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 39 atoms. PyMOL>color cyan,ss s Executive: Colored 19 atoms. PyMOL>color gray,ss ""+l Executive: Colored 2024 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: 1.29 sec. = 2783.9 frames/hour (1.29 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: 5.08 sec. = 708.7 frames/hour (6.37 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, 4.2834367752075195, 2.9735822677612305, 3.9945862293243408, 3.5230531692504883, 4.66162109375, 2.6412005424499512, 3.2952597141265869, 2.8305442333221436, 4.7417616844177246, 4.3277802467346191, 4.3584675788879395, 3.5825674533843994, 2.9846765995025635, 4.2708854675292969, 3.2240829467773438, 3.9902827739715576, 3.7809996604919434, 3.1261568069458008, 4.0484352111816406] -> 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 = 1.090 "obj and name CA" index = 2 rmsd = 1.131 "obj and name CA" index = 3 rmsd = 0.941 "obj and name CA" index = 4 rmsd = 1.057 "obj and name CA" index = 5 rmsd = 1.095 "obj and name CA" index = 6 rmsd = 0.837 "obj and name CA" index = 7 rmsd = 0.904 "obj and name CA" index = 8 rmsd = 1.233 "obj and name CA" index = 9 rmsd = 1.221 "obj and name CA" index = 10 rmsd = 1.269 "obj and name CA" index = 11 rmsd = 1.520 "obj and name CA" index = 12 rmsd = 1.948 "obj and name CA" index = 13 rmsd = 1.946 "obj and name CA" index = 14 rmsd = 2.006 "obj and name CA" index = 15 rmsd = 1.998 "obj and name CA" index = 16 rmsd = 1.662 "obj and name CA" index = 17 rmsd = 1.810 "obj and name CA" index = 18 rmsd = 1.304 "obj and name CA" index = 19 rmsd = 1.167 "obj and name CA" index = 20 rmsd = 1.217 "obj and name CA" index = 21 rmsd = 1.805 "obj and name CA" index = 22 rmsd = 2.008 "obj and name CA" index = 23 rmsd = 2.441 "obj and name CA" index = 24 rmsd = 2.394 "obj and name CA" index = 25 rmsd = 1.688 "obj and name CA" index = 26 rmsd = 1.739 "obj and name CA" index = 27 rmsd = 1.460 "obj and name CA" index = 28 rmsd = 0.989 "obj and name CA" index = 29 rmsd = 0.801 "obj and name CA" index = 30 rmsd = 0.914 "obj and name CA" index = 31 rmsd = 1.075 "obj and name CA" index = 32 rmsd = 1.430 "obj and name CA" index = 33 rmsd = 1.849 "obj and name CA" index = 34 rmsd = 2.685 "obj and name CA" index = 35 rmsd = 3.143 "obj and name CA" index = 36 rmsd = 3.039 "obj and name CA" index = 37 rmsd = 2.842 "obj and name CA" index = 38 rmsd = 2.860 "obj and name CA" index = 39 rmsd = 2.164 "obj and name CA" index = 40 rmsd = 1.641 "obj and name CA" index = 41 rmsd = 1.031 "obj and name CA" index = 42 rmsd = 0.827 "obj and name CA" index = 43 rmsd = 0.581 "obj and name CA" index = 44 rmsd = 0.682 "obj and name CA" index = 45 rmsd = 0.827 "obj and name CA" index = 46 rmsd = 0.881 "obj and name CA" index = 47 rmsd = 1.005 "obj and name CA" index = 48 rmsd = 1.053 "obj and name CA" index = 49 rmsd = 1.261 "obj and name CA" index = 50 rmsd = 1.336 "obj and name CA" index = 51 rmsd = 1.486 "obj and name CA" index = 52 rmsd = 1.753 "obj and name CA" index = 53 rmsd = 1.691 "obj and name CA" index = 54 rmsd = 2.107 "obj and name CA" index = 55 rmsd = 1.776 "obj and name CA" index = 56 rmsd = 1.880 "obj and name CA" index = 57 rmsd = 1.358 "obj and name CA" index = 58 rmsd = 1.111 "obj and name CA" index = 59 rmsd = 0.756 "obj and name CA" index = 60 rmsd = 0.604 "obj and name CA" index = 61 rmsd = 0.413 "obj and name CA" index = 62 rmsd = 0.495 "obj and name CA" index = 63 rmsd = 0.658 "obj and name CA" index = 64 rmsd = 0.845 "obj and name CA" index = 65 rmsd = 1.133 "obj and name CA" index = 66 rmsd = 1.251 "obj and name CA" index = 67 rmsd = 1.516 "obj and name CA" index = 68 rmsd = 1.503 "obj and name CA" index = 69 rmsd = 1.630 "obj and name CA" index = 70 rmsd = 1.391 "obj and name CA" index = 71 rmsd = 1.189 "obj and name CA" index = 72 rmsd = 1.503 "obj and name CA" index = 73 rmsd = 1.566 "obj and name CA" index = 74 rmsd = 1.212 "obj and name CA" index = 75 rmsd = 1.152 "obj and name CA" index = 76 rmsd = 1.640 "obj and name CA" index = 77 rmsd = 1.361 "obj and name CA" index = 78 rmsd = 1.050 "obj and name CA" index = 79 rmsd = 0.878 "obj and name CA" index = 80 rmsd = 0.650 "obj and name CA" index = 81 rmsd = 0.681 "obj and name CA" index = 82 rmsd = 1.041 "obj and name CA" index = 83 rmsd = 0.860 "obj and name CA" index = 84 rmsd = 1.728 "obj and name CA" index = 85 rmsd = 2.678 "obj and name CA" index = 86 rmsd = 2.645 "obj and name CA" index = 87 rmsd = 2.056 "obj and name CA" index = 88 rmsd = 1.447 "obj and name CA" index = 89 rmsd = 1.759 "obj and name CA" index = 90 rmsd = 1.366 "obj and name CA" index = 91 rmsd = 0.976 "obj and name CA" index = 92 rmsd = 0.724 "obj and name CA" index = 93 rmsd = 0.521 "obj and name CA" index = 94 rmsd = 0.494 "obj and name CA" index = 95 rmsd = 0.450 "obj and name CA" index = 96 rmsd = 0.580 "obj and name CA" index = 97 rmsd = 0.766 "obj and name CA" index = 98 rmsd = 0.708 "obj and name CA" index = 99 rmsd = 0.925 "obj and name CA" index = 100 rmsd = 0.999 "obj and name CA" index = 101 rmsd = 1.202 "obj and name CA" index = 102 rmsd = 1.243 "obj and name CA" index = 103 rmsd = 1.391 "obj and name CA" index = 104 rmsd = 1.208 "obj and name CA" index = 105 rmsd = 0.843 "obj and name CA" index = 106 rmsd = 1.052 "obj and name CA" index = 107 rmsd = 1.184 "obj and name CA" index = 108 rmsd = 1.071 "obj and name CA" index = 109 rmsd = 1.050 "obj and name CA" index = 110 rmsd = 1.250 "obj and name CA" index = 111 rmsd = 1.442 "obj and name CA" index = 112 rmsd = 1.272 "obj and name CA" index = 113 rmsd = 1.463 "obj and name CA" index = 114 rmsd = 1.848 "obj and name CA" index = 115 rmsd = 1.777 "obj and name CA" index = 116 rmsd = 1.828 "obj and name CA" index = 117 rmsd = 2.074 "obj and name CA" index = 118 rmsd = 2.462 "obj and name CA" index = 119 rmsd = 3.302 "obj and name CA" index = 120 rmsd = 4.192 "obj and name CA" index = 121 rmsd = 5.422 "obj and name CA" index = 122 rmsd = 6.819 "obj and name CA" index = 123 rmsd = 8.708 "obj and name CA" index = 124 rmsd = 9.730 "obj and name CA" index = 125 rmsd = 11.254 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 117 atoms. PyMOL>color cyan,ss s Executive: Colored 57 atoms. PyMOL>color gray,ss ""+l Executive: Colored 4104 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: 2.23 sec. = 1613.6 frames/hour (8.60 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit