PyMOL>load ./selSi.pdb,obj HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 27-MAY-10 2KYI TITLE SOLUTION NMR STRUCTURE OF DSY0195(21-82) PROTEIN FROM TITLE 2 DESULFITOBACTERIUM HAFNIENSE. NORTHEAST STRUCTURAL GENOMICS TITLE 3 CONSORTIUM TARGET DHR8C COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES 21-82; 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 48 atoms. PyMOL>color cyan,ss s Executive: Colored 1125 atoms. PyMOL>color gray,ss ""+l Executive: Colored 1117 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: 1.38 sec. = 2603.9 frames/hour (1.38 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: 5.62 sec. = 640.1 frames/hour (7.01 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, 3.8347282409667969, 2.7598874568939209, 3.3542602062225342, 4.2667980194091797, 5.3405122756958008, 3.3703656196594238, 3.3757345676422119, 3.8949935436248779, 2.8661279678344727, 4.3767752647399902, 3.4818630218505859, 2.4252057075500488, 3.2890348434448242, 3.1827125549316406, 3.9752440452575684, 2.870201587677002, 3.8208892345428467, 4.4411396980285645, 3.5570104122161865] -> 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, 699, 718, 730, 749, 771, 781, 788, 805, 821, 836, 852, 867, 874, 893, 912, 924, 934, 953, 969, 990, 1004, 1023, 1038, 1056, 1074, 1092, 1110, 1128, 1147, 1166, 1178, 1192, 1216, 1233, 1253, 1272, 1283, 1302, 1316, 1323, 1339, 1350, 1372, 1388, 1405, 1416, 1436, 1448, 1462, 1484, 1499, 1518, 1537, 1556, 1571, 1585, 1604, 1621, 1628, 1644, 1663, 1674, 1693, 1715, 1722, 1737, 1759, 1778, 1785, 1804, 1826, 1844, 1863, 1875, 1894, 1916, 1926, 1933, 1950, 1966, 1981, 1997, 2012, 2019, 2038, 2057, 2069, 2079, 2098, 2114, 2135, 2149, 2168, 2183, 2201, 2219, 2237, 2255, 2273] "obj and name CA" index = 1 rmsd = 3.759 "obj and name CA" index = 2 rmsd = 2.266 "obj and name CA" index = 3 rmsd = 1.455 "obj and name CA" index = 4 rmsd = 1.169 "obj and name CA" index = 5 rmsd = 0.906 "obj and name CA" index = 6 rmsd = 0.697 "obj and name CA" index = 7 rmsd = 0.538 "obj and name CA" index = 8 rmsd = 0.495 "obj and name CA" index = 9 rmsd = 0.460 "obj and name CA" index = 10 rmsd = 0.574 "obj and name CA" index = 11 rmsd = 0.828 "obj and name CA" index = 12 rmsd = 0.777 "obj and name CA" index = 13 rmsd = 1.034 "obj and name CA" index = 14 rmsd = 1.111 "obj and name CA" index = 15 rmsd = 1.038 "obj and name CA" index = 16 rmsd = 1.156 "obj and name CA" index = 17 rmsd = 1.290 "obj and name CA" index = 18 rmsd = 1.234 "obj and name CA" index = 19 rmsd = 1.231 "obj and name CA" index = 20 rmsd = 1.106 "obj and name CA" index = 21 rmsd = 1.167 "obj and name CA" index = 22 rmsd = 1.134 "obj and name CA" index = 23 rmsd = 0.979 "obj and name CA" index = 24 rmsd = 0.995 "obj and name CA" index = 25 rmsd = 0.868 "obj and name CA" index = 26 rmsd = 0.998 "obj and name CA" index = 27 rmsd = 0.937 "obj and name CA" index = 28 rmsd = 1.186 "obj and name CA" index = 29 rmsd = 1.492 "obj and name CA" index = 30 rmsd = 1.057 "obj and name CA" index = 31 rmsd = 0.982 "obj and name CA" index = 32 rmsd = 0.768 "obj and name CA" index = 33 rmsd = 0.900 "obj and name CA" index = 34 rmsd = 0.825 "obj and name CA" index = 35 rmsd = 1.022 "obj and name CA" index = 36 rmsd = 1.138 "obj and name CA" index = 37 rmsd = 1.277 "obj and name CA" index = 38 rmsd = 1.132 "obj and name CA" index = 39 rmsd = 0.938 "obj and name CA" index = 40 rmsd = 1.021 "obj and name CA" index = 41 rmsd = 1.631 "obj and name CA" index = 42 rmsd = 2.423 "obj and name CA" index = 43 rmsd = 2.534 "obj and name CA" index = 44 rmsd = 2.713 "obj and name CA" index = 45 rmsd = 2.234 "obj and name CA" index = 46 rmsd = 1.658 "obj and name CA" index = 47 rmsd = 2.115 "obj and name CA" index = 48 rmsd = 1.463 "obj and name CA" index = 49 rmsd = 0.876 "obj and name CA" index = 50 rmsd = 0.739 "obj and name CA" index = 51 rmsd = 0.738 "obj and name CA" index = 52 rmsd = 0.703 "obj and name CA" index = 53 rmsd = 0.799 "obj and name CA" index = 54 rmsd = 0.844 "obj and name CA" index = 55 rmsd = 0.934 "obj and name CA" index = 56 rmsd = 1.085 "obj and name CA" index = 57 rmsd = 0.985 "obj and name CA" index = 58 rmsd = 1.143 "obj and name CA" index = 59 rmsd = 1.044 "obj and name CA" index = 60 rmsd = 0.921 "obj and name CA" index = 61 rmsd = 1.061 "obj and name CA" index = 62 rmsd = 1.023 "obj and name CA" index = 63 rmsd = 1.456 "obj and name CA" index = 64 rmsd = 1.951 "obj and name CA" index = 65 rmsd = 2.967 "obj and name CA" index = 66 rmsd = 3.945 "obj and name CA" index = 67 rmsd = 5.294 "obj and name CA" index = 68 rmsd = 6.770 "obj and name CA" index = 69 rmsd = 8.579 "obj and name CA" index = 70 rmsd = 9.804 "obj and name CA" index = 71 rmsd = 11.408 "obj and name CA" index = 72 rmsd = 3.735 "obj and name CA" index = 73 rmsd = 2.181 "obj and name CA" index = 74 rmsd = 1.317 "obj and name CA" index = 75 rmsd = 1.091 "obj and name CA" index = 76 rmsd = 0.728 "obj and name CA" index = 77 rmsd = 0.682 "obj and name CA" index = 78 rmsd = 0.566 "obj and name CA" index = 79 rmsd = 0.614 "obj and name CA" index = 80 rmsd = 0.649 "obj and name CA" index = 81 rmsd = 0.927 "obj and name CA" index = 82 rmsd = 1.067 "obj and name CA" index = 83 rmsd = 0.880 "obj and name CA" index = 84 rmsd = 1.014 "obj and name CA" index = 85 rmsd = 1.040 "obj and name CA" index = 86 rmsd = 1.100 "obj and name CA" index = 87 rmsd = 1.276 "obj and name CA" index = 88 rmsd = 1.356 "obj and name CA" index = 89 rmsd = 1.367 "obj and name CA" index = 90 rmsd = 1.426 "obj and name CA" index = 91 rmsd = 1.398 "obj and name CA" index = 92 rmsd = 1.236 "obj and name CA" index = 93 rmsd = 1.108 "obj and name CA" index = 94 rmsd = 1.087 "obj and name CA" index = 95 rmsd = 1.091 "obj and name CA" index = 96 rmsd = 0.960 "obj and name CA" index = 97 rmsd = 1.036 "obj and name CA" index = 98 rmsd = 0.954 "obj and name CA" index = 99 rmsd = 1.251 "obj and name CA" index = 100 rmsd = 1.708 "obj and name CA" index = 101 rmsd = 1.288 "obj and name CA" index = 102 rmsd = 1.126 "obj and name CA" index = 103 rmsd = 0.844 "obj and name CA" index = 104 rmsd = 0.968 "obj and name CA" index = 105 rmsd = 0.859 "obj and name CA" index = 106 rmsd = 0.952 "obj and name CA" index = 107 rmsd = 1.035 "obj and name CA" index = 108 rmsd = 1.239 "obj and name CA" index = 109 rmsd = 1.236 "obj and name CA" index = 110 rmsd = 1.105 "obj and name CA" index = 111 rmsd = 1.321 "obj and name CA" index = 112 rmsd = 1.900 "obj and name CA" index = 113 rmsd = 2.081 "obj and name CA" index = 114 rmsd = 2.637 "obj and name CA" index = 115 rmsd = 2.684 "obj and name CA" index = 116 rmsd = 2.259 "obj and name CA" index = 117 rmsd = 1.696 "obj and name CA" index = 118 rmsd = 2.368 "obj and name CA" index = 119 rmsd = 2.192 "obj and name CA" index = 120 rmsd = 0.996 "obj and name CA" index = 121 rmsd = 0.921 "obj and name CA" index = 122 rmsd = 0.925 "obj and name CA" index = 123 rmsd = 0.869 "obj and name CA" index = 124 rmsd = 0.884 "obj and name CA" index = 125 rmsd = 0.890 "obj and name CA" index = 126 rmsd = 0.928 "obj and name CA" index = 127 rmsd = 0.988 "obj and name CA" index = 128 rmsd = 0.830 "obj and name CA" index = 129 rmsd = 1.002 "obj and name CA" index = 130 rmsd = 0.907 "obj and name CA" index = 131 rmsd = 0.899 "obj and name CA" index = 132 rmsd = 1.013 "obj and name CA" index = 133 rmsd = 0.906 "obj and name CA" index = 134 rmsd = 1.148 "obj and name CA" index = 135 rmsd = 1.960 "obj and name CA" index = 136 rmsd = 3.189 "obj and name CA" index = 137 rmsd = 4.584 "obj and name CA" index = 138 rmsd = 5.008 "obj and name CA" index = 139 rmsd = 6.755 "obj and name CA" index = 140 rmsd = 8.356 "obj and name CA" index = 141 rmsd = 10.309 "obj and name CA" index = 142 rmsd = 12.062 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 96 atoms. PyMOL>color cyan,ss s Executive: Colored 2323 atoms. PyMOL>color gray,ss ""+l Executive: Colored 2303 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: 2.18 sec. = 1654.6 frames/hour (9.18 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit