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 87 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 1939 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: 1.69 sec. = 2134.8 frames/hour (1.69 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 369 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 369 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: 5.52 sec. = 652.8 frames/hour (7.20 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, 1.832154393196106, 2.0526962280273438, 2.4648110866546631, 1.7815344333648682, 2.4427788257598877, 2.4493358135223389, 2.5643141269683838, 1.9118896722793579, 3.339080810546875, 2.4212861061096191, 2.1479220390319824, 1.660724401473999, 2.0557866096496582, 1.9682586193084717, 2.8167855739593506, 1.8077114820480347, 2.6191885471343994, 2.7556228637695312, 2.6902365684509277] -> atom index_map = [None, 2, 21, 40, 51, 68, 82, 101, 120, 135, 152, 166, 181, 198, 215, 234, 249, 265, 275, 290, 312, 319, 329, 341, 365, 386, 403, 418, 425, 447, 461, 472, 486, 503, 514, 535, 547, 567, 587, 602, 616, 635, 657, 671, 681, 697, 712, 727, 741, 753, 768, 787, 797, 807, 831, 855, 865, 880, 887, 897, 916, 931, 950, 969, 991, 1007, 1031, 1055, 1069, 1091, 1112, 1128, 1145, 1167, 1182, 1199, 1218, 1233, 1243, 1259, 1281, 1293, 1307, 1327, 1346, 1361, 1380, 1396, 1415, 1432, 1443, 1464, 1480, 1497, 1514, 1533, 1550, 1572, 1594, 1618, 1638, 1660, 1672, 1691, 1705, 1720, 1731, 1747, 1766, 1787, 1801, 1820, 1837, 1847, 1863, 1885, 1897, 1912, 1931, 1941, 1965, 1980, 1992, 2003] "obj and name CA" index = 1 rmsd = 7.707 "obj and name CA" index = 2 rmsd = 5.888 "obj and name CA" index = 3 rmsd = 4.195 "obj and name CA" index = 4 rmsd = 2.951 "obj and name CA" index = 5 rmsd = 2.370 "obj and name CA" index = 6 rmsd = 1.208 "obj and name CA" index = 7 rmsd = 0.924 "obj and name CA" index = 8 rmsd = 0.895 "obj and name CA" index = 9 rmsd = 0.848 "obj and name CA" index = 10 rmsd = 0.563 "obj and name CA" index = 11 rmsd = 0.567 "obj and name CA" index = 12 rmsd = 0.621 "obj and name CA" index = 13 rmsd = 0.531 "obj and name CA" index = 14 rmsd = 0.442 "obj and name CA" index = 15 rmsd = 0.544 "obj and name CA" index = 16 rmsd = 0.562 "obj and name CA" index = 17 rmsd = 0.490 "obj and name CA" index = 18 rmsd = 0.521 "obj and name CA" index = 19 rmsd = 0.652 "obj and name CA" index = 20 rmsd = 0.711 "obj and name CA" index = 21 rmsd = 0.688 "obj and name CA" index = 22 rmsd = 0.823 "obj and name CA" index = 23 rmsd = 0.968 "obj and name CA" index = 24 rmsd = 1.024 "obj and name CA" index = 25 rmsd = 1.155 "obj and name CA" index = 26 rmsd = 1.357 "obj and name CA" index = 27 rmsd = 1.436 "obj and name CA" index = 28 rmsd = 2.724 "obj and name CA" index = 29 rmsd = 3.534 "obj and name CA" index = 30 rmsd = 4.543 "obj and name CA" index = 31 rmsd = 4.662 "obj and name CA" index = 32 rmsd = 4.904 "obj and name CA" index = 33 rmsd = 4.212 "obj and name CA" index = 34 rmsd = 2.610 "obj and name CA" index = 35 rmsd = 2.562 "obj and name CA" index = 36 rmsd = 1.939 "obj and name CA" index = 37 rmsd = 1.787 "obj and name CA" index = 38 rmsd = 1.842 "obj and name CA" index = 39 rmsd = 1.648 "obj and name CA" index = 40 rmsd = 1.337 "obj and name CA" index = 41 rmsd = 0.784 "obj and name CA" index = 42 rmsd = 0.808 "obj and name CA" index = 43 rmsd = 0.724 "obj and name CA" index = 44 rmsd = 0.581 "obj and name CA" index = 45 rmsd = 0.553 "obj and name CA" index = 46 rmsd = 0.652 "obj and name CA" index = 47 rmsd = 0.560 "obj and name CA" index = 48 rmsd = 0.548 "obj and name CA" index = 49 rmsd = 0.685 "obj and name CA" index = 50 rmsd = 0.667 "obj and name CA" index = 51 rmsd = 0.595 "obj and name CA" index = 52 rmsd = 0.701 "obj and name CA" index = 53 rmsd = 0.744 "obj and name CA" index = 54 rmsd = 0.575 "obj and name CA" index = 55 rmsd = 0.618 "obj and name CA" index = 56 rmsd = 0.756 "obj and name CA" index = 57 rmsd = 0.648 "obj and name CA" index = 58 rmsd = 0.548 "obj and name CA" index = 59 rmsd = 0.681 "obj and name CA" index = 60 rmsd = 0.747 "obj and name CA" index = 61 rmsd = 0.685 "obj and name CA" index = 62 rmsd = 0.737 "obj and name CA" index = 63 rmsd = 0.971 "obj and name CA" index = 64 rmsd = 1.085 "obj and name CA" index = 65 rmsd = 1.154 "obj and name CA" index = 66 rmsd = 1.080 "obj and name CA" index = 67 rmsd = 1.176 "obj and name CA" index = 68 rmsd = 1.047 "obj and name CA" index = 69 rmsd = 1.039 "obj and name CA" index = 70 rmsd = 0.786 "obj and name CA" index = 71 rmsd = 0.875 "obj and name CA" index = 72 rmsd = 0.870 "obj and name CA" index = 73 rmsd = 0.853 "obj and name CA" index = 74 rmsd = 0.676 "obj and name CA" index = 75 rmsd = 0.585 "obj and name CA" index = 76 rmsd = 0.668 "obj and name CA" index = 77 rmsd = 0.553 "obj and name CA" index = 78 rmsd = 0.444 "obj and name CA" index = 79 rmsd = 0.466 "obj and name CA" index = 80 rmsd = 0.547 "obj and name CA" index = 81 rmsd = 0.514 "obj and name CA" index = 82 rmsd = 0.466 "obj and name CA" index = 83 rmsd = 0.530 "obj and name CA" index = 84 rmsd = 0.593 "obj and name CA" index = 85 rmsd = 0.599 "obj and name CA" index = 86 rmsd = 0.646 "obj and name CA" index = 87 rmsd = 0.708 "obj and name CA" index = 88 rmsd = 0.798 "obj and name CA" index = 89 rmsd = 0.957 "obj and name CA" index = 90 rmsd = 0.950 "obj and name CA" index = 91 rmsd = 0.928 "obj and name CA" index = 92 rmsd = 1.091 "obj and name CA" index = 93 rmsd = 1.121 "obj and name CA" index = 94 rmsd = 1.174 "obj and name CA" index = 95 rmsd = 1.415 "obj and name CA" index = 96 rmsd = 1.265 "obj and name CA" index = 97 rmsd = 1.178 "obj and name CA" index = 98 rmsd = 0.982 "obj and name CA" index = 99 rmsd = 0.769 "obj and name CA" index = 100 rmsd = 0.800 "obj and name CA" index = 101 rmsd = 0.812 "obj and name CA" index = 102 rmsd = 0.669 "obj and name CA" index = 103 rmsd = 0.511 "obj and name CA" index = 104 rmsd = 0.567 "obj and name CA" index = 105 rmsd = 0.611 "obj and name CA" index = 106 rmsd = 0.443 "obj and name CA" index = 107 rmsd = 0.381 "obj and name CA" index = 108 rmsd = 0.485 "obj and name CA" index = 109 rmsd = 0.489 "obj and name CA" index = 110 rmsd = 0.449 "obj and name CA" index = 111 rmsd = 0.527 "obj and name CA" index = 112 rmsd = 0.548 "obj and name CA" index = 113 rmsd = 0.571 "obj and name CA" index = 114 rmsd = 0.705 "obj and name CA" index = 115 rmsd = 0.836 "obj and name CA" index = 116 rmsd = 0.869 "obj and name CA" index = 117 rmsd = 0.944 "obj and name CA" index = 118 rmsd = 1.209 "obj and name CA" index = 119 rmsd = 1.299 "obj and name CA" index = 120 rmsd = 1.346 "obj and name CA" index = 121 rmsd = 1.923 "obj and name CA" index = 122 rmsd = 3.862 "obj and name CA" index = 123 rmsd = 5.730 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 261 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 3914 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: 1.99 sec. = 1809.5 frames/hour (9.19 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit