PyMOL>load ./selSi.pdb,obj HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 29-DEC-08 2KCU TITLE NMR SOLUTION STRUCTURE OF AN UNCHARACTERIZED PROTEIN FROM TITLE 2 CHLOROBIUM TEPIDUM. NORTHEAST STRUCTURAL GENOMICS TARGET TITLE 3 CTR107 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN CTR107; COMPND 3 CHAIN: A; COMPND 4 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 491 atoms. PyMOL>color cyan,ss s Executive: Colored 786 atoms. PyMOL>color gray,ss ""+l Executive: Colored 1218 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: 1.76 sec. = 2040.0 frames/hour (1.76 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 498 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 498 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: 8.78 sec. = 410.0 frames/hour (10.54 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, 3.8697898387908936, 3.3429310321807861, 5.953916072845459, 3.6766870021820068, 4.2717819213867188, 4.436553955078125, 6.3718156814575195, 7.7977733612060547, 4.8756256103515625, 7.3722877502441406, 5.4027299880981445, 8.5213661193847656, 3.2624778747558594, 7.2046270370483398, 5.1823520660400391, 7.0604677200317383, 6.9341506958007812, 6.5438847541809082, 5.6960344314575195] -> atom index_map = [None, 2, 21, 33, 53, 68, 79, 96, 116, 132, 143, 158, 177, 199, 214, 233, 243, 257, 273, 287, 297, 316, 335, 354, 378, 392, 409, 423, 433, 450, 461, 476, 495, 502, 513, 532, 552, 567, 577, 584, 605, 623, 635, 654, 673, 690, 709, 728, 738, 745, 762, 769, 791, 802, 816, 827, 834, 848, 862, 882, 892, 916, 937, 957, 964, 981, 992, 1002, 1009, 1023, 1043, 1058, 1074, 1089, 1109, 1116, 1136, 1150, 1166, 1181, 1188, 1195, 1211, 1226, 1233, 1244, 1251, 1275, 1291, 1307, 1321, 1328, 1347, 1361, 1375, 1386, 1393, 1415, 1425, 1435, 1446, 1457, 1476, 1497, 1516, 1523, 1537, 1558, 1565, 1580, 1599, 1614, 1624, 1640, 1661, 1673, 1683, 1702, 1719, 1741, 1765, 1781, 1793, 1805, 1819, 1826, 1846, 1858, 1877, 1888, 1895, 1910, 1920, 1941, 1956, 1975, 1996, 2015, 2027, 2041, 2055, 2065, 2080, 2094, 2104, 2118, 2130, 2147, 2166, 2190, 2204, 2228, 2244, 2255, 2274, 2291, 2310, 2328, 2343, 2354, 2373, 2388, 2406, 2424, 2442, 2460, 2478] "obj and name CA" index = 1 rmsd = 11.687 "obj and name CA" index = 2 rmsd = 10.806 "obj and name CA" index = 3 rmsd = 9.098 "obj and name CA" index = 4 rmsd = 7.049 "obj and name CA" index = 5 rmsd = 5.331 "obj and name CA" index = 6 rmsd = 3.388 "obj and name CA" index = 7 rmsd = 1.558 "obj and name CA" index = 8 rmsd = 1.320 "obj and name CA" index = 9 rmsd = 1.125 "obj and name CA" index = 10 rmsd = 1.318 "obj and name CA" index = 11 rmsd = 1.299 "obj and name CA" index = 12 rmsd = 1.504 "obj and name CA" index = 13 rmsd = 1.533 "obj and name CA" index = 14 rmsd = 1.418 "obj and name CA" index = 15 rmsd = 1.501 "obj and name CA" index = 16 rmsd = 1.622 "obj and name CA" index = 17 rmsd = 1.481 "obj and name CA" index = 18 rmsd = 1.614 "obj and name CA" index = 19 rmsd = 1.257 "obj and name CA" index = 20 rmsd = 1.137 "obj and name CA" index = 21 rmsd = 1.562 "obj and name CA" index = 22 rmsd = 1.917 "obj and name CA" index = 23 rmsd = 2.004 "obj and name CA" index = 24 rmsd = 2.149 "obj and name CA" index = 25 rmsd = 2.615 "obj and name CA" index = 26 rmsd = 2.837 "obj and name CA" index = 27 rmsd = 3.837 "obj and name CA" index = 28 rmsd = 4.819 "obj and name CA" index = 29 rmsd = 4.079 "obj and name CA" index = 30 rmsd = 3.381 "obj and name CA" index = 31 rmsd = 2.743 "obj and name CA" index = 32 rmsd = 2.819 "obj and name CA" index = 33 rmsd = 2.723 "obj and name CA" index = 34 rmsd = 2.271 "obj and name CA" index = 35 rmsd = 2.019 "obj and name CA" index = 36 rmsd = 2.391 "obj and name CA" index = 37 rmsd = 2.289 "obj and name CA" index = 38 rmsd = 1.795 "obj and name CA" index = 39 rmsd = 1.808 "obj and name CA" index = 40 rmsd = 2.001 "obj and name CA" index = 41 rmsd = 1.719 "obj and name CA" index = 42 rmsd = 1.464 "obj and name CA" index = 43 rmsd = 1.955 "obj and name CA" index = 44 rmsd = 1.862 "obj and name CA" index = 45 rmsd = 1.692 "obj and name CA" index = 46 rmsd = 1.618 "obj and name CA" index = 47 rmsd = 2.185 "obj and name CA" index = 48 rmsd = 2.526 "obj and name CA" index = 49 rmsd = 2.539 "obj and name CA" index = 50 rmsd = 2.643 "obj and name CA" index = 51 rmsd = 2.062 "obj and name CA" index = 52 rmsd = 1.677 "obj and name CA" index = 53 rmsd = 1.162 "obj and name CA" index = 54 rmsd = 1.478 "obj and name CA" index = 55 rmsd = 1.285 "obj and name CA" index = 56 rmsd = 1.131 "obj and name CA" index = 57 rmsd = 1.007 "obj and name CA" index = 58 rmsd = 0.978 "obj and name CA" index = 59 rmsd = 1.163 "obj and name CA" index = 60 rmsd = 1.316 "obj and name CA" index = 61 rmsd = 1.849 "obj and name CA" index = 62 rmsd = 2.121 "obj and name CA" index = 63 rmsd = 2.747 "obj and name CA" index = 64 rmsd = 2.737 "obj and name CA" index = 65 rmsd = 3.785 "obj and name CA" index = 66 rmsd = 3.614 "obj and name CA" index = 67 rmsd = 3.796 "obj and name CA" index = 68 rmsd = 3.288 "obj and name CA" index = 69 rmsd = 2.914 "obj and name CA" index = 70 rmsd = 2.377 "obj and name CA" index = 71 rmsd = 1.835 "obj and name CA" index = 72 rmsd = 1.538 "obj and name CA" index = 73 rmsd = 1.427 "obj and name CA" index = 74 rmsd = 1.296 "obj and name CA" index = 75 rmsd = 1.087 "obj and name CA" index = 76 rmsd = 1.225 "obj and name CA" index = 77 rmsd = 1.332 "obj and name CA" index = 78 rmsd = 2.141 "obj and name CA" index = 79 rmsd = 2.612 "obj and name CA" index = 80 rmsd = 2.592 "obj and name CA" index = 81 rmsd = 2.114 "obj and name CA" index = 82 rmsd = 2.406 "obj and name CA" index = 83 rmsd = 2.031 "obj and name CA" index = 84 rmsd = 2.569 "obj and name CA" index = 85 rmsd = 2.789 "obj and name CA" index = 86 rmsd = 2.344 "obj and name CA" index = 87 rmsd = 1.611 "obj and name CA" index = 88 rmsd = 1.903 "obj and name CA" index = 89 rmsd = 1.955 "obj and name CA" index = 90 rmsd = 2.238 "obj and name CA" index = 91 rmsd = 1.840 "obj and name CA" index = 92 rmsd = 1.695 "obj and name CA" index = 93 rmsd = 2.168 "obj and name CA" index = 94 rmsd = 2.013 "obj and name CA" index = 95 rmsd = 1.898 "obj and name CA" index = 96 rmsd = 1.617 "obj and name CA" index = 97 rmsd = 1.230 "obj and name CA" index = 98 rmsd = 1.083 "obj and name CA" index = 99 rmsd = 1.068 "obj and name CA" index = 100 rmsd = 1.055 "obj and name CA" index = 101 rmsd = 1.091 "obj and name CA" index = 102 rmsd = 1.322 "obj and name CA" index = 103 rmsd = 1.585 "obj and name CA" index = 104 rmsd = 2.141 "obj and name CA" index = 105 rmsd = 2.529 "obj and name CA" index = 106 rmsd = 2.280 "obj and name CA" index = 107 rmsd = 2.349 "obj and name CA" index = 108 rmsd = 1.996 "obj and name CA" index = 109 rmsd = 1.594 "obj and name CA" index = 110 rmsd = 1.504 "obj and name CA" index = 111 rmsd = 1.731 "obj and name CA" index = 112 rmsd = 1.470 "obj and name CA" index = 113 rmsd = 1.456 "obj and name CA" index = 114 rmsd = 1.758 "obj and name CA" index = 115 rmsd = 1.580 "obj and name CA" index = 116 rmsd = 1.533 "obj and name CA" index = 117 rmsd = 1.899 "obj and name CA" index = 118 rmsd = 1.969 "obj and name CA" index = 119 rmsd = 1.719 "obj and name CA" index = 120 rmsd = 1.928 "obj and name CA" index = 121 rmsd = 2.146 "obj and name CA" index = 122 rmsd = 2.100 "obj and name CA" index = 123 rmsd = 2.083 "obj and name CA" index = 124 rmsd = 2.392 "obj and name CA" index = 125 rmsd = 2.610 "obj and name CA" index = 126 rmsd = 3.068 "obj and name CA" index = 127 rmsd = 3.532 "obj and name CA" index = 128 rmsd = 3.761 "obj and name CA" index = 129 rmsd = 4.039 "obj and name CA" index = 130 rmsd = 2.108 "obj and name CA" index = 131 rmsd = 1.376 "obj and name CA" index = 132 rmsd = 1.088 "obj and name CA" index = 133 rmsd = 1.131 "obj and name CA" index = 134 rmsd = 1.056 "obj and name CA" index = 135 rmsd = 1.290 "obj and name CA" index = 136 rmsd = 1.818 "obj and name CA" index = 137 rmsd = 2.725 "obj and name CA" index = 138 rmsd = 3.107 "obj and name CA" index = 139 rmsd = 3.584 "obj and name CA" index = 140 rmsd = 4.341 "obj and name CA" index = 141 rmsd = 3.332 "obj and name CA" index = 142 rmsd = 3.069 "obj and name CA" index = 143 rmsd = 3.258 "obj and name CA" index = 144 rmsd = 3.424 "obj and name CA" index = 145 rmsd = 3.067 "obj and name CA" index = 146 rmsd = 2.604 "obj and name CA" index = 147 rmsd = 1.887 "obj and name CA" index = 148 rmsd = 1.461 "obj and name CA" index = 149 rmsd = 1.157 "obj and name CA" index = 150 rmsd = 1.013 "obj and name CA" index = 151 rmsd = 0.974 "obj and name CA" index = 152 rmsd = 0.975 "obj and name CA" index = 153 rmsd = 1.150 "obj and name CA" index = 154 rmsd = 2.098 "obj and name CA" index = 155 rmsd = 2.297 "obj and name CA" index = 156 rmsd = 4.288 "obj and name CA" index = 157 rmsd = 5.304 "obj and name CA" index = 158 rmsd = 5.409 "obj and name CA" index = 159 rmsd = 6.496 "obj and name CA" index = 160 rmsd = 7.913 "obj and name CA" index = 161 rmsd = 9.660 "obj and name CA" index = 162 rmsd = 11.238 "obj and name CA" index = 163 rmsd = 12.911 "obj and name CA" index = 164 rmsd = 14.370 "obj and name CA" index = 165 rmsd = 16.113 "obj and name CA" index = 166 rmsd = 18.188 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 1006 atoms. PyMOL>color cyan,ss s Executive: Colored 1599 atoms. PyMOL>color gray,ss ""+l Executive: Colored 2551 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: 2.29 sec. = 1572.1 frames/hour (12.83 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit