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 Executive: Colored 89 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 2050 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: 1.78 sec. = 2020.1 frames/hour (1.78 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: 5.89 sec. = 611.4 frames/hour (7.67 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, 3.0604169368743896, 2.4809634685516357, 2.4622447490692139, 1.460237979888916, 2.469505786895752, 3.1892104148864746, 2.7029671669006348, 2.729724645614624, 2.8687911033630371, 2.9117364883422852, 2.44919753074646, 3.3381004333496094, 2.3160715103149414, 2.9170567989349365, 2.5726909637451172, 2.8378543853759766, 2.3591024875640869, 2.0302224159240723, 2.3619091510772705] -> 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, 1476, 1492, 1507, 1514, 1534, 1551, 1566, 1585, 1596, 1615, 1629, 1644, 1666, 1681, 1697, 1719, 1741, 1760, 1782, 1797, 1809, 1825, 1849, 1871, 1890, 1906, 1925, 1945, 1955, 1971, 1985, 1996, 2015, 2030, 2047, 2064, 2081, 2098, 2115] "obj and name CA" index = 1 rmsd = 5.890 "obj and name CA" index = 2 rmsd = 4.171 "obj and name CA" index = 3 rmsd = 2.140 "obj and name CA" index = 4 rmsd = 1.636 "obj and name CA" index = 5 rmsd = 0.946 "obj and name CA" index = 6 rmsd = 0.769 "obj and name CA" index = 7 rmsd = 0.562 "obj and name CA" index = 8 rmsd = 0.625 "obj and name CA" index = 9 rmsd = 0.673 "obj and name CA" index = 10 rmsd = 0.544 "obj and name CA" index = 11 rmsd = 0.577 "obj and name CA" index = 12 rmsd = 0.770 "obj and name CA" index = 13 rmsd = 0.759 "obj and name CA" index = 14 rmsd = 0.654 "obj and name CA" index = 15 rmsd = 0.868 "obj and name CA" index = 16 rmsd = 1.044 "obj and name CA" index = 17 rmsd = 0.902 "obj and name CA" index = 18 rmsd = 0.878 "obj and name CA" index = 19 rmsd = 1.241 "obj and name CA" index = 20 rmsd = 1.241 "obj and name CA" index = 21 rmsd = 0.991 "obj and name CA" index = 22 rmsd = 0.932 "obj and name CA" index = 23 rmsd = 0.751 "obj and name CA" index = 24 rmsd = 0.883 "obj and name CA" index = 25 rmsd = 0.843 "obj and name CA" index = 26 rmsd = 0.640 "obj and name CA" index = 27 rmsd = 0.560 "obj and name CA" index = 28 rmsd = 0.606 "obj and name CA" index = 29 rmsd = 0.620 "obj and name CA" index = 30 rmsd = 0.722 "obj and name CA" index = 31 rmsd = 0.589 "obj and name CA" index = 32 rmsd = 0.511 "obj and name CA" index = 33 rmsd = 0.455 "obj and name CA" index = 34 rmsd = 0.442 "obj and name CA" index = 35 rmsd = 0.516 "obj and name CA" index = 36 rmsd = 0.456 "obj and name CA" index = 37 rmsd = 0.470 "obj and name CA" index = 38 rmsd = 0.504 "obj and name CA" index = 39 rmsd = 0.551 "obj and name CA" index = 40 rmsd = 0.643 "obj and name CA" index = 41 rmsd = 0.700 "obj and name CA" index = 42 rmsd = 0.776 "obj and name CA" index = 43 rmsd = 0.908 "obj and name CA" index = 44 rmsd = 1.083 "obj and name CA" index = 45 rmsd = 1.211 "obj and name CA" index = 46 rmsd = 1.425 "obj and name CA" index = 47 rmsd = 1.062 "obj and name CA" index = 48 rmsd = 1.094 "obj and name CA" index = 49 rmsd = 1.193 "obj and name CA" index = 50 rmsd = 0.867 "obj and name CA" index = 51 rmsd = 0.887 "obj and name CA" index = 52 rmsd = 1.179 "obj and name CA" index = 53 rmsd = 1.316 "obj and name CA" index = 54 rmsd = 1.173 "obj and name CA" index = 55 rmsd = 1.485 "obj and name CA" index = 56 rmsd = 1.707 "obj and name CA" index = 57 rmsd = 1.830 "obj and name CA" index = 58 rmsd = 2.337 "obj and name CA" index = 59 rmsd = 1.566 "obj and name CA" index = 60 rmsd = 1.181 "obj and name CA" index = 61 rmsd = 1.554 "obj and name CA" index = 62 rmsd = 1.366 "obj and name CA" index = 63 rmsd = 1.226 "obj and name CA" index = 64 rmsd = 0.928 "obj and name CA" index = 65 rmsd = 0.744 "obj and name CA" index = 66 rmsd = 0.913 "obj and name CA" index = 67 rmsd = 1.074 "obj and name CA" index = 68 rmsd = 0.873 "obj and name CA" index = 69 rmsd = 0.780 "obj and name CA" index = 70 rmsd = 1.007 "obj and name CA" index = 71 rmsd = 0.963 "obj and name CA" index = 72 rmsd = 1.082 "obj and name CA" index = 73 rmsd = 1.177 "obj and name CA" index = 74 rmsd = 1.591 "obj and name CA" index = 75 rmsd = 1.399 "obj and name CA" index = 76 rmsd = 1.072 "obj and name CA" index = 77 rmsd = 1.004 "obj and name CA" index = 78 rmsd = 1.030 "obj and name CA" index = 79 rmsd = 0.746 "obj and name CA" index = 80 rmsd = 0.747 "obj and name CA" index = 81 rmsd = 0.884 "obj and name CA" index = 82 rmsd = 0.664 "obj and name CA" index = 83 rmsd = 0.668 "obj and name CA" index = 84 rmsd = 0.838 "obj and name CA" index = 85 rmsd = 0.868 "obj and name CA" index = 86 rmsd = 0.860 "obj and name CA" index = 87 rmsd = 1.054 "obj and name CA" index = 88 rmsd = 1.179 "obj and name CA" index = 89 rmsd = 1.384 "obj and name CA" index = 90 rmsd = 1.843 "obj and name CA" index = 91 rmsd = 1.943 "obj and name CA" index = 92 rmsd = 1.756 "obj and name CA" index = 93 rmsd = 2.589 "obj and name CA" index = 94 rmsd = 3.766 "obj and name CA" index = 95 rmsd = 4.159 "obj and name CA" index = 96 rmsd = 3.573 "obj and name CA" index = 97 rmsd = 3.246 "obj and name CA" index = 98 rmsd = 2.160 "obj and name CA" index = 99 rmsd = 1.172 "obj and name CA" index = 100 rmsd = 0.977 "obj and name CA" index = 101 rmsd = 0.992 "obj and name CA" index = 102 rmsd = 1.150 "obj and name CA" index = 103 rmsd = 0.868 "obj and name CA" index = 104 rmsd = 0.597 "obj and name CA" index = 105 rmsd = 1.027 "obj and name CA" index = 106 rmsd = 1.065 "obj and name CA" index = 107 rmsd = 0.771 "obj and name CA" index = 108 rmsd = 0.786 "obj and name CA" index = 109 rmsd = 0.901 "obj and name CA" index = 110 rmsd = 0.748 "obj and name CA" index = 111 rmsd = 0.593 "obj and name CA" index = 112 rmsd = 0.614 "obj and name CA" index = 113 rmsd = 0.682 "obj and name CA" index = 114 rmsd = 0.699 "obj and name CA" index = 115 rmsd = 0.676 "obj and name CA" index = 116 rmsd = 0.723 "obj and name CA" index = 117 rmsd = 0.763 "obj and name CA" index = 118 rmsd = 0.830 "obj and name CA" index = 119 rmsd = 0.906 "obj and name CA" index = 120 rmsd = 0.983 "obj and name CA" index = 121 rmsd = 1.010 "obj and name CA" index = 122 rmsd = 1.109 "obj and name CA" index = 123 rmsd = 1.381 "obj and name CA" index = 124 rmsd = 2.910 "obj and name CA" index = 125 rmsd = 4.540 "obj and name CA" index = 126 rmsd = 5.443 "obj and name CA" index = 127 rmsd = 5.754 "obj and name CA" index = 128 rmsd = 6.919 "obj and name CA" index = 129 rmsd = 9.090 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 267 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 4132 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: 2.18 sec. = 1650.0 frames/hour (9.85 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit