj and name CA" index = 137 rmsd = 15.572 "obj and name CA" index = 138 rmsd = 16.686 "obj and name CA" index = 139 rmsd = 18.030 "obj and name CA" index = 140 rmsd = 19.212 "obj and name CA" index = 141 rmsd = 20.714 "obj and name CA" index = 142 rmsd = 21.615 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 51 atoms. PyMOL>color gray,ss ""+l Executive: Colored 4482 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: 2.32 sec. = 1554.6 frames/hour (8.89 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit