PyMOL>load ./selSi.pdb,obj HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 24-FEB-09 2KFP TITLE SOLUTION NMR STRUCTURE OF PSPTO_3016 FROM PSEUDOMONAS TITLE 2 SYRINGAE. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET TITLE 3 PSR293. COMPND MOL_ID: 1; COMPND 2 MOLECULE: PSPTO_3016 PROTEIN; 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 675 atoms. PyMOL>color cyan,ss s Executive: Colored 411 atoms. PyMOL>color gray,ss ""+l Executive: Colored 985 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: 1.38 sec. = 2607.8 frames/hour (1.38 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 375 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 375 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: 4.59 sec. = 783.8 frames/hour (5.97 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, 2.6098406314849854, 2.5040247440338135, 1.7360329627990723, 1.9738372564315796, 1.6028110980987549, 3.3664019107818604, 2.4562797546386719, 1.3641307353973389, 1.7630255222320557, 1.4412528276443481, 1.6661609411239624, 3.088651180267334, 1.916010856628418, 2.3113267421722412, 2.1528584957122803, 2.6838748455047607, 2.4959619045257568, 2.0069544315338135, 1.6850287914276123] -> atom index_map = [None, 2, 21, 35, 59, 76, 93, 113, 132, 144, 165, 175, 192, 214, 236, 257, 269, 283, 305, 319, 331, 348, 362, 386, 401, 423, 443, 457, 469, 490, 500, 516, 536, 560, 577, 588, 600, 614, 626, 648, 672, 693, 703, 722, 741, 758, 770, 789, 803, 813, 828, 850, 869, 876, 895, 909, 916, 928, 950, 974, 990, 1002, 1018, 1037, 1049, 1068, 1090, 1106, 1123, 1137, 1152, 1171, 1187, 1194, 1205, 1224, 1248, 1270, 1292, 1306, 1313, 1332, 1353, 1367, 1377, 1398, 1415, 1432, 1446, 1468, 1483, 1500, 1524, 1543, 1557, 1573, 1592, 1611, 1625, 1632, 1646, 1665, 1672, 1682, 1704, 1719, 1738, 1755, 1766, 1785, 1804, 1819, 1831, 1842, 1862, 1879, 1898, 1912, 1936, 1955, 1970, 1987, 2004, 2021, 2038, 2055] "obj and name CA" index = 1 rmsd = 1.197 "obj and name CA" index = 2 rmsd = 1.016 "obj and name CA" index = 3 rmsd = 0.777 "obj and name CA" index = 4 rmsd = 0.963 "obj and name CA" index = 5 rmsd = 0.881 "obj and name CA" index = 6 rmsd = 0.656 "obj and name CA" index = 7 rmsd = 0.817 "obj and name CA" index = 8 rmsd = 0.982 "obj and name CA" index = 9 rmsd = 0.849 "obj and name CA" index = 10 rmsd = 0.862 "obj and name CA" index = 11 rmsd = 1.123 "obj and name CA" index = 12 rmsd = 1.275 "obj and name CA" index = 13 rmsd = 1.289 "obj and name CA" index = 14 rmsd = 1.489 "obj and name CA" index = 15 rmsd = 1.431 "obj and name CA" index = 16 rmsd = 1.286 "obj and name CA" index = 17 rmsd = 1.219 "obj and name CA" index = 18 rmsd = 0.961 "obj and name CA" index = 19 rmsd = 0.915 "obj and name CA" index = 20 rmsd = 1.031 "obj and name CA" index = 21 rmsd = 1.299 "obj and name CA" index = 22 rmsd = 1.182 "obj and name CA" index = 23 rmsd = 1.343 "obj and name CA" index = 24 rmsd = 1.388 "obj and name CA" index = 25 rmsd = 1.142 "obj and name CA" index = 26 rmsd = 1.175 "obj and name CA" index = 27 rmsd = 1.030 "obj and name CA" index = 28 rmsd = 0.752 "obj and name CA" index = 29 rmsd = 0.729 "obj and name CA" index = 30 rmsd = 0.812 "obj and name CA" index = 31 rmsd = 0.940 "obj and name CA" index = 32 rmsd = 1.152 "obj and name CA" index = 33 rmsd = 1.232 "obj and name CA" index = 34 rmsd = 1.617 "obj and name CA" index = 35 rmsd = 1.638 "obj and name CA" index = 36 rmsd = 1.668 "obj and name CA" index = 37 rmsd = 1.979 "obj and name CA" index = 38 rmsd = 2.077 "obj and name CA" index = 39 rmsd = 1.567 "obj and name CA" index = 40 rmsd = 0.955 "obj and name CA" index = 41 rmsd = 0.725 "obj and name CA" index = 42 rmsd = 0.719 "obj and name CA" index = 43 rmsd = 0.439 "obj and name CA" index = 44 rmsd = 0.444 "obj and name CA" index = 45 rmsd = 0.572 "obj and name CA" index = 46 rmsd = 0.678 "obj and name CA" index = 47 rmsd = 0.962 "obj and name CA" index = 48 rmsd = 0.894 "obj and name CA" index = 49 rmsd = 1.121 "obj and name CA" index = 50 rmsd = 1.130 "obj and name CA" index = 51 rmsd = 1.063 "obj and name CA" index = 52 rmsd = 1.401 "obj and name CA" index = 53 rmsd = 1.230 "obj and name CA" index = 54 rmsd = 1.876 "obj and name CA" index = 55 rmsd = 1.498 "obj and name CA" index = 56 rmsd = 1.391 "obj and name CA" index = 57 rmsd = 1.257 "obj and name CA" index = 58 rmsd = 1.012 "obj and name CA" index = 59 rmsd = 0.660 "obj and name CA" index = 60 rmsd = 0.469 "obj and name CA" index = 61 rmsd = 0.289 "obj and name CA" index = 62 rmsd = 0.313 "obj and name CA" index = 63 rmsd = 0.483 "obj and name CA" index = 64 rmsd = 0.840 "obj and name CA" index = 65 rmsd = 0.837 "obj and name CA" index = 66 rmsd = 0.850 "obj and name CA" index = 67 rmsd = 0.993 "obj and name CA" index = 68 rmsd = 1.052 "obj and name CA" index = 69 rmsd = 1.166 "obj and name CA" index = 70 rmsd = 1.030 "obj and name CA" index = 71 rmsd = 0.901 "obj and name CA" index = 72 rmsd = 0.995 "obj and name CA" index = 73 rmsd = 1.044 "obj and name CA" index = 74 rmsd = 0.842 "obj and name CA" index = 75 rmsd = 0.700 "obj and name CA" index = 76 rmsd = 1.048 "obj and name CA" index = 77 rmsd = 0.827 "obj and name CA" index = 78 rmsd = 0.772 "obj and name CA" index = 79 rmsd = 0.715 "obj and name CA" index = 80 rmsd = 0.542 "obj and name CA" index = 81 rmsd = 0.625 "obj and name CA" index = 82 rmsd = 0.696 "obj and name CA" index = 83 rmsd = 0.618 "obj and name CA" index = 84 rmsd = 1.079 "obj and name CA" index = 85 rmsd = 1.907 "obj and name CA" index = 86 rmsd = 1.948 "obj and name CA" index = 87 rmsd = 1.383 "obj and name CA" index = 88 rmsd = 1.024 "obj and name CA" index = 89 rmsd = 1.083 "obj and name CA" index = 90 rmsd = 0.995 "obj and name CA" index = 91 rmsd = 0.678 "obj and name CA" index = 92 rmsd = 0.564 "obj and name CA" index = 93 rmsd = 0.368 "obj and name CA" index = 94 rmsd = 0.339 "obj and name CA" index = 95 rmsd = 0.360 "obj and name CA" index = 96 rmsd = 0.433 "obj and name CA" index = 97 rmsd = 0.652 "obj and name CA" index = 98 rmsd = 0.715 "obj and name CA" index = 99 rmsd = 0.720 "obj and name CA" index = 100 rmsd = 0.975 "obj and name CA" index = 101 rmsd = 0.801 "obj and name CA" index = 102 rmsd = 0.818 "obj and name CA" index = 103 rmsd = 0.871 "obj and name CA" index = 104 rmsd = 0.768 "obj and name CA" index = 105 rmsd = 0.674 "obj and name CA" index = 106 rmsd = 0.904 "obj and name CA" index = 107 rmsd = 0.953 "obj and name CA" index = 108 rmsd = 0.845 "obj and name CA" index = 109 rmsd = 0.914 "obj and name CA" index = 110 rmsd = 1.115 "obj and name CA" index = 111 rmsd = 1.125 "obj and name CA" index = 112 rmsd = 1.052 "obj and name CA" index = 113 rmsd = 1.187 "obj and name CA" index = 114 rmsd = 1.329 "obj and name CA" index = 115 rmsd = 1.507 "obj and name CA" index = 116 rmsd = 1.453 "obj and name CA" index = 117 rmsd = 1.442 "obj and name CA" index = 118 rmsd = 1.809 "obj and name CA" index = 119 rmsd = 2.734 "obj and name CA" index = 120 rmsd = 3.065 "obj and name CA" index = 121 rmsd = 4.032 "obj and name CA" index = 122 rmsd = 5.065 "obj and name CA" index = 123 rmsd = 6.213 "obj and name CA" index = 124 rmsd = 7.825 "obj and name CA" index = 125 rmsd = 9.203 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 1386 atoms. PyMOL>color cyan,ss s Executive: Colored 845 atoms. PyMOL>color gray,ss ""+l Executive: Colored 2036 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: 1.54 sec. = 2340.5 frames/hour (7.51 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit