PyMOL>load ./selSi.pdb,obj HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 09-OCT-04 1XPW TITLE SOLUTION NMR STRUCTURE OF HUMAN PROTEIN HSPCO34. NORTHEAST TITLE 2 STRUCTURAL GENOMICS TARGET HR1958 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LOC51668 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HSPC034; 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 133 atoms. PyMOL>color cyan,ss s Executive: Colored 1140 atoms. PyMOL>color gray,ss ""+l Executive: Colored 976 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. = 2242.7 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 429 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 429 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: 8.25 sec. = 436.4 frames/hour (9.86 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, 1.4195681810379028, 0.9713892936706543, 1.1223839521408081, 1.5539118051528931, 1.0146093368530273, 1.1802670955657959, 1.2139972448348999, 1.3590738773345947, 1.2617090940475464, 1.3052822351455688, 1.2356065511703491, 0.96903228759765625, 1.1137268543243408, 1.0680762529373169, 1.2460185289382935, 1.2471921443939209, 1.2072341442108154, 1.3288410902023315, 1.2789069414138794] -> atom index_map = [None, 2, 19, 43, 65, 84, 96, 115, 126, 145, 156, 167, 182, 189, 200, 215, 231, 250, 269, 279, 293, 304, 315, 327, 342, 364, 381, 395, 409, 424, 438, 457, 476, 488, 495, 509, 523, 538, 552, 572, 596, 610, 624, 638, 645, 662, 682, 696, 713, 728, 748, 767, 786, 797, 817, 834, 856, 873, 889, 913, 932, 947, 971, 990, 1006, 1025, 1042, 1053, 1074, 1094, 1110, 1127, 1141, 1160, 1182, 1201, 1216, 1238, 1249, 1263, 1274, 1296, 1311, 1325, 1341, 1353, 1373, 1388, 1405, 1429, 1448, 1463, 1485, 1497, 1516, 1532, 1549, 1563, 1578, 1585, 1602, 1621, 1638, 1652, 1667, 1682, 1701, 1717, 1727, 1744, 1751, 1762, 1772, 1786, 1807, 1826, 1850, 1870, 1889, 1908, 1924, 1935, 1945, 1965, 1977, 1994, 2014, 2024, 2035, 2051, 2068, 2079, 2095, 2106, 2116, 2131, 2138, 2152, 2168, 2184, 2195, 2209, 2228, 2239] "obj and name CA" index = 1 rmsd = 2.450 "obj and name CA" index = 2 rmsd = 1.124 "obj and name CA" index = 3 rmsd = 0.819 "obj and name CA" index = 4 rmsd = 0.729 "obj and name CA" index = 5 rmsd = 0.608 "obj and name CA" index = 6 rmsd = 0.386 "obj and name CA" index = 7 rmsd = 0.576 "obj and name CA" index = 8 rmsd = 0.568 "obj and name CA" index = 9 rmsd = 0.659 "obj and name CA" index = 10 rmsd = 0.843 "obj and name CA" index = 11 rmsd = 0.582 "obj and name CA" index = 12 rmsd = 0.644 "obj and name CA" index = 13 rmsd = 0.381 "obj and name CA" index = 14 rmsd = 0.508 "obj and name CA" index = 15 rmsd = 0.439 "obj and name CA" index = 16 rmsd = 0.477 "obj and name CA" index = 17 rmsd = 0.590 "obj and name CA" index = 18 rmsd = 0.506 "obj and name CA" index = 19 rmsd = 0.709 "obj and name CA" index = 20 rmsd = 0.754 "obj and name CA" index = 21 rmsd = 0.958 "obj and name CA" index = 22 rmsd = 0.976 "obj and name CA" index = 23 rmsd = 1.284 "obj and name CA" index = 24 rmsd = 1.492 "obj and name CA" index = 25 rmsd = 1.221 "obj and name CA" index = 26 rmsd = 0.994 "obj and name CA" index = 27 rmsd = 0.804 "obj and name CA" index = 28 rmsd = 0.977 "obj and name CA" index = 29 rmsd = 1.146 "obj and name CA" index = 30 rmsd = 0.898 "obj and name CA" index = 31 rmsd = 1.111 "obj and name CA" index = 32 rmsd = 1.106 "obj and name CA" index = 33 rmsd = 1.765 "obj and name CA" index = 34 rmsd = 1.301 "obj and name CA" index = 35 rmsd = 1.544 "obj and name CA" index = 36 rmsd = 1.720 "obj and name CA" index = 37 rmsd = 1.488 "obj and name CA" index = 38 rmsd = 0.963 "obj and name CA" index = 39 rmsd = 0.577 "obj and name CA" index = 40 rmsd = 0.599 "obj and name CA" index = 41 rmsd = 0.702 "obj and name CA" index = 42 rmsd = 0.817 "obj and name CA" index = 43 rmsd = 0.791 "obj and name CA" index = 44 rmsd = 0.749 "obj and name CA" index = 45 rmsd = 0.617 "obj and name CA" index = 46 rmsd = 0.549 "obj and name CA" index = 47 rmsd = 0.637 "obj and name CA" index = 48 rmsd = 0.471 "obj and name CA" index = 49 rmsd = 0.356 "obj and name CA" index = 50 rmsd = 0.321 "obj and name CA" index = 51 rmsd = 0.350 "obj and name CA" index = 52 rmsd = 0.469 "obj and name CA" index = 53 rmsd = 0.448 "obj and name CA" index = 54 rmsd = 0.584 "obj and name CA" index = 55 rmsd = 0.506 "obj and name CA" index = 56 rmsd = 0.597 "obj and name CA" index = 57 rmsd = 0.455 "obj and name CA" index = 58 rmsd = 0.488 "obj and name CA" index = 59 rmsd = 0.392 "obj and name CA" index = 60 rmsd = 0.483 "obj and name CA" index = 61 rmsd = 0.451 "obj and name CA" index = 62 rmsd = 0.433 "obj and name CA" index = 63 rmsd = 0.380 "obj and name CA" index = 64 rmsd = 0.445 "obj and name CA" index = 65 rmsd = 0.570 "obj and name CA" index = 66 rmsd = 0.525 "obj and name CA" index = 67 rmsd = 0.529 "obj and name CA" index = 68 rmsd = 0.684 "obj and name CA" index = 69 rmsd = 0.413 "obj and name CA" index = 70 rmsd = 0.477 "obj and name CA" index = 71 rmsd = 0.373 "obj and name CA" index = 72 rmsd = 0.334 "obj and name CA" index = 73 rmsd = 0.401 "obj and name CA" index = 74 rmsd = 0.383 "obj and name CA" index = 75 rmsd = 0.399 "obj and name CA" index = 76 rmsd = 0.421 "obj and name CA" index = 77 rmsd = 0.423 "obj and name CA" index = 78 rmsd = 0.471 "obj and name CA" index = 79 rmsd = 0.700 "obj and name CA" index = 80 rmsd = 0.952 "obj and name CA" index = 81 rmsd = 0.710 "obj and name CA" index = 82 rmsd = 0.726 "obj and name CA" index = 83 rmsd = 0.755 "obj and name CA" index = 84 rmsd = 0.818 "obj and name CA" index = 85 rmsd = 0.714 "obj and name CA" index = 86 rmsd = 0.671 "obj and name CA" index = 87 rmsd = 0.685 "obj and name CA" index = 88 rmsd = 0.468 "obj and name CA" index = 89 rmsd = 0.457 "obj and name CA" index = 90 rmsd = 0.536 "obj and name CA" index = 91 rmsd = 0.740 "obj and name CA" index = 92 rmsd = 0.623 "obj and name CA" index = 93 rmsd = 0.893 "obj and name CA" index = 94 rmsd = 1.068 "obj and name CA" index = 95 rmsd = 1.479 "obj and name CA" index = 96 rmsd = 1.375 "obj and name CA" index = 97 rmsd = 1.579 "obj and name CA" index = 98 rmsd = 1.786 "obj and name CA" index = 99 rmsd = 1.408 "obj and name CA" index = 100 rmsd = 1.245 "obj and name CA" index = 101 rmsd = 1.390 "obj and name CA" index = 102 rmsd = 0.928 "obj and name CA" index = 103 rmsd = 0.736 "obj and name CA" index = 104 rmsd = 0.603 "obj and name CA" index = 105 rmsd = 0.517 "obj and name CA" index = 106 rmsd = 0.516 "obj and name CA" index = 107 rmsd = 0.504 "obj and name CA" index = 108 rmsd = 0.550 "obj and name CA" index = 109 rmsd = 0.529 "obj and name CA" index = 110 rmsd = 0.428 "obj and name CA" index = 111 rmsd = 0.317 "obj and name CA" index = 112 rmsd = 0.334 "obj and name CA" index = 113 rmsd = 0.303 "obj and name CA" index = 114 rmsd = 0.359 "obj and name CA" index = 115 rmsd = 0.383 "obj and name CA" index = 116 rmsd = 0.318 "obj and name CA" index = 117 rmsd = 0.358 "obj and name CA" index = 118 rmsd = 0.372 "obj and name CA" index = 119 rmsd = 0.400 "obj and name CA" index = 120 rmsd = 0.430 "obj and name CA" index = 121 rmsd = 0.398 "obj and name CA" index = 122 rmsd = 0.602 "obj and name CA" index = 123 rmsd = 0.694 "obj and name CA" index = 124 rmsd = 0.836 "obj and name CA" index = 125 rmsd = 0.802 "obj and name CA" index = 126 rmsd = 0.701 "obj and name CA" index = 127 rmsd = 0.568 "obj and name CA" index = 128 rmsd = 0.467 "obj and name CA" index = 129 rmsd = 0.899 "obj and name CA" index = 130 rmsd = 0.953 "obj and name CA" index = 131 rmsd = 0.772 "obj and name CA" index = 132 rmsd = 0.516 "obj and name CA" index = 133 rmsd = 0.413 "obj and name CA" index = 134 rmsd = 0.394 "obj and name CA" index = 135 rmsd = 0.482 "obj and name CA" index = 136 rmsd = 0.627 "obj and name CA" index = 137 rmsd = 0.524 "obj and name CA" index = 138 rmsd = 0.632 "obj and name CA" index = 139 rmsd = 0.758 "obj and name CA" index = 140 rmsd = 1.245 "obj and name CA" index = 141 rmsd = 2.028 "obj and name CA" index = 142 rmsd = 4.016 "obj and name CA" index = 143 rmsd = 5.097 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 270 atoms. PyMOL>color cyan,ss s Executive: Colored 2332 atoms. PyMOL>color gray,ss ""+l Executive: Colored 2039 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: 2.09 sec. = 1720.0 frames/hour (11.95 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit