PyMOL>load ./selSi.pdb,obj HEADER LIPID BINDING PROTEIN 22-DEC-09 2KRT TITLE SOLUTION NMR STRUCTURE OF A CONSERVED HYPOTHETICAL MEMBRANE TITLE 2 LIPOPROTEIN OBTAINED FROM UREAPLASMA PARVUM: NORTHEAST TITLE 3 STRUCTURAL GENOMICS CONSORTIUM TARGET UUR17A (139-239) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CONSERVED HYPOTHETICAL MEMBRANE LIPOPROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 128-239; COMPND 5 ENGINEERED: YES ObjectMolecule: Read secondary structure assignments. 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 418 atoms. PyMOL>color cyan,ss s Executive: Colored 620 atoms. PyMOL>color gray,ss ""+l Executive: Colored 975 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: 1.18 sec. = 3045.2 frames/hour (1.18 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 363 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 363 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: 3.90 sec. = 922.5 frames/hour (5.08 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, 2.3035321235656738, 2.1583225727081299, 1.8155093193054199, 1.7712711095809937, 2.7552869319915771, 1.3176561594009399, 1.8497251272201538, 2.8779034614562988, 2.0226094722747803, 1.8956153392791748, 1.4625366926193237, 2.3416142463684082, 2.7210309505462646, 2.6681993007659912, 1.9738373756408691, 2.8170492649078369, 2.8151144981384277, 1.7306336164474487, 2.2255618572235107] -> atom index_map = [None, 2, 21, 40, 51, 68, 78, 92, 107, 119, 139, 161, 183, 202, 218, 232, 246, 265, 289, 308, 330, 342, 356, 376, 388, 408, 430, 449, 459, 469, 489, 503, 517, 534, 548, 569, 581, 598, 617, 636, 650, 661, 678, 697, 718, 740, 754, 775, 796, 813, 820, 839, 854, 873, 890, 907, 925, 947, 968, 985, 999, 1014, 1033, 1045, 1064, 1086, 1105, 1124, 1138, 1158, 1177, 1198, 1212, 1224, 1231, 1243, 1263, 1270, 1281, 1291, 1305, 1327, 1341, 1348, 1362, 1381, 1403, 1422, 1433, 1452, 1469, 1488, 1502, 1514, 1536, 1558, 1572, 1586, 1603, 1619, 1640, 1661, 1683, 1702, 1721, 1736, 1752, 1763, 1770, 1790, 1812, 1823, 1837, 1851, 1872, 1891, 1906, 1924, 1942, 1960, 1978, 1996] "obj and name CA" index = 1 rmsd = 3.841 "obj and name CA" index = 2 rmsd = 2.525 "obj and name CA" index = 3 rmsd = 2.049 "obj and name CA" index = 4 rmsd = 1.538 "obj and name CA" index = 5 rmsd = 1.179 "obj and name CA" index = 6 rmsd = 1.092 "obj and name CA" index = 7 rmsd = 1.029 "obj and name CA" index = 8 rmsd = 0.897 "obj and name CA" index = 9 rmsd = 0.860 "obj and name CA" index = 10 rmsd = 0.798 "obj and name CA" index = 11 rmsd = 0.786 "obj and name CA" index = 12 rmsd = 0.699 "obj and name CA" index = 13 rmsd = 0.519 "obj and name CA" index = 14 rmsd = 0.709 "obj and name CA" index = 15 rmsd = 0.782 "obj and name CA" index = 16 rmsd = 0.506 "obj and name CA" index = 17 rmsd = 0.495 "obj and name CA" index = 18 rmsd = 0.491 "obj and name CA" index = 19 rmsd = 0.775 "obj and name CA" index = 20 rmsd = 0.679 "obj and name CA" index = 21 rmsd = 0.532 "obj and name CA" index = 22 rmsd = 0.537 "obj and name CA" index = 23 rmsd = 0.650 "obj and name CA" index = 24 rmsd = 0.611 "obj and name CA" index = 25 rmsd = 0.755 "obj and name CA" index = 26 rmsd = 0.795 "obj and name CA" index = 27 rmsd = 0.942 "obj and name CA" index = 28 rmsd = 1.090 "obj and name CA" index = 29 rmsd = 1.072 "obj and name CA" index = 30 rmsd = 1.097 "obj and name CA" index = 31 rmsd = 1.256 "obj and name CA" index = 32 rmsd = 1.092 "obj and name CA" index = 33 rmsd = 0.913 "obj and name CA" index = 34 rmsd = 0.769 "obj and name CA" index = 35 rmsd = 0.939 "obj and name CA" index = 36 rmsd = 1.146 "obj and name CA" index = 37 rmsd = 1.051 "obj and name CA" index = 38 rmsd = 1.002 "obj and name CA" index = 39 rmsd = 0.963 "obj and name CA" index = 40 rmsd = 1.085 "obj and name CA" index = 41 rmsd = 1.048 "obj and name CA" index = 42 rmsd = 0.851 "obj and name CA" index = 43 rmsd = 0.885 "obj and name CA" index = 44 rmsd = 0.986 "obj and name CA" index = 45 rmsd = 0.936 "obj and name CA" index = 46 rmsd = 1.114 "obj and name CA" index = 47 rmsd = 1.306 "obj and name CA" index = 48 rmsd = 1.072 "obj and name CA" index = 49 rmsd = 0.863 "obj and name CA" index = 50 rmsd = 0.673 "obj and name CA" index = 51 rmsd = 0.701 "obj and name CA" index = 52 rmsd = 0.563 "obj and name CA" index = 53 rmsd = 0.654 "obj and name CA" index = 54 rmsd = 0.769 "obj and name CA" index = 55 rmsd = 0.936 "obj and name CA" index = 56 rmsd = 0.862 "obj and name CA" index = 57 rmsd = 0.849 "obj and name CA" index = 58 rmsd = 0.774 "obj and name CA" index = 59 rmsd = 1.022 "obj and name CA" index = 60 rmsd = 0.948 "obj and name CA" index = 61 rmsd = 0.679 "obj and name CA" index = 62 rmsd = 0.552 "obj and name CA" index = 63 rmsd = 0.477 "obj and name CA" index = 64 rmsd = 0.606 "obj and name CA" index = 65 rmsd = 0.481 "obj and name CA" index = 66 rmsd = 0.672 "obj and name CA" index = 67 rmsd = 0.719 "obj and name CA" index = 68 rmsd = 0.703 "obj and name CA" index = 69 rmsd = 0.795 "obj and name CA" index = 70 rmsd = 0.818 "obj and name CA" index = 71 rmsd = 1.140 "obj and name CA" index = 72 rmsd = 1.797 "obj and name CA" index = 73 rmsd = 1.714 "obj and name CA" index = 74 rmsd = 1.294 "obj and name CA" index = 75 rmsd = 1.260 "obj and name CA" index = 76 rmsd = 1.406 "obj and name CA" index = 77 rmsd = 1.297 "obj and name CA" index = 78 rmsd = 0.984 "obj and name CA" index = 79 rmsd = 1.104 "obj and name CA" index = 80 rmsd = 1.264 "obj and name CA" index = 81 rmsd = 1.313 "obj and name CA" index = 82 rmsd = 0.969 "obj and name CA" index = 83 rmsd = 0.699 "obj and name CA" index = 84 rmsd = 0.588 "obj and name CA" index = 85 rmsd = 0.594 "obj and name CA" index = 86 rmsd = 0.534 "obj and name CA" index = 87 rmsd = 0.503 "obj and name CA" index = 88 rmsd = 0.428 "obj and name CA" index = 89 rmsd = 0.469 "obj and name CA" index = 90 rmsd = 0.441 "obj and name CA" index = 91 rmsd = 0.615 "obj and name CA" index = 92 rmsd = 0.886 "obj and name CA" index = 93 rmsd = 0.965 "obj and name CA" index = 94 rmsd = 1.205 "obj and name CA" index = 95 rmsd = 1.200 "obj and name CA" index = 96 rmsd = 1.034 "obj and name CA" index = 97 rmsd = 0.947 "obj and name CA" index = 98 rmsd = 0.731 "obj and name CA" index = 99 rmsd = 0.637 "obj and name CA" index = 100 rmsd = 0.632 "obj and name CA" index = 101 rmsd = 0.582 "obj and name CA" index = 102 rmsd = 0.612 "obj and name CA" index = 103 rmsd = 0.615 "obj and name CA" index = 104 rmsd = 0.723 "obj and name CA" index = 105 rmsd = 0.629 "obj and name CA" index = 106 rmsd = 0.815 "obj and name CA" index = 107 rmsd = 0.967 "obj and name CA" index = 108 rmsd = 0.928 "obj and name CA" index = 109 rmsd = 1.111 "obj and name CA" index = 110 rmsd = 1.301 "obj and name CA" index = 111 rmsd = 1.164 "obj and name CA" index = 112 rmsd = 1.455 "obj and name CA" index = 113 rmsd = 1.581 "obj and name CA" index = 114 rmsd = 1.323 "obj and name CA" index = 115 rmsd = 1.619 "obj and name CA" index = 116 rmsd = 1.982 "obj and name CA" index = 117 rmsd = 2.940 "obj and name CA" index = 118 rmsd = 4.264 "obj and name CA" index = 119 rmsd = 5.892 "obj and name CA" index = 120 rmsd = 7.178 "obj and name CA" index = 121 rmsd = 8.616 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 863 atoms. PyMOL>color cyan,ss s Executive: Colored 1268 atoms. PyMOL>color gray,ss ""+l Executive: Colored 2016 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: 1.30 sec. = 2773.1 frames/hour (6.38 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit