PyMOL>load ./selSi.pdb,obj HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 23-JUN-06 2HFI TITLE SOLUTION NMR STRUCTURE OF PROTEIN YPPE FROM BACILLUS TITLE 2 SUBTILIS. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET TITLE 3 SR213 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN YPPE; 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 1603 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 428 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: 1.54 sec. = 2334.9 frames/hour (1.54 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 369 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 369 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: 5.57 sec. = 646.3 frames/hour (7.11 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, 2.095196008682251, 1.9351829290390015, 2.1693909168243408, 2.6234219074249268, 3.1401333808898926, 2.6385641098022461, 2.4425961971282959, 2.5051510334014893, 2.176316499710083, 3.0007233619689941, 2.3101742267608643, 1.9829663038253784, 2.382502555847168, 2.7567088603973389, 1.8725167512893677, 2.5072309970855713, 1.8672587871551514, 2.1937024593353271, 2.4934897422790527] -> atom index_map = [None, 2, 21, 40, 51, 68, 82, 101, 120, 135, 152, 166, 181, 198, 215, 234, 249, 265, 275, 290, 312, 319, 329, 341, 365, 386, 403, 418, 425, 447, 461, 472, 486, 504, 515, 536, 548, 568, 588, 603, 617, 636, 658, 672, 682, 698, 713, 728, 742, 754, 769, 788, 798, 808, 832, 856, 866, 881, 888, 898, 917, 932, 951, 970, 992, 1008, 1032, 1056, 1070, 1092, 1113, 1129, 1147, 1169, 1184, 1201, 1220, 1235, 1245, 1261, 1283, 1295, 1309, 1329, 1348, 1363, 1382, 1398, 1417, 1434, 1445, 1466, 1482, 1500, 1518, 1537, 1555, 1577, 1599, 1623, 1643, 1665, 1677, 1696, 1710, 1725, 1736, 1752, 1771, 1792, 1806, 1825, 1843, 1853, 1869, 1891, 1903, 1918, 1937, 1947, 1971, 1986, 1998, 2009] "obj and name CA" index = 1 rmsd = 8.250 "obj and name CA" index = 2 rmsd = 6.106 "obj and name CA" index = 3 rmsd = 4.378 "obj and name CA" index = 4 rmsd = 2.810 "obj and name CA" index = 5 rmsd = 1.428 "obj and name CA" index = 6 rmsd = 0.892 "obj and name CA" index = 7 rmsd = 0.864 "obj and name CA" index = 8 rmsd = 0.989 "obj and name CA" index = 9 rmsd = 0.811 "obj and name CA" index = 10 rmsd = 0.552 "obj and name CA" index = 11 rmsd = 0.738 "obj and name CA" index = 12 rmsd = 0.736 "obj and name CA" index = 13 rmsd = 0.539 "obj and name CA" index = 14 rmsd = 0.586 "obj and name CA" index = 15 rmsd = 0.763 "obj and name CA" index = 16 rmsd = 0.734 "obj and name CA" index = 17 rmsd = 0.641 "obj and name CA" index = 18 rmsd = 0.786 "obj and name CA" index = 19 rmsd = 0.940 "obj and name CA" index = 20 rmsd = 0.886 "obj and name CA" index = 21 rmsd = 0.841 "obj and name CA" index = 22 rmsd = 0.927 "obj and name CA" index = 23 rmsd = 1.061 "obj and name CA" index = 24 rmsd = 1.061 "obj and name CA" index = 25 rmsd = 1.200 "obj and name CA" index = 26 rmsd = 1.396 "obj and name CA" index = 27 rmsd = 1.493 "obj and name CA" index = 28 rmsd = 2.769 "obj and name CA" index = 29 rmsd = 3.738 "obj and name CA" index = 30 rmsd = 4.692 "obj and name CA" index = 31 rmsd = 4.701 "obj and name CA" index = 32 rmsd = 4.718 "obj and name CA" index = 33 rmsd = 4.104 "obj and name CA" index = 34 rmsd = 2.280 "obj and name CA" index = 35 rmsd = 2.020 "obj and name CA" index = 36 rmsd = 1.453 "obj and name CA" index = 37 rmsd = 1.252 "obj and name CA" index = 38 rmsd = 1.436 "obj and name CA" index = 39 rmsd = 1.542 "obj and name CA" index = 40 rmsd = 1.224 "obj and name CA" index = 41 rmsd = 0.993 "obj and name CA" index = 42 rmsd = 1.064 "obj and name CA" index = 43 rmsd = 0.831 "obj and name CA" index = 44 rmsd = 0.742 "obj and name CA" index = 45 rmsd = 0.786 "obj and name CA" index = 46 rmsd = 0.709 "obj and name CA" index = 47 rmsd = 0.643 "obj and name CA" index = 48 rmsd = 0.620 "obj and name CA" index = 49 rmsd = 0.707 "obj and name CA" index = 50 rmsd = 0.681 "obj and name CA" index = 51 rmsd = 0.588 "obj and name CA" index = 52 rmsd = 0.635 "obj and name CA" index = 53 rmsd = 0.752 "obj and name CA" index = 54 rmsd = 0.556 "obj and name CA" index = 55 rmsd = 0.496 "obj and name CA" index = 56 rmsd = 0.643 "obj and name CA" index = 57 rmsd = 0.621 "obj and name CA" index = 58 rmsd = 0.538 "obj and name CA" index = 59 rmsd = 0.677 "obj and name CA" index = 60 rmsd = 0.739 "obj and name CA" index = 61 rmsd = 0.719 "obj and name CA" index = 62 rmsd = 0.797 "obj and name CA" index = 63 rmsd = 1.050 "obj and name CA" index = 64 rmsd = 1.046 "obj and name CA" index = 65 rmsd = 1.168 "obj and name CA" index = 66 rmsd = 1.119 "obj and name CA" index = 67 rmsd = 1.372 "obj and name CA" index = 68 rmsd = 1.191 "obj and name CA" index = 69 rmsd = 0.740 "obj and name CA" index = 70 rmsd = 0.687 "obj and name CA" index = 71 rmsd = 0.780 "obj and name CA" index = 72 rmsd = 0.731 "obj and name CA" index = 73 rmsd = 0.789 "obj and name CA" index = 74 rmsd = 0.642 "obj and name CA" index = 75 rmsd = 0.584 "obj and name CA" index = 76 rmsd = 0.713 "obj and name CA" index = 77 rmsd = 0.644 "obj and name CA" index = 78 rmsd = 0.520 "obj and name CA" index = 79 rmsd = 0.635 "obj and name CA" index = 80 rmsd = 0.689 "obj and name CA" index = 81 rmsd = 0.598 "obj and name CA" index = 82 rmsd = 0.485 "obj and name CA" index = 83 rmsd = 0.563 "obj and name CA" index = 84 rmsd = 0.715 "obj and name CA" index = 85 rmsd = 0.690 "obj and name CA" index = 86 rmsd = 0.644 "obj and name CA" index = 87 rmsd = 0.788 "obj and name CA" index = 88 rmsd = 1.018 "obj and name CA" index = 89 rmsd = 1.000 "obj and name CA" index = 90 rmsd = 1.061 "obj and name CA" index = 91 rmsd = 1.288 "obj and name CA" index = 92 rmsd = 1.223 "obj and name CA" index = 93 rmsd = 1.332 "obj and name CA" index = 94 rmsd = 1.271 "obj and name CA" index = 95 rmsd = 1.752 "obj and name CA" index = 96 rmsd = 1.683 "obj and name CA" index = 97 rmsd = 1.457 "obj and name CA" index = 98 rmsd = 1.199 "obj and name CA" index = 99 rmsd = 0.969 "obj and name CA" index = 100 rmsd = 1.006 "obj and name CA" index = 101 rmsd = 0.900 "obj and name CA" index = 102 rmsd = 0.723 "obj and name CA" index = 103 rmsd = 0.626 "obj and name CA" index = 104 rmsd = 0.555 "obj and name CA" index = 105 rmsd = 0.572 "obj and name CA" index = 106 rmsd = 0.474 "obj and name CA" index = 107 rmsd = 0.483 "obj and name CA" index = 108 rmsd = 0.542 "obj and name CA" index = 109 rmsd = 0.478 "obj and name CA" index = 110 rmsd = 0.452 "obj and name CA" index = 111 rmsd = 0.537 "obj and name CA" index = 112 rmsd = 0.621 "obj and name CA" index = 113 rmsd = 0.610 "obj and name CA" index = 114 rmsd = 0.676 "obj and name CA" index = 115 rmsd = 0.843 "obj and name CA" index = 116 rmsd = 0.960 "obj and name CA" index = 117 rmsd = 0.986 "obj and name CA" index = 118 rmsd = 1.162 "obj and name CA" index = 119 rmsd = 1.268 "obj and name CA" index = 120 rmsd = 1.387 "obj and name CA" index = 121 rmsd = 1.829 "obj and name CA" index = 122 rmsd = 3.783 "obj and name CA" index = 123 rmsd = 5.426 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 3291 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 894 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: 1.90 sec. = 1892.4 frames/hour (9.01 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit