PyMOL>load ./selSi.pdb,obj HEADER ANTIVIRAL PROTEIN 29-JUN-09 2KKZ TITLE SOLUTION NMR STRUCTURE OF THE MONOMERIC W187R MUTANT OF TITLE 2 A/UDORN NS1 EFFECTOR DOMAIN. NORTHEAST STRUCTURAL GENOMICS TITLE 3 TARGET OR8C[W187R]. COMPND MOL_ID: 1; COMPND 2 MOLECULE: NON-STRUCTURAL PROTEIN NS1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES 85-215; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: 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 113 atoms. PyMOL>color cyan,ss s Executive: Colored 417 atoms. PyMOL>color gray,ss ""+l Executive: Colored 1607 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: 1.20 sec. = 2990.6 frames/hour (1.20 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 402 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 402 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: 5.08 sec. = 709.2 frames/hour (6.28 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, 10.119256019592285, 5.5249500274658203, 8.8206548690795898, 10.207952499389648, 9.6649703979492188, 2.1507678031921387, 9.3035392761230469, 8.0441884994506836, 12.972832679748535, 8.3158950805664062, 10.431637763977051, 3.5908102989196777, 11.167181968688965, 2.1786773204803467, 10.379415512084961, 9.1111602783203125, 6.1471328735351562, 10.752981185913086, 3.2357480525970459] -> atom index_map = [None, 2, 21, 35, 45, 56, 80, 101, 120, 134, 146, 163, 177, 196, 211, 226, 245, 256, 280, 292, 316, 336, 353, 372, 389, 403, 425, 442, 464, 480, 495, 502, 516, 535, 546, 565, 589, 608, 620, 637, 647, 666, 683, 695, 717, 731, 750, 767, 786, 808, 818, 832, 852, 863, 879, 898, 918, 930, 954, 973, 988, 1002, 1021, 1040, 1059, 1078, 1102, 1112, 1132, 1146, 1161, 1176, 1183, 1193, 1212, 1228, 1235, 1250, 1269, 1280, 1294, 1313, 1327, 1338, 1358, 1372, 1379, 1396, 1410, 1429, 1444, 1456, 1472, 1494, 1508, 1518, 1537, 1544, 1560, 1579, 1598, 1605, 1612, 1631, 1646, 1670, 1684, 1696, 1710, 1724, 1740, 1764, 1780, 1791, 1813, 1827, 1846, 1863, 1887, 1907, 1917, 1941, 1948, 1959, 1970, 1984, 1999, 2013, 2020, 2044, 2058, 2072, 2091, 2105, 2124] "obj and name CA" index = 1 rmsd = 5.472 "obj and name CA" index = 2 rmsd = 4.229 "obj and name CA" index = 3 rmsd = 3.998 "obj and name CA" index = 4 rmsd = 3.124 "obj and name CA" index = 5 rmsd = 2.940 "obj and name CA" index = 6 rmsd = 2.543 "obj and name CA" index = 7 rmsd = 2.217 "obj and name CA" index = 8 rmsd = 2.299 "obj and name CA" index = 9 rmsd = 2.194 "obj and name CA" index = 10 rmsd = 2.092 "obj and name CA" index = 11 rmsd = 2.669 "obj and name CA" index = 12 rmsd = 2.755 "obj and name CA" index = 13 rmsd = 2.753 "obj and name CA" index = 14 rmsd = 2.041 "obj and name CA" index = 15 rmsd = 1.634 "obj and name CA" index = 16 rmsd = 2.004 "obj and name CA" index = 17 rmsd = 1.859 "obj and name CA" index = 18 rmsd = 1.877 "obj and name CA" index = 19 rmsd = 1.525 "obj and name CA" index = 20 rmsd = 1.970 "obj and name CA" index = 21 rmsd = 2.443 "obj and name CA" index = 22 rmsd = 3.011 "obj and name CA" index = 23 rmsd = 3.513 "obj and name CA" index = 24 rmsd = 3.191 "obj and name CA" index = 25 rmsd = 3.594 "obj and name CA" index = 26 rmsd = 3.566 "obj and name CA" index = 27 rmsd = 3.715 "obj and name CA" index = 28 rmsd = 3.668 "obj and name CA" index = 29 rmsd = 3.688 "obj and name CA" index = 30 rmsd = 3.867 "obj and name CA" index = 31 rmsd = 3.309 "obj and name CA" index = 32 rmsd = 2.659 "obj and name CA" index = 33 rmsd = 2.590 "obj and name CA" index = 34 rmsd = 2.588 "obj and name CA" index = 35 rmsd = 2.466 "obj and name CA" index = 36 rmsd = 3.006 "obj and name CA" index = 37 rmsd = 3.154 "obj and name CA" index = 38 rmsd = 4.021 "obj and name CA" index = 39 rmsd = 4.028 "obj and name CA" index = 40 rmsd = 3.715 "obj and name CA" index = 41 rmsd = 4.442 "obj and name CA" index = 42 rmsd = 4.889 "obj and name CA" index = 43 rmsd = 4.185 "obj and name CA" index = 44 rmsd = 3.999 "obj and name CA" index = 45 rmsd = 3.211 "obj and name CA" index = 46 rmsd = 2.743 "obj and name CA" index = 47 rmsd = 2.187 "obj and name CA" index = 48 rmsd = 1.701 "obj and name CA" index = 49 rmsd = 1.084 "obj and name CA" index = 50 rmsd = 1.326 "obj and name CA" index = 51 rmsd = 1.524 "obj and name CA" index = 52 rmsd = 2.119 "obj and name CA" index = 53 rmsd = 2.268 "obj and name CA" index = 54 rmsd = 2.726 "obj and name CA" index = 55 rmsd = 3.018 "obj and name CA" index = 56 rmsd = 2.697 "obj and name CA" index = 57 rmsd = 2.341 "obj and name CA" index = 58 rmsd = 1.928 "obj and name CA" index = 59 rmsd = 2.213 "obj and name CA" index = 60 rmsd = 2.058 "obj and name CA" index = 61 rmsd = 1.498 "obj and name CA" index = 62 rmsd = 1.526 "obj and name CA" index = 63 rmsd = 0.985 "obj and name CA" index = 64 rmsd = 0.920 "obj and name CA" index = 65 rmsd = 1.204 "obj and name CA" index = 66 rmsd = 1.958 "obj and name CA" index = 67 rmsd = 2.205 "obj and name CA" index = 68 rmsd = 2.980 "obj and name CA" index = 69 rmsd = 3.597 "obj and name CA" index = 70 rmsd = 3.329 "obj and name CA" index = 71 rmsd = 2.700 "obj and name CA" index = 72 rmsd = 2.392 "obj and name CA" index = 73 rmsd = 1.765 "obj and name CA" index = 74 rmsd = 2.232 "obj and name CA" index = 75 rmsd = 2.014 "obj and name CA" index = 76 rmsd = 1.468 "obj and name CA" index = 77 rmsd = 1.593 "obj and name CA" index = 78 rmsd = 1.612 "obj and name CA" index = 79 rmsd = 2.227 "obj and name CA" index = 80 rmsd = 2.889 "obj and name CA" index = 81 rmsd = 3.362 "obj and name CA" index = 82 rmsd = 4.203 "obj and name CA" index = 83 rmsd = 3.729 "obj and name CA" index = 84 rmsd = 3.727 "obj and name CA" index = 85 rmsd = 3.655 "obj and name CA" index = 86 rmsd = 2.997 "obj and name CA" index = 87 rmsd = 2.863 "obj and name CA" index = 88 rmsd = 2.383 "obj and name CA" index = 89 rmsd = 3.104 "obj and name CA" index = 90 rmsd = 3.038 "obj and name CA" index = 91 rmsd = 2.292 "obj and name CA" index = 92 rmsd = 2.809 "obj and name CA" index = 93 rmsd = 3.387 "obj and name CA" index = 94 rmsd = 2.806 "obj and name CA" index = 95 rmsd = 2.568 "obj and name CA" index = 96 rmsd = 3.478 "obj and name CA" index = 97 rmsd = 3.631 "obj and name CA" index = 98 rmsd = 2.997 "obj and name CA" index = 99 rmsd = 3.494 "obj and name CA" index = 100 rmsd = 4.266 "obj and name CA" index = 101 rmsd = 4.051 "obj and name CA" index = 102 rmsd = 3.909 "obj and name CA" index = 103 rmsd = 4.646 "obj and name CA" index = 104 rmsd = 5.120 "obj and name CA" index = 105 rmsd = 4.779 "obj and name CA" index = 106 rmsd = 5.159 "obj and name CA" index = 107 rmsd = 4.536 "obj and name CA" index = 108 rmsd = 4.446 "obj and name CA" index = 109 rmsd = 3.819 "obj and name CA" index = 110 rmsd = 3.469 "obj and name CA" index = 111 rmsd = 2.820 "obj and name CA" index = 112 rmsd = 2.506 "obj and name CA" index = 113 rmsd = 2.972 "obj and name CA" index = 114 rmsd = 2.349 "obj and name CA" index = 115 rmsd = 2.046 "obj and name CA" index = 116 rmsd = 2.743 "obj and name CA" index = 117 rmsd = 2.722 "obj and name CA" index = 118 rmsd = 2.099 "obj and name CA" index = 119 rmsd = 2.211 "obj and name CA" index = 120 rmsd = 2.802 "obj and name CA" index = 121 rmsd = 3.188 "obj and name CA" index = 122 rmsd = 2.691 "obj and name CA" index = 123 rmsd = 3.507 "obj and name CA" index = 124 rmsd = 4.697 "obj and name CA" index = 125 rmsd = 6.629 "obj and name CA" index = 126 rmsd = 8.764 "obj and name CA" index = 127 rmsd = 11.256 "obj and name CA" index = 128 rmsd = 13.679 "obj and name CA" index = 129 rmsd = 16.205 "obj and name CA" index = 130 rmsd = 18.612 "obj and name CA" index = 131 rmsd = 20.845 "obj and name CA" index = 132 rmsd = 23.226 "obj and name CA" index = 133 rmsd = 26.201 "obj and name CA" index = 134 rmsd = 28.945 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 255 atoms. PyMOL>color cyan,ss s Executive: Colored 878 atoms. PyMOL>color gray,ss ""+l Executive: Colored 3275 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: 1.58 sec. = 2283.1 frames/hour (7.86 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit