PyMOL>load ./selSi.pdb,obj HEADER STRUCTURAL GENOMICS 23-MAY-07 2JPU TITLE SOLUTION STRUCTURE OF NESG TARGET SSR10, ORF C02003 PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ORF C02003 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HYPOTHETICAL PROTEIN; 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 1662 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 477 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: 1.67 sec. = 2159.8 frames/hour (1.67 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 387 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 387 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: 6.21 sec. = 579.4 frames/hour (7.88 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, 2.1565160751342773, 1.6168248653411865, 2.448307991027832, 2.3111600875854492, 3.1384279727935791, 2.2777252197265625, 2.9559791088104248, 3.2828500270843506, 3.5271615982055664, 1.9609556198120117, 2.5482912063598633, 2.9161934852600098, 3.4754369258880615, 2.9578311443328857, 1.9183305501937866, 2.1065661907196045, 2.2743782997131348, 2.8922502994537354, 2.1442885398864746] -> atom index_map = [None, 2, 21, 32, 51, 62, 76, 87, 97, 112, 128, 149, 170, 185, 200, 210, 225, 240, 260, 279, 290, 312, 319, 331, 350, 366, 383, 393, 404, 419, 441, 462, 483, 505, 515, 525, 540, 555, 565, 584, 606, 625, 644, 660, 679, 694, 708, 722, 741, 763, 778, 797, 811, 825, 839, 855, 877, 891, 913, 920, 944, 968, 990, 1001, 1016, 1030, 1049, 1069, 1091, 1101, 1112, 1134, 1153, 1172, 1196, 1207, 1221, 1235, 1249, 1264, 1283, 1297, 1316, 1335, 1359, 1381, 1392, 1402, 1426, 1440, 1459, 1477, 1493, 1508, 1515, 1535, 1553, 1568, 1587, 1598, 1617, 1631, 1646, 1668, 1683, 1699, 1721, 1743, 1762, 1784, 1799, 1811, 1827, 1851, 1873, 1892, 1908, 1927, 1947, 1957, 1973, 1987, 1998, 2017, 2032, 2050, 2068, 2086, 2104, 2122] "obj and name CA" index = 1 rmsd = 5.318 "obj and name CA" index = 2 rmsd = 3.505 "obj and name CA" index = 3 rmsd = 1.689 "obj and name CA" index = 4 rmsd = 1.594 "obj and name CA" index = 5 rmsd = 0.896 "obj and name CA" index = 6 rmsd = 0.871 "obj and name CA" index = 7 rmsd = 0.658 "obj and name CA" index = 8 rmsd = 0.781 "obj and name CA" index = 9 rmsd = 0.813 "obj and name CA" index = 10 rmsd = 0.705 "obj and name CA" index = 11 rmsd = 0.705 "obj and name CA" index = 12 rmsd = 0.796 "obj and name CA" index = 13 rmsd = 0.787 "obj and name CA" index = 14 rmsd = 0.678 "obj and name CA" index = 15 rmsd = 0.782 "obj and name CA" index = 16 rmsd = 0.883 "obj and name CA" index = 17 rmsd = 0.807 "obj and name CA" index = 18 rmsd = 0.851 "obj and name CA" index = 19 rmsd = 1.213 "obj and name CA" index = 20 rmsd = 1.206 "obj and name CA" index = 21 rmsd = 1.129 "obj and name CA" index = 22 rmsd = 0.897 "obj and name CA" index = 23 rmsd = 0.784 "obj and name CA" index = 24 rmsd = 0.848 "obj and name CA" index = 25 rmsd = 0.811 "obj and name CA" index = 26 rmsd = 0.585 "obj and name CA" index = 27 rmsd = 0.663 "obj and name CA" index = 28 rmsd = 0.739 "obj and name CA" index = 29 rmsd = 0.720 "obj and name CA" index = 30 rmsd = 0.821 "obj and name CA" index = 31 rmsd = 0.672 "obj and name CA" index = 32 rmsd = 0.589 "obj and name CA" index = 33 rmsd = 0.524 "obj and name CA" index = 34 rmsd = 0.540 "obj and name CA" index = 35 rmsd = 0.509 "obj and name CA" index = 36 rmsd = 0.577 "obj and name CA" index = 37 rmsd = 0.611 "obj and name CA" index = 38 rmsd = 0.569 "obj and name CA" index = 39 rmsd = 0.700 "obj and name CA" index = 40 rmsd = 0.723 "obj and name CA" index = 41 rmsd = 0.722 "obj and name CA" index = 42 rmsd = 0.825 "obj and name CA" index = 43 rmsd = 1.042 "obj and name CA" index = 44 rmsd = 1.298 "obj and name CA" index = 45 rmsd = 1.244 "obj and name CA" index = 46 rmsd = 1.293 "obj and name CA" index = 47 rmsd = 0.995 "obj and name CA" index = 48 rmsd = 1.122 "obj and name CA" index = 49 rmsd = 1.098 "obj and name CA" index = 50 rmsd = 0.869 "obj and name CA" index = 51 rmsd = 1.024 "obj and name CA" index = 52 rmsd = 1.209 "obj and name CA" index = 53 rmsd = 1.108 "obj and name CA" index = 54 rmsd = 1.248 "obj and name CA" index = 55 rmsd = 1.605 "obj and name CA" index = 56 rmsd = 1.703 "obj and name CA" index = 57 rmsd = 1.731 "obj and name CA" index = 58 rmsd = 2.436 "obj and name CA" index = 59 rmsd = 1.751 "obj and name CA" index = 60 rmsd = 1.000 "obj and name CA" index = 61 rmsd = 1.583 "obj and name CA" index = 62 rmsd = 1.207 "obj and name CA" index = 63 rmsd = 1.282 "obj and name CA" index = 64 rmsd = 1.046 "obj and name CA" index = 65 rmsd = 0.773 "obj and name CA" index = 66 rmsd = 0.861 "obj and name CA" index = 67 rmsd = 0.954 "obj and name CA" index = 68 rmsd = 0.827 "obj and name CA" index = 69 rmsd = 0.769 "obj and name CA" index = 70 rmsd = 0.908 "obj and name CA" index = 71 rmsd = 1.015 "obj and name CA" index = 72 rmsd = 1.022 "obj and name CA" index = 73 rmsd = 1.142 "obj and name CA" index = 74 rmsd = 1.613 "obj and name CA" index = 75 rmsd = 1.549 "obj and name CA" index = 76 rmsd = 1.150 "obj and name CA" index = 77 rmsd = 1.019 "obj and name CA" index = 78 rmsd = 0.967 "obj and name CA" index = 79 rmsd = 0.839 "obj and name CA" index = 80 rmsd = 0.757 "obj and name CA" index = 81 rmsd = 0.860 "obj and name CA" index = 82 rmsd = 0.771 "obj and name CA" index = 83 rmsd = 0.582 "obj and name CA" index = 84 rmsd = 0.702 "obj and name CA" index = 85 rmsd = 0.757 "obj and name CA" index = 86 rmsd = 0.674 "obj and name CA" index = 87 rmsd = 0.749 "obj and name CA" index = 88 rmsd = 0.840 "obj and name CA" index = 89 rmsd = 0.947 "obj and name CA" index = 90 rmsd = 1.331 "obj and name CA" index = 91 rmsd = 1.522 "obj and name CA" index = 92 rmsd = 1.553 "obj and name CA" index = 93 rmsd = 1.947 "obj and name CA" index = 94 rmsd = 3.714 "obj and name CA" index = 95 rmsd = 3.735 "obj and name CA" index = 96 rmsd = 2.897 "obj and name CA" index = 97 rmsd = 2.853 "obj and name CA" index = 98 rmsd = 1.371 "obj and name CA" index = 99 rmsd = 1.318 "obj and name CA" index = 100 rmsd = 1.171 "obj and name CA" index = 101 rmsd = 1.059 "obj and name CA" index = 102 rmsd = 1.028 "obj and name CA" index = 103 rmsd = 0.935 "obj and name CA" index = 104 rmsd = 0.888 "obj and name CA" index = 105 rmsd = 1.072 "obj and name CA" index = 106 rmsd = 0.888 "obj and name CA" index = 107 rmsd = 0.696 "obj and name CA" index = 108 rmsd = 0.866 "obj and name CA" index = 109 rmsd = 0.964 "obj and name CA" index = 110 rmsd = 0.781 "obj and name CA" index = 111 rmsd = 0.630 "obj and name CA" index = 112 rmsd = 0.790 "obj and name CA" index = 113 rmsd = 0.834 "obj and name CA" index = 114 rmsd = 0.746 "obj and name CA" index = 115 rmsd = 0.736 "obj and name CA" index = 116 rmsd = 0.828 "obj and name CA" index = 117 rmsd = 0.952 "obj and name CA" index = 118 rmsd = 0.937 "obj and name CA" index = 119 rmsd = 0.899 "obj and name CA" index = 120 rmsd = 1.044 "obj and name CA" index = 121 rmsd = 1.368 "obj and name CA" index = 122 rmsd = 1.395 "obj and name CA" index = 123 rmsd = 1.441 "obj and name CA" index = 124 rmsd = 2.531 "obj and name CA" index = 125 rmsd = 4.159 "obj and name CA" index = 126 rmsd = 5.369 "obj and name CA" index = 127 rmsd = 6.155 "obj and name CA" index = 128 rmsd = 6.597 "obj and name CA" index = 129 rmsd = 8.487 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 3413 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 994 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: 2.13 sec. = 1690.2 frames/hour (10.01 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit