PyMOL>load ./selSi.pdb,obj HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 31-DEC-08 2KCZ TITLE SOLUTION NMR STRUCTURE OF THE C-TERMINAL DOMAIN OF PROTEIN TITLE 2 DR_A0006 FROM DEINOCOCCUS RADIODURANS. NORTHEAST TITLE 3 STRUCTURAL GENOMICS CONSORTIUM TARGET DRR147D COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN DR_A0006; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 98-243; 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 671 atoms. PyMOL>color cyan,ss s Executive: Colored 446 atoms. PyMOL>color gray,ss ""+l Executive: Colored 1329 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: 1.53 sec. = 2354.7 frames/hour (1.53 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 465 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 465 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: 7.22 sec. = 498.7 frames/hour (8.75 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, 6.0423555374145508, 5.8057155609130859, 6.9475851058959961, 7.3250899314880371, 7.6142497062683105, 7.5414724349975586, 9.1359672546386719, 6.4001898765563965, 6.7153868675231934, 8.7230720520019531, 7.8264908790588379, 9.9417791366577148, 7.4455804824829102, 3.4816784858703613, 6.6814312934875488, 9.1540803909301758, 8.5319242477416992, 7.684420108795166, 8.8282690048217773] -> atom index_map = [None, 2, 21, 28, 43, 57, 73, 89, 113, 125, 135, 151, 165, 184, 191, 213, 227, 237, 252, 269, 288, 309, 319, 335, 359, 383, 395, 414, 428, 435, 454, 468, 487, 506, 523, 537, 555, 574, 598, 609, 625, 640, 656, 675, 687, 699, 721, 745, 756, 780, 804, 818, 834, 849, 859, 873, 883, 897, 916, 923, 933, 949, 960, 984, 999, 1009, 1024, 1043, 1057, 1067, 1079, 1094, 1108, 1115, 1137, 1161, 1180, 1190, 1214, 1238, 1249, 1268, 1282, 1289, 1299, 1323, 1342, 1357, 1371, 1382, 1389, 1404, 1420, 1439, 1459, 1483, 1497, 1507, 1521, 1528, 1538, 1562, 1569, 1583, 1598, 1614, 1630, 1646, 1670, 1689, 1703, 1724, 1748, 1762, 1776, 1783, 1790, 1801, 1811, 1818, 1828, 1844, 1863, 1873, 1897, 1914, 1934, 1948, 1965, 1980, 1994, 2005, 2022, 2039, 2058, 2082, 2094, 2106, 2125, 2142, 2166, 2186, 2208, 2232, 2247, 2264, 2279, 2298, 2305, 2324, 2339, 2357, 2375, 2393, 2411, 2429] "obj and name CA" index = 1 rmsd = 8.193 "obj and name CA" index = 2 rmsd = 6.881 "obj and name CA" index = 3 rmsd = 5.469 "obj and name CA" index = 4 rmsd = 4.171 "obj and name CA" index = 5 rmsd = 3.116 "obj and name CA" index = 6 rmsd = 2.473 "obj and name CA" index = 7 rmsd = 2.140 "obj and name CA" index = 8 rmsd = 2.125 "obj and name CA" index = 9 rmsd = 1.924 "obj and name CA" index = 10 rmsd = 2.035 "obj and name CA" index = 11 rmsd = 2.093 "obj and name CA" index = 12 rmsd = 2.202 "obj and name CA" index = 13 rmsd = 2.412 "obj and name CA" index = 14 rmsd = 2.344 "obj and name CA" index = 15 rmsd = 2.345 "obj and name CA" index = 16 rmsd = 2.017 "obj and name CA" index = 17 rmsd = 2.313 "obj and name CA" index = 18 rmsd = 2.330 "obj and name CA" index = 19 rmsd = 1.938 "obj and name CA" index = 20 rmsd = 1.912 "obj and name CA" index = 21 rmsd = 2.099 "obj and name CA" index = 22 rmsd = 2.211 "obj and name CA" index = 23 rmsd = 2.523 "obj and name CA" index = 24 rmsd = 2.673 "obj and name CA" index = 25 rmsd = 3.147 "obj and name CA" index = 26 rmsd = 2.665 "obj and name CA" index = 27 rmsd = 3.521 "obj and name CA" index = 28 rmsd = 3.566 "obj and name CA" index = 29 rmsd = 3.889 "obj and name CA" index = 30 rmsd = 5.939 "obj and name CA" index = 31 rmsd = 5.444 "obj and name CA" index = 32 rmsd = 5.694 "obj and name CA" index = 33 rmsd = 7.344 "obj and name CA" index = 34 rmsd = 7.581 "obj and name CA" index = 35 rmsd = 8.623 "obj and name CA" index = 36 rmsd = 8.694 "obj and name CA" index = 37 rmsd = 7.866 "obj and name CA" index = 38 rmsd = 7.167 "obj and name CA" index = 39 rmsd = 5.232 "obj and name CA" index = 40 rmsd = 5.672 "obj and name CA" index = 41 rmsd = 4.666 "obj and name CA" index = 42 rmsd = 5.054 "obj and name CA" index = 43 rmsd = 5.834 "obj and name CA" index = 44 rmsd = 5.383 "obj and name CA" index = 45 rmsd = 4.554 "obj and name CA" index = 46 rmsd = 3.855 "obj and name CA" index = 47 rmsd = 3.499 "obj and name CA" index = 48 rmsd = 4.666 "obj and name CA" index = 49 rmsd = 5.164 "obj and name CA" index = 50 rmsd = 5.627 "obj and name CA" index = 51 rmsd = 6.036 "obj and name CA" index = 52 rmsd = 8.067 "obj and name CA" index = 53 rmsd = 7.906 "obj and name CA" index = 54 rmsd = 7.425 "obj and name CA" index = 55 rmsd = 6.689 "obj and name CA" index = 56 rmsd = 4.511 "obj and name CA" index = 57 rmsd = 5.284 "obj and name CA" index = 58 rmsd = 7.488 "obj and name CA" index = 59 rmsd = 7.303 "obj and name CA" index = 60 rmsd = 5.491 "obj and name CA" index = 61 rmsd = 4.831 "obj and name CA" index = 62 rmsd = 4.566 "obj and name CA" index = 63 rmsd = 3.468 "obj and name CA" index = 64 rmsd = 2.688 "obj and name CA" index = 65 rmsd = 2.548 "obj and name CA" index = 66 rmsd = 2.277 "obj and name CA" index = 67 rmsd = 2.529 "obj and name CA" index = 68 rmsd = 2.088 "obj and name CA" index = 69 rmsd = 2.168 "obj and name CA" index = 70 rmsd = 2.278 "obj and name CA" index = 71 rmsd = 2.615 "obj and name CA" index = 72 rmsd = 1.949 "obj and name CA" index = 73 rmsd = 1.726 "obj and name CA" index = 74 rmsd = 1.431 "obj and name CA" index = 75 rmsd = 1.342 "obj and name CA" index = 76 rmsd = 1.613 "obj and name CA" index = 77 rmsd = 2.008 "obj and name CA" index = 78 rmsd = 2.578 "obj and name CA" index = 79 rmsd = 3.527 "obj and name CA" index = 80 rmsd = 3.155 "obj and name CA" index = 81 rmsd = 3.878 "obj and name CA" index = 82 rmsd = 4.140 "obj and name CA" index = 83 rmsd = 3.762 "obj and name CA" index = 84 rmsd = 4.410 "obj and name CA" index = 85 rmsd = 3.886 "obj and name CA" index = 86 rmsd = 3.794 "obj and name CA" index = 87 rmsd = 2.677 "obj and name CA" index = 88 rmsd = 2.186 "obj and name CA" index = 89 rmsd = 2.194 "obj and name CA" index = 90 rmsd = 1.636 "obj and name CA" index = 91 rmsd = 1.330 "obj and name CA" index = 92 rmsd = 1.342 "obj and name CA" index = 93 rmsd = 1.479 "obj and name CA" index = 94 rmsd = 1.652 "obj and name CA" index = 95 rmsd = 1.880 "obj and name CA" index = 96 rmsd = 2.000 "obj and name CA" index = 97 rmsd = 2.313 "obj and name CA" index = 98 rmsd = 3.017 "obj and name CA" index = 99 rmsd = 2.999 "obj and name CA" index = 100 rmsd = 2.966 "obj and name CA" index = 101 rmsd = 2.413 "obj and name CA" index = 102 rmsd = 1.893 "obj and name CA" index = 103 rmsd = 1.771 "obj and name CA" index = 104 rmsd = 1.537 "obj and name CA" index = 105 rmsd = 1.558 "obj and name CA" index = 106 rmsd = 1.712 "obj and name CA" index = 107 rmsd = 1.851 "obj and name CA" index = 108 rmsd = 2.127 "obj and name CA" index = 109 rmsd = 2.198 "obj and name CA" index = 110 rmsd = 2.600 "obj and name CA" index = 111 rmsd = 2.577 "obj and name CA" index = 112 rmsd = 3.062 "obj and name CA" index = 113 rmsd = 3.912 "obj and name CA" index = 114 rmsd = 4.979 "obj and name CA" index = 115 rmsd = 6.194 "obj and name CA" index = 116 rmsd = 7.286 "obj and name CA" index = 117 rmsd = 7.570 "obj and name CA" index = 118 rmsd = 6.690 "obj and name CA" index = 119 rmsd = 7.181 "obj and name CA" index = 120 rmsd = 8.307 "obj and name CA" index = 121 rmsd = 8.125 "obj and name CA" index = 122 rmsd = 7.795 "obj and name CA" index = 123 rmsd = 8.990 "obj and name CA" index = 124 rmsd = 9.701 "obj and name CA" index = 125 rmsd = 9.635 "obj and name CA" index = 126 rmsd = 9.428 "obj and name CA" index = 127 rmsd = 9.018 "obj and name CA" index = 128 rmsd = 7.632 "obj and name CA" index = 129 rmsd = 7.195 "obj and name CA" index = 130 rmsd = 6.620 "obj and name CA" index = 131 rmsd = 6.463 "obj and name CA" index = 132 rmsd = 5.467 "obj and name CA" index = 133 rmsd = 3.204 "obj and name CA" index = 134 rmsd = 3.221 "obj and name CA" index = 135 rmsd = 3.895 "obj and name CA" index = 136 rmsd = 3.712 "obj and name CA" index = 137 rmsd = 2.700 "obj and name CA" index = 138 rmsd = 3.121 "obj and name CA" index = 139 rmsd = 3.498 "obj and name CA" index = 140 rmsd = 2.840 "obj and name CA" index = 141 rmsd = 2.591 "obj and name CA" index = 142 rmsd = 3.223 "obj and name CA" index = 143 rmsd = 3.250 "obj and name CA" index = 144 rmsd = 2.717 "obj and name CA" index = 145 rmsd = 3.142 "obj and name CA" index = 146 rmsd = 3.650 "obj and name CA" index = 147 rmsd = 3.606 "obj and name CA" index = 148 rmsd = 4.080 "obj and name CA" index = 149 rmsd = 5.977 "obj and name CA" index = 150 rmsd = 7.805 "obj and name CA" index = 151 rmsd = 9.715 "obj and name CA" index = 152 rmsd = 11.932 "obj and name CA" index = 153 rmsd = 14.226 "obj and name CA" index = 154 rmsd = 16.358 "obj and name CA" index = 155 rmsd = 18.124 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 1369 atoms. PyMOL>color cyan,ss s Executive: Colored 908 atoms. PyMOL>color gray,ss ""+l Executive: Colored 2770 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: 2.02 sec. = 1784.1 frames/hour (10.77 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit