PyMOL>load ./selSi.pdb,obj 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 PyMOL>color cyan,ss s Executive: Colored 61 atoms. PyMOL>color gray,ss ""+l Executive: Colored 1629 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: 1.26 sec. = 2864.9 frames/hour (1.26 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 324 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 324 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: 4.43 sec. = 811.8 frames/hour (5.69 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, 0.79960191249847412, 0.81209659576416016, 0.79234081506729126, 0.74077624082565308, 0.74444019794464111, 0.823128342628479, 0.72062456607818604, 0.60658156871795654, 0.71989786624908447, 0.73954033851623535, 0.67194062471389771, 0.63548922538757324, 0.67973250150680542, 0.62093675136566162, 0.65085327625274658, 0.61171829700469971, 0.77051073312759399, 0.67581433057785034, 0.68605989217758179] -> atom index_map = [None, 2, 21, 36, 56, 70, 82, 101, 115, 131, 146, 165, 187, 194, 208, 220, 236, 252, 259, 275, 289, 311, 330, 340, 355, 376, 391, 407, 424, 440, 462, 476, 495, 502, 509, 528, 535, 551, 565, 576, 590, 612, 628, 652, 668, 689, 708, 722, 729, 743, 762, 783, 805, 819, 843, 857, 873, 884, 903, 910, 924, 946, 961, 976, 998, 1014, 1033, 1047, 1067, 1078, 1102, 1116, 1130, 1144, 1161, 1176, 1183, 1200, 1221, 1245, 1264, 1278, 1288, 1302, 1318, 1330, 1345, 1360, 1374, 1388, 1404, 1420, 1435, 1454, 1468, 1483, 1497, 1511, 1525, 1541, 1551, 1565, 1585, 1597, 1613, 1624, 1640, 1656, 1675] "obj and name CA" index = 1 rmsd = 1.440 "obj and name CA" index = 2 rmsd = 0.937 "obj and name CA" index = 3 rmsd = 0.482 "obj and name CA" index = 4 rmsd = 0.343 "obj and name CA" index = 5 rmsd = 0.361 "obj and name CA" index = 6 rmsd = 0.438 "obj and name CA" index = 7 rmsd = 0.527 "obj and name CA" index = 8 rmsd = 0.323 "obj and name CA" index = 9 rmsd = 0.345 "obj and name CA" index = 10 rmsd = 0.194 "obj and name CA" index = 11 rmsd = 0.218 "obj and name CA" index = 12 rmsd = 0.217 "obj and name CA" index = 13 rmsd = 0.322 "obj and name CA" index = 14 rmsd = 0.371 "obj and name CA" index = 15 rmsd = 0.247 "obj and name CA" index = 16 rmsd = 0.243 "obj and name CA" index = 17 rmsd = 0.299 "obj and name CA" index = 18 rmsd = 0.377 "obj and name CA" index = 19 rmsd = 0.501 "obj and name CA" index = 20 rmsd = 0.496 "obj and name CA" index = 21 rmsd = 0.493 "obj and name CA" index = 22 rmsd = 0.346 "obj and name CA" index = 23 rmsd = 0.311 "obj and name CA" index = 24 rmsd = 0.229 "obj and name CA" index = 25 rmsd = 0.302 "obj and name CA" index = 26 rmsd = 0.231 "obj and name CA" index = 27 rmsd = 0.220 "obj and name CA" index = 28 rmsd = 0.262 "obj and name CA" index = 29 rmsd = 0.442 "obj and name CA" index = 30 rmsd = 0.249 "obj and name CA" index = 31 rmsd = 0.340 "obj and name CA" index = 32 rmsd = 0.293 "obj and name CA" index = 33 rmsd = 0.388 "obj and name CA" index = 34 rmsd = 0.418 "obj and name CA" index = 35 rmsd = 0.330 "obj and name CA" index = 36 rmsd = 0.292 "obj and name CA" index = 37 rmsd = 0.462 "obj and name CA" index = 38 rmsd = 0.610 "obj and name CA" index = 39 rmsd = 0.384 "obj and name CA" index = 40 rmsd = 0.369 "obj and name CA" index = 41 rmsd = 0.325 "obj and name CA" index = 42 rmsd = 0.293 "obj and name CA" index = 43 rmsd = 0.225 "obj and name CA" index = 44 rmsd = 0.271 "obj and name CA" index = 45 rmsd = 0.274 "obj and name CA" index = 46 rmsd = 0.425 "obj and name CA" index = 47 rmsd = 0.382 "obj and name CA" index = 48 rmsd = 0.355 "obj and name CA" index = 49 rmsd = 0.331 "obj and name CA" index = 50 rmsd = 0.305 "obj and name CA" index = 51 rmsd = 0.334 "obj and name CA" index = 52 rmsd = 0.354 "obj and name CA" index = 53 rmsd = 0.379 "obj and name CA" index = 54 rmsd = 0.407 "obj and name CA" index = 55 rmsd = 0.410 "obj and name CA" index = 56 rmsd = 0.399 "obj and name CA" index = 57 rmsd = 0.291 "obj and name CA" index = 58 rmsd = 0.317 "obj and name CA" index = 59 rmsd = 0.346 "obj and name CA" index = 60 rmsd = 0.364 "obj and name CA" index = 61 rmsd = 0.370 "obj and name CA" index = 62 rmsd = 0.353 "obj and name CA" index = 63 rmsd = 0.332 "obj and name CA" index = 64 rmsd = 0.471 "obj and name CA" index = 65 rmsd = 0.387 "obj and name CA" index = 66 rmsd = 0.323 "obj and name CA" index = 67 rmsd = 0.376 "obj and name CA" index = 68 rmsd = 0.319 "obj and name CA" index = 69 rmsd = 0.435 "obj and name CA" index = 70 rmsd = 0.467 "obj and name CA" index = 71 rmsd = 0.413 "obj and name CA" index = 72 rmsd = 0.874 "obj and name CA" index = 73 rmsd = 0.386 "obj and name CA" index = 74 rmsd = 0.382 "obj and name CA" index = 75 rmsd = 0.363 "obj and name CA" index = 76 rmsd = 0.355 "obj and name CA" index = 77 rmsd = 0.369 "obj and name CA" index = 78 rmsd = 0.329 "obj and name CA" index = 79 rmsd = 0.223 "obj and name CA" index = 80 rmsd = 0.235 "obj and name CA" index = 81 rmsd = 0.281 "obj and name CA" index = 82 rmsd = 0.273 "obj and name CA" index = 83 rmsd = 0.403 "obj and name CA" index = 84 rmsd = 0.514 "obj and name CA" index = 85 rmsd = 0.658 "obj and name CA" index = 86 rmsd = 0.791 "obj and name CA" index = 87 rmsd = 0.741 "obj and name CA" index = 88 rmsd = 0.801 "obj and name CA" index = 89 rmsd = 0.552 "obj and name CA" index = 90 rmsd = 0.616 "obj and name CA" index = 91 rmsd = 0.737 "obj and name CA" index = 92 rmsd = 0.720 "obj and name CA" index = 93 rmsd = 0.809 "obj and name CA" index = 94 rmsd = 0.975 "obj and name CA" index = 95 rmsd = 0.985 "obj and name CA" index = 96 rmsd = 0.869 "obj and name CA" index = 97 rmsd = 0.524 "obj and name CA" index = 98 rmsd = 0.451 "obj and name CA" index = 99 rmsd = 0.320 "obj and name CA" index = 100 rmsd = 0.236 "obj and name CA" index = 101 rmsd = 0.239 "obj and name CA" index = 102 rmsd = 0.296 "obj and name CA" index = 103 rmsd = 0.271 "obj and name CA" index = 104 rmsd = 0.250 "obj and name CA" index = 105 rmsd = 0.271 "obj and name CA" index = 106 rmsd = 0.350 "obj and name CA" index = 107 rmsd = 0.515 "obj and name CA" index = 108 rmsd = 0.709 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h PyMOL>color cyan,ss s Executive: Colored 183 atoms. PyMOL>color gray,ss ""+l Executive: Colored 3304 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: 1.63 sec. = 2210.4 frames/hour (7.32 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit