PyMOL>load ./selSi.pdb,obj HEADER SIGNALING PROTEIN 09-APR-09 2KHN TITLE NMR SOLUTION STRUCTURE OF THE EH 1 DOMAIN FROM HUMAN TITLE 2 INTERSECTIN-1 PROTEIN. NORTHEAST STRUCTURAL GENOMICS TITLE 3 CONSORTIUM TARGET HR3646E. COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTERSECTIN-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-111; COMPND 5 SYNONYM: SH3 DOMAIN-CONTAINING PROTEIN 1A, SH3P17; COMPND 6 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 1008 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 895 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: 0.80 sec. = 4517.8 frames/hour (0.80 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 363 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 363 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: 3.21 sec. = 1123.0 frames/hour (4.00 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, 6.0091171264648438, 9.1067228317260742, 8.9841623306274414, 5.5088443756103516, 7.9848570823669434, 6.576988697052002, 9.8877706527709961, 4.211082935333252, 17.852611541748047, 6.2374296188354492, 8.8787469863891602, 20.203792572021484, 15.007684707641602, 15.293244361877441, 20.842227935791016, 13.652859687805176, 17.936805725097656, 14.692873001098633, 14.361031532287598] -> atom index_map = [None, 2, 21, 28, 46, 64, 82, 100, 118, 136, 147, 165, 182, 192, 209, 229, 243, 257, 271, 291, 298, 305, 316, 335, 347, 361, 385, 395, 414, 428, 444, 459, 474, 498, 508, 530, 548, 560, 577, 594, 614, 632, 643, 662, 684, 698, 717, 728, 735, 755, 774, 788, 795, 807, 824, 834, 858, 872, 892, 912, 932, 949, 960, 967, 986, 1000, 1017, 1031, 1047, 1066, 1076, 1093, 1112, 1136, 1146, 1165, 1175, 1187, 1204, 1218, 1232, 1244, 1251, 1275, 1292, 1304, 1321, 1337, 1352, 1372, 1383, 1402, 1412, 1429, 1451, 1470, 1489, 1511, 1530, 1552, 1571, 1588, 1595, 1616, 1633, 1652, 1666, 1677, 1687, 1706, 1720, 1734, 1750, 1767, 1789, 1806, 1823, 1837, 1853, 1863, 1882, 1893] "obj and name CA" index = 1 rmsd = 35.978 "obj and name CA" index = 2 rmsd = 34.810 "obj and name CA" index = 3 rmsd = 33.329 "obj and name CA" index = 4 rmsd = 31.824 "obj and name CA" index = 5 rmsd = 29.916 "obj and name CA" index = 6 rmsd = 27.981 "obj and name CA" index = 7 rmsd = 25.855 "obj and name CA" index = 8 rmsd = 23.816 "obj and name CA" index = 9 rmsd = 21.422 "obj and name CA" index = 10 rmsd = 19.225 "obj and name CA" index = 11 rmsd = 16.724 "obj and name CA" index = 12 rmsd = 14.576 "obj and name CA" index = 13 rmsd = 12.334 "obj and name CA" index = 14 rmsd = 10.448 "obj and name CA" index = 15 rmsd = 8.856 "obj and name CA" index = 16 rmsd = 7.748 "obj and name CA" index = 17 rmsd = 6.720 "obj and name CA" index = 18 rmsd = 6.526 "obj and name CA" index = 19 rmsd = 5.764 "obj and name CA" index = 20 rmsd = 5.856 "obj and name CA" index = 21 rmsd = 5.555 "obj and name CA" index = 22 rmsd = 4.920 "obj and name CA" index = 23 rmsd = 4.617 "obj and name CA" index = 24 rmsd = 3.684 "obj and name CA" index = 25 rmsd = 2.972 "obj and name CA" index = 26 rmsd = 3.887 "obj and name CA" index = 27 rmsd = 4.687 "obj and name CA" index = 28 rmsd = 5.829 "obj and name CA" index = 29 rmsd = 7.227 "obj and name CA" index = 30 rmsd = 6.910 "obj and name CA" index = 31 rmsd = 5.494 "obj and name CA" index = 32 rmsd = 6.319 "obj and name CA" index = 33 rmsd = 7.302 "obj and name CA" index = 34 rmsd = 6.194 "obj and name CA" index = 35 rmsd = 5.888 "obj and name CA" index = 36 rmsd = 7.257 "obj and name CA" index = 37 rmsd = 7.139 "obj and name CA" index = 38 rmsd = 5.870 "obj and name CA" index = 39 rmsd = 6.437 "obj and name CA" index = 40 rmsd = 7.528 "obj and name CA" index = 41 rmsd = 6.712 "obj and name CA" index = 42 rmsd = 6.167 "obj and name CA" index = 43 rmsd = 7.431 "obj and name CA" index = 44 rmsd = 7.993 "obj and name CA" index = 45 rmsd = 9.129 "obj and name CA" index = 46 rmsd = 10.212 "obj and name CA" index = 47 rmsd = 9.456 "obj and name CA" index = 48 rmsd = 8.360 "obj and name CA" index = 49 rmsd = 7.214 "obj and name CA" index = 50 rmsd = 6.766 "obj and name CA" index = 51 rmsd = 5.802 "obj and name CA" index = 52 rmsd = 5.861 "obj and name CA" index = 53 rmsd = 5.755 "obj and name CA" index = 54 rmsd = 4.810 "obj and name CA" index = 55 rmsd = 4.318 "obj and name CA" index = 56 rmsd = 4.576 "obj and name CA" index = 57 rmsd = 4.338 "obj and name CA" index = 58 rmsd = 3.245 "obj and name CA" index = 59 rmsd = 3.501 "obj and name CA" index = 60 rmsd = 3.902 "obj and name CA" index = 61 rmsd = 3.166 "obj and name CA" index = 62 rmsd = 3.225 "obj and name CA" index = 63 rmsd = 2.763 "obj and name CA" index = 64 rmsd = 3.470 "obj and name CA" index = 65 rmsd = 3.697 "obj and name CA" index = 66 rmsd = 3.932 "obj and name CA" index = 67 rmsd = 2.846 "obj and name CA" index = 68 rmsd = 2.720 "obj and name CA" index = 69 rmsd = 3.464 "obj and name CA" index = 70 rmsd = 2.961 "obj and name CA" index = 71 rmsd = 2.367 "obj and name CA" index = 72 rmsd = 3.469 "obj and name CA" index = 73 rmsd = 3.957 "obj and name CA" index = 74 rmsd = 3.362 "obj and name CA" index = 75 rmsd = 3.852 "obj and name CA" index = 76 rmsd = 4.955 "obj and name CA" index = 77 rmsd = 5.102 "obj and name CA" index = 78 rmsd = 6.293 "obj and name CA" index = 79 rmsd = 6.024 "obj and name CA" index = 80 rmsd = 6.868 "obj and name CA" index = 81 rmsd = 6.395 "obj and name CA" index = 82 rmsd = 6.573 "obj and name CA" index = 83 rmsd = 6.019 "obj and name CA" index = 84 rmsd = 6.986 "obj and name CA" index = 85 rmsd = 6.937 "obj and name CA" index = 86 rmsd = 6.584 "obj and name CA" index = 87 rmsd = 5.351 "obj and name CA" index = 88 rmsd = 4.961 "obj and name CA" index = 89 rmsd = 5.151 "obj and name CA" index = 90 rmsd = 4.027 "obj and name CA" index = 91 rmsd = 3.281 "obj and name CA" index = 92 rmsd = 3.559 "obj and name CA" index = 93 rmsd = 3.005 "obj and name CA" index = 94 rmsd = 1.979 "obj and name CA" index = 95 rmsd = 2.078 "obj and name CA" index = 96 rmsd = 2.676 "obj and name CA" index = 97 rmsd = 2.216 "obj and name CA" index = 98 rmsd = 1.915 "obj and name CA" index = 99 rmsd = 2.608 "obj and name CA" index = 100 rmsd = 3.321 "obj and name CA" index = 101 rmsd = 3.415 "obj and name CA" index = 102 rmsd = 2.807 "obj and name CA" index = 103 rmsd = 2.822 "obj and name CA" index = 104 rmsd = 2.588 "obj and name CA" index = 105 rmsd = 3.327 "obj and name CA" index = 106 rmsd = 3.747 "obj and name CA" index = 107 rmsd = 3.622 "obj and name CA" index = 108 rmsd = 2.985 "obj and name CA" index = 109 rmsd = 2.954 "obj and name CA" index = 110 rmsd = 3.897 "obj and name CA" index = 111 rmsd = 3.956 "obj and name CA" index = 112 rmsd = 3.807 "obj and name CA" index = 113 rmsd = 4.772 "obj and name CA" index = 114 rmsd = 5.589 "obj and name CA" index = 115 rmsd = 6.747 "obj and name CA" index = 116 rmsd = 8.021 "obj and name CA" index = 117 rmsd = 9.149 "obj and name CA" index = 118 rmsd = 10.239 "obj and name CA" index = 119 rmsd = 11.076 "obj and name CA" index = 120 rmsd = 11.947 "obj and name CA" index = 121 rmsd = 12.327 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 2072 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 1855 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: 1.68 sec. = 2140.9 frames/hour (5.68 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit