PyMOL>load ./selSi.pdb,obj HEADER ISOMERASE 16-JAN-08 2JZT TITLE SOLUTION NMR STRUCTURE OF Q8ZP25_SALTY FROM SALMONELLA TITLE 2 TYPHIMURIUM. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TITLE 3 TARGET STR70 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE THIOL-DISULFIDE ISOMERASE AND COMPND 3 THIOREDOXIN; COMPND 4 CHAIN: A; 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 837 atoms. PyMOL>color cyan,ss s Executive: Colored 330 atoms. PyMOL>color gray,ss ""+l Executive: Colored 1089 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: 1.61 sec. = 2233.8 frames/hour (1.61 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: 6.36 sec. = 566.1 frames/hour (7.97 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, 4.735476016998291, 9.6098413467407227, 4.643195629119873, 6.5751395225524902, 8.2278051376342773, 5.0865726470947266, 7.4975504875183105, 10.531834602355957, 5.3511056900024414, 4.923149585723877, 8.7883949279785156, 10.484036445617676, 8.478485107421875, 10.521121978759766, 9.6044387817382812, 8.5360307693481445, 5.5508570671081543, 11.090522766113281, 8.987187385559082] -> atom index_map = [None, 2, 21, 31, 45, 57, 71, 85, 105, 116, 126, 145, 169, 186, 210, 229, 248, 262, 286, 293, 317, 334, 348, 364, 379, 389, 400, 414, 430, 442, 454, 478, 497, 519, 543, 559, 566, 578, 585, 601, 620, 639, 658, 669, 680, 692, 706, 730, 754, 768, 782, 797, 813, 824, 836, 850, 864, 880, 897, 916, 926, 941, 960, 979, 1003, 1018, 1038, 1052, 1069, 1089, 1101, 1125, 1142, 1158, 1168, 1184, 1194, 1206, 1225, 1240, 1257, 1268, 1283, 1293, 1312, 1319, 1331, 1355, 1375, 1389, 1405, 1429, 1453, 1473, 1487, 1497, 1511, 1530, 1546, 1566, 1580, 1592, 1599, 1621, 1640, 1664, 1671, 1681, 1700, 1711, 1718, 1737, 1755, 1769, 1793, 1803, 1818, 1837, 1856, 1870, 1889, 1906, 1930, 1941, 1960, 1976, 1988, 2002, 2016, 2026, 2036, 2053, 2068, 2082, 2098, 2115, 2134, 2149, 2167, 2185, 2203, 2221, 2239] "obj and name CA" index = 1 rmsd = 13.640 "obj and name CA" index = 2 rmsd = 11.637 "obj and name CA" index = 3 rmsd = 9.870 "obj and name CA" index = 4 rmsd = 8.881 "obj and name CA" index = 5 rmsd = 6.482 "obj and name CA" index = 6 rmsd = 5.599 "obj and name CA" index = 7 rmsd = 4.266 "obj and name CA" index = 8 rmsd = 2.911 "obj and name CA" index = 9 rmsd = 3.056 "obj and name CA" index = 10 rmsd = 2.609 "obj and name CA" index = 11 rmsd = 2.424 "obj and name CA" index = 12 rmsd = 3.059 "obj and name CA" index = 13 rmsd = 3.207 "obj and name CA" index = 14 rmsd = 2.983 "obj and name CA" index = 15 rmsd = 3.463 "obj and name CA" index = 16 rmsd = 4.006 "obj and name CA" index = 17 rmsd = 3.956 "obj and name CA" index = 18 rmsd = 4.093 "obj and name CA" index = 19 rmsd = 3.347 "obj and name CA" index = 20 rmsd = 3.711 "obj and name CA" index = 21 rmsd = 3.393 "obj and name CA" index = 22 rmsd = 3.736 "obj and name CA" index = 23 rmsd = 4.180 "obj and name CA" index = 24 rmsd = 4.532 "obj and name CA" index = 25 rmsd = 5.430 "obj and name CA" index = 26 rmsd = 5.218 "obj and name CA" index = 27 rmsd = 4.309 "obj and name CA" index = 28 rmsd = 4.858 "obj and name CA" index = 29 rmsd = 5.539 "obj and name CA" index = 30 rmsd = 4.696 "obj and name CA" index = 31 rmsd = 4.095 "obj and name CA" index = 32 rmsd = 5.095 "obj and name CA" index = 33 rmsd = 5.347 "obj and name CA" index = 34 rmsd = 4.529 "obj and name CA" index = 35 rmsd = 4.188 "obj and name CA" index = 36 rmsd = 3.367 "obj and name CA" index = 37 rmsd = 2.798 "obj and name CA" index = 38 rmsd = 2.027 "obj and name CA" index = 39 rmsd = 2.033 "obj and name CA" index = 40 rmsd = 1.457 "obj and name CA" index = 41 rmsd = 1.706 "obj and name CA" index = 42 rmsd = 1.812 "obj and name CA" index = 43 rmsd = 2.257 "obj and name CA" index = 44 rmsd = 2.442 "obj and name CA" index = 45 rmsd = 3.625 "obj and name CA" index = 46 rmsd = 4.624 "obj and name CA" index = 47 rmsd = 5.245 "obj and name CA" index = 48 rmsd = 5.051 "obj and name CA" index = 49 rmsd = 5.445 "obj and name CA" index = 50 rmsd = 6.113 "obj and name CA" index = 51 rmsd = 5.594 "obj and name CA" index = 52 rmsd = 5.106 "obj and name CA" index = 53 rmsd = 3.855 "obj and name CA" index = 54 rmsd = 3.077 "obj and name CA" index = 55 rmsd = 2.053 "obj and name CA" index = 56 rmsd = 2.645 "obj and name CA" index = 57 rmsd = 3.034 "obj and name CA" index = 58 rmsd = 2.215 "obj and name CA" index = 59 rmsd = 3.003 "obj and name CA" index = 60 rmsd = 3.507 "obj and name CA" index = 61 rmsd = 2.759 "obj and name CA" index = 62 rmsd = 2.748 "obj and name CA" index = 63 rmsd = 3.423 "obj and name CA" index = 64 rmsd = 3.174 "obj and name CA" index = 65 rmsd = 2.937 "obj and name CA" index = 66 rmsd = 3.735 "obj and name CA" index = 67 rmsd = 3.809 "obj and name CA" index = 68 rmsd = 3.703 "obj and name CA" index = 69 rmsd = 3.983 "obj and name CA" index = 70 rmsd = 3.254 "obj and name CA" index = 71 rmsd = 3.409 "obj and name CA" index = 72 rmsd = 2.765 "obj and name CA" index = 73 rmsd = 2.774 "obj and name CA" index = 74 rmsd = 2.289 "obj and name CA" index = 75 rmsd = 2.609 "obj and name CA" index = 76 rmsd = 2.750 "obj and name CA" index = 77 rmsd = 2.662 "obj and name CA" index = 78 rmsd = 3.361 "obj and name CA" index = 79 rmsd = 3.458 "obj and name CA" index = 80 rmsd = 2.791 "obj and name CA" index = 81 rmsd = 3.483 "obj and name CA" index = 82 rmsd = 4.172 "obj and name CA" index = 83 rmsd = 3.699 "obj and name CA" index = 84 rmsd = 3.496 "obj and name CA" index = 85 rmsd = 4.522 "obj and name CA" index = 86 rmsd = 4.771 "obj and name CA" index = 87 rmsd = 4.153 "obj and name CA" index = 88 rmsd = 4.640 "obj and name CA" index = 89 rmsd = 3.650 "obj and name CA" index = 90 rmsd = 4.428 "obj and name CA" index = 91 rmsd = 3.793 "obj and name CA" index = 92 rmsd = 3.071 "obj and name CA" index = 93 rmsd = 2.403 "obj and name CA" index = 94 rmsd = 1.716 "obj and name CA" index = 95 rmsd = 1.248 "obj and name CA" index = 96 rmsd = 1.859 "obj and name CA" index = 97 rmsd = 1.851 "obj and name CA" index = 98 rmsd = 2.706 "obj and name CA" index = 99 rmsd = 3.121 "obj and name CA" index = 100 rmsd = 4.070 "obj and name CA" index = 101 rmsd = 4.183 "obj and name CA" index = 102 rmsd = 3.874 "obj and name CA" index = 103 rmsd = 3.226 "obj and name CA" index = 104 rmsd = 2.607 "obj and name CA" index = 105 rmsd = 2.484 "obj and name CA" index = 106 rmsd = 2.088 "obj and name CA" index = 107 rmsd = 1.665 "obj and name CA" index = 108 rmsd = 2.641 "obj and name CA" index = 109 rmsd = 3.710 "obj and name CA" index = 110 rmsd = 4.698 "obj and name CA" index = 111 rmsd = 4.628 "obj and name CA" index = 112 rmsd = 4.444 "obj and name CA" index = 113 rmsd = 3.998 "obj and name CA" index = 114 rmsd = 4.371 "obj and name CA" index = 115 rmsd = 3.772 "obj and name CA" index = 116 rmsd = 2.770 "obj and name CA" index = 117 rmsd = 2.701 "obj and name CA" index = 118 rmsd = 2.710 "obj and name CA" index = 119 rmsd = 2.346 "obj and name CA" index = 120 rmsd = 1.530 "obj and name CA" index = 121 rmsd = 1.689 "obj and name CA" index = 122 rmsd = 1.822 "obj and name CA" index = 123 rmsd = 1.753 "obj and name CA" index = 124 rmsd = 1.836 "obj and name CA" index = 125 rmsd = 2.172 "obj and name CA" index = 126 rmsd = 2.496 "obj and name CA" index = 127 rmsd = 3.268 "obj and name CA" index = 128 rmsd = 4.165 "obj and name CA" index = 129 rmsd = 5.292 "obj and name CA" index = 130 rmsd = 6.413 "obj and name CA" index = 131 rmsd = 6.959 "obj and name CA" index = 132 rmsd = 7.529 "obj and name CA" index = 133 rmsd = 8.852 "obj and name CA" index = 134 rmsd = 10.081 "obj and name CA" index = 135 rmsd = 11.418 "obj and name CA" index = 136 rmsd = 13.038 "obj and name CA" index = 137 rmsd = 14.491 "obj and name CA" index = 138 rmsd = 15.623 "obj and name CA" index = 139 rmsd = 17.092 "obj and name CA" index = 140 rmsd = 18.416 "obj and name CA" index = 141 rmsd = 19.287 "obj and name CA" index = 142 rmsd = 19.860 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 1717 atoms. PyMOL>color cyan,ss s Executive: Colored 676 atoms. PyMOL>color gray,ss ""+l Executive: Colored 2261 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: 1.80 sec. = 2000.9 frames/hour (9.77 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit