PyMOL>load ./selSi.pdb,obj HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 19-JUN-07 2JR2 TITLE SOLUTION NMR STRUCTURE OF HOMODIMER CPS_2611 FROM COLWELLIA TITLE 2 PSYCHRERYTHRAEA. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET TITLE 3 CSR4. COMPND MOL_ID: 1; COMPND 2 MOLECULE: UPF0352 PROTEIN CPS_2611; COMPND 3 CHAIN: A, B; 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 1905 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 555 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: 2.02 sec. = 1783.8 frames/hour (2.02 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 456 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 456 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: 5.94 sec. = 606.1 frames/hour (7.96 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, 4.4888849258422852, 3.6556437015533447, 4.01458740234375, 3.3630380630493164, 2.0562169551849365, 4.2870635986328125, 4.0260171890258789, 4.5853285789489746, 3.6763200759887695, 3.3718104362487793, 3.1358165740966797, 2.5747113227844238, 3.25266432762146, 2.984086275100708, 3.226306676864624, 3.1335077285766602, 1.9583749771118164, 3.8572378158569336, 4.1662631034851074] -> atom index_map = [None, 2, 21, 35, 54, 70, 81, 103, 124, 135, 149, 164, 188, 204, 219, 241, 260, 279, 296, 308, 327, 346, 358, 374, 393, 409, 431, 446, 461, 477, 491, 505, 517, 536, 546, 565, 582, 593, 612, 619, 633, 643, 659, 673, 687, 706, 725, 735, 752, 768, 782, 797, 808, 830, 854, 870, 880, 896, 912, 924, 938, 958, 972, 994, 1004, 1023, 1045, 1062, 1073, 1089, 1108, 1123, 1141, 1159, 1177, 1195, 1213, 1232, 1251, 1265, 1284, 1300, 1311, 1333, 1354, 1365, 1379, 1394, 1418, 1434, 1449, 1471, 1490, 1509, 1526, 1538, 1557, 1576, 1588, 1604, 1623, 1639, 1661, 1676, 1691, 1707, 1721, 1735, 1747, 1766, 1776, 1795, 1812, 1823, 1842, 1849, 1863, 1873, 1889, 1903, 1917, 1936, 1955, 1965, 1982, 1998, 2012, 2027, 2038, 2060, 2084, 2100, 2110, 2126, 2142, 2154, 2168, 2188, 2202, 2224, 2234, 2253, 2275, 2292, 2303, 2319, 2338, 2353, 2371, 2389, 2407, 2425, 2443] "obj and name CA" index = 1 rmsd = 9.406 "obj and name CA" index = 2 rmsd = 7.204 "obj and name CA" index = 3 rmsd = 5.128 "obj and name CA" index = 4 rmsd = 4.026 "obj and name CA" index = 5 rmsd = 2.476 "obj and name CA" index = 6 rmsd = 2.697 "obj and name CA" index = 7 rmsd = 1.440 "obj and name CA" index = 8 rmsd = 1.262 "obj and name CA" index = 9 rmsd = 1.180 "obj and name CA" index = 10 rmsd = 1.169 "obj and name CA" index = 11 rmsd = 1.015 "obj and name CA" index = 12 rmsd = 0.913 "obj and name CA" index = 13 rmsd = 0.916 "obj and name CA" index = 14 rmsd = 0.896 "obj and name CA" index = 15 rmsd = 0.734 "obj and name CA" index = 16 rmsd = 0.638 "obj and name CA" index = 17 rmsd = 0.673 "obj and name CA" index = 18 rmsd = 0.673 "obj and name CA" index = 19 rmsd = 0.583 "obj and name CA" index = 20 rmsd = 0.595 "obj and name CA" index = 21 rmsd = 0.595 "obj and name CA" index = 22 rmsd = 0.642 "obj and name CA" index = 23 rmsd = 0.552 "obj and name CA" index = 24 rmsd = 0.674 "obj and name CA" index = 25 rmsd = 0.826 "obj and name CA" index = 26 rmsd = 0.819 "obj and name CA" index = 27 rmsd = 0.851 "obj and name CA" index = 28 rmsd = 0.764 "obj and name CA" index = 29 rmsd = 0.785 "obj and name CA" index = 30 rmsd = 0.809 "obj and name CA" index = 31 rmsd = 0.928 "obj and name CA" index = 32 rmsd = 0.763 "obj and name CA" index = 33 rmsd = 0.580 "obj and name CA" index = 34 rmsd = 0.589 "obj and name CA" index = 35 rmsd = 0.701 "obj and name CA" index = 36 rmsd = 0.616 "obj and name CA" index = 37 rmsd = 0.526 "obj and name CA" index = 38 rmsd = 0.641 "obj and name CA" index = 39 rmsd = 0.695 "obj and name CA" index = 40 rmsd = 0.614 "obj and name CA" index = 41 rmsd = 0.577 "obj and name CA" index = 42 rmsd = 0.747 "obj and name CA" index = 43 rmsd = 0.812 "obj and name CA" index = 44 rmsd = 0.816 "obj and name CA" index = 45 rmsd = 0.734 "obj and name CA" index = 46 rmsd = 0.995 "obj and name CA" index = 47 rmsd = 1.030 "obj and name CA" index = 48 rmsd = 1.098 "obj and name CA" index = 49 rmsd = 1.272 "obj and name CA" index = 50 rmsd = 1.309 "obj and name CA" index = 51 rmsd = 1.381 "obj and name CA" index = 52 rmsd = 0.996 "obj and name CA" index = 53 rmsd = 0.792 "obj and name CA" index = 54 rmsd = 0.810 "obj and name CA" index = 55 rmsd = 0.828 "obj and name CA" index = 56 rmsd = 0.723 "obj and name CA" index = 57 rmsd = 0.614 "obj and name CA" index = 58 rmsd = 0.722 "obj and name CA" index = 59 rmsd = 0.725 "obj and name CA" index = 60 rmsd = 0.557 "obj and name CA" index = 61 rmsd = 0.592 "obj and name CA" index = 62 rmsd = 0.771 "obj and name CA" index = 63 rmsd = 0.718 "obj and name CA" index = 64 rmsd = 0.612 "obj and name CA" index = 65 rmsd = 0.719 "obj and name CA" index = 66 rmsd = 0.857 "obj and name CA" index = 67 rmsd = 0.712 "obj and name CA" index = 68 rmsd = 0.759 "obj and name CA" index = 69 rmsd = 0.959 "obj and name CA" index = 70 rmsd = 1.098 "obj and name CA" index = 71 rmsd = 1.145 "obj and name CA" index = 72 rmsd = 2.607 "obj and name CA" index = 73 rmsd = 3.047 "obj and name CA" index = 74 rmsd = 4.264 "obj and name CA" index = 75 rmsd = 5.353 "obj and name CA" index = 76 rmsd = 7.206 "obj and name CA" index = 77 rmsd = 9.634 "obj and name CA" index = 78 rmsd = 7.891 "obj and name CA" index = 79 rmsd = 5.940 "obj and name CA" index = 80 rmsd = 4.478 "obj and name CA" index = 81 rmsd = 3.271 "obj and name CA" index = 82 rmsd = 2.486 "obj and name CA" index = 83 rmsd = 1.248 "obj and name CA" index = 84 rmsd = 1.193 "obj and name CA" index = 85 rmsd = 1.159 "obj and name CA" index = 86 rmsd = 1.163 "obj and name CA" index = 87 rmsd = 0.986 "obj and name CA" index = 88 rmsd = 0.842 "obj and name CA" index = 89 rmsd = 0.871 "obj and name CA" index = 90 rmsd = 0.832 "obj and name CA" index = 91 rmsd = 0.717 "obj and name CA" index = 92 rmsd = 0.714 "obj and name CA" index = 93 rmsd = 0.771 "obj and name CA" index = 94 rmsd = 0.728 "obj and name CA" index = 95 rmsd = 0.659 "obj and name CA" index = 96 rmsd = 0.716 "obj and name CA" index = 97 rmsd = 0.855 "obj and name CA" index = 98 rmsd = 0.813 "obj and name CA" index = 99 rmsd = 0.803 "obj and name CA" index = 100 rmsd = 0.956 "obj and name CA" index = 101 rmsd = 1.073 "obj and name CA" index = 102 rmsd = 1.083 "obj and name CA" index = 103 rmsd = 1.173 "obj and name CA" index = 104 rmsd = 0.966 "obj and name CA" index = 105 rmsd = 0.950 "obj and name CA" index = 106 rmsd = 0.887 "obj and name CA" index = 107 rmsd = 0.965 "obj and name CA" index = 108 rmsd = 0.860 "obj and name CA" index = 109 rmsd = 0.672 "obj and name CA" index = 110 rmsd = 0.641 "obj and name CA" index = 111 rmsd = 0.688 "obj and name CA" index = 112 rmsd = 0.576 "obj and name CA" index = 113 rmsd = 0.486 "obj and name CA" index = 114 rmsd = 0.548 "obj and name CA" index = 115 rmsd = 0.630 "obj and name CA" index = 116 rmsd = 0.594 "obj and name CA" index = 117 rmsd = 0.563 "obj and name CA" index = 118 rmsd = 0.690 "obj and name CA" index = 119 rmsd = 0.741 "obj and name CA" index = 120 rmsd = 0.767 "obj and name CA" index = 121 rmsd = 0.738 "obj and name CA" index = 122 rmsd = 0.880 "obj and name CA" index = 123 rmsd = 0.960 "obj and name CA" index = 124 rmsd = 0.960 "obj and name CA" index = 125 rmsd = 1.197 "obj and name CA" index = 126 rmsd = 1.140 "obj and name CA" index = 127 rmsd = 1.312 "obj and name CA" index = 128 rmsd = 1.029 "obj and name CA" index = 129 rmsd = 0.872 "obj and name CA" index = 130 rmsd = 0.852 "obj and name CA" index = 131 rmsd = 0.925 "obj and name CA" index = 132 rmsd = 0.859 "obj and name CA" index = 133 rmsd = 0.725 "obj and name CA" index = 134 rmsd = 0.792 "obj and name CA" index = 135 rmsd = 0.864 "obj and name CA" index = 136 rmsd = 0.749 "obj and name CA" index = 137 rmsd = 0.677 "obj and name CA" index = 138 rmsd = 0.768 "obj and name CA" index = 139 rmsd = 0.833 "obj and name CA" index = 140 rmsd = 0.842 "obj and name CA" index = 141 rmsd = 0.886 "obj and name CA" index = 142 rmsd = 0.984 "obj and name CA" index = 143 rmsd = 0.916 "obj and name CA" index = 144 rmsd = 0.949 "obj and name CA" index = 145 rmsd = 1.227 "obj and name CA" index = 146 rmsd = 1.374 "obj and name CA" index = 147 rmsd = 1.336 "obj and name CA" index = 148 rmsd = 2.388 "obj and name CA" index = 149 rmsd = 4.260 "obj and name CA" index = 150 rmsd = 5.951 "obj and name CA" index = 151 rmsd = 7.891 "obj and name CA" index = 152 rmsd = 9.439 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 3916 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 1156 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: 2.59 sec. = 1389.2 frames/hour (10.55 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit