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 26 atoms. PyMOL>color cyan,ss s Executive: Colored 26 atoms. PyMOL>color gray,ss ""+l Executive: Colored 1720 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: 1.83 sec. = 1964.3 frames/hour (1.83 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 348 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 348 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: 8.47 sec. = 425.2 frames/hour (10.30 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, 2.239799976348877, 2.03568434715271, 2.0787975788116455, 1.9594526290893555, 2.1245641708374023, 2.1079151630401611, 2.7974789142608643, 2.1252541542053223, 1.8449491262435913, 2.4428200721740723, 2.689617395401001, 2.1062424182891846, 2.4803769588470459, 2.4952590465545654, 2.4159121513366699, 2.33526611328125, 1.7887072563171387, 2.4907212257385254, 2.0897665023803711] -> atom index_map = [None, 2, 21, 35, 54, 73, 94, 116, 135, 154, 165, 189, 199, 214, 238, 250, 260, 270, 292, 302, 319, 326, 350, 370, 385, 392, 403, 413, 429, 441, 460, 470, 482, 489, 509, 528, 545, 564, 575, 585, 592, 607, 624, 634, 651, 666, 680, 690, 700, 722, 746, 766, 790, 797, 814, 824, 838, 857, 873, 892, 911, 921, 937, 952, 962, 977, 991, 1010, 1017, 1032, 1044, 1063, 1085, 1109, 1124, 1134, 1145, 1169, 1176, 1183, 1193, 1217, 1237, 1251, 1268, 1287, 1308, 1332, 1346, 1365, 1384, 1400, 1411, 1426, 1442, 1456, 1480, 1495, 1505, 1517, 1536, 1548, 1567, 1579, 1589, 1601, 1608, 1624, 1638, 1655, 1674, 1681, 1693, 1710, 1729, 1739, 1758] "obj and name CA" index = 1 rmsd = 3.890 "obj and name CA" index = 2 rmsd = 1.382 "obj and name CA" index = 3 rmsd = 0.954 "obj and name CA" index = 4 rmsd = 0.758 "obj and name CA" index = 5 rmsd = 0.646 "obj and name CA" index = 6 rmsd = 0.665 "obj and name CA" index = 7 rmsd = 0.540 "obj and name CA" index = 8 rmsd = 0.625 "obj and name CA" index = 9 rmsd = 0.772 "obj and name CA" index = 10 rmsd = 0.796 "obj and name CA" index = 11 rmsd = 0.918 "obj and name CA" index = 12 rmsd = 0.795 "obj and name CA" index = 13 rmsd = 0.645 "obj and name CA" index = 14 rmsd = 0.759 "obj and name CA" index = 15 rmsd = 0.760 "obj and name CA" index = 16 rmsd = 0.603 "obj and name CA" index = 17 rmsd = 0.632 "obj and name CA" index = 18 rmsd = 0.749 "obj and name CA" index = 19 rmsd = 0.707 "obj and name CA" index = 20 rmsd = 0.710 "obj and name CA" index = 21 rmsd = 0.759 "obj and name CA" index = 22 rmsd = 0.702 "obj and name CA" index = 23 rmsd = 1.156 "obj and name CA" index = 24 rmsd = 1.403 "obj and name CA" index = 25 rmsd = 1.785 "obj and name CA" index = 26 rmsd = 2.183 "obj and name CA" index = 27 rmsd = 1.792 "obj and name CA" index = 28 rmsd = 1.198 "obj and name CA" index = 29 rmsd = 1.752 "obj and name CA" index = 30 rmsd = 2.044 "obj and name CA" index = 31 rmsd = 1.712 "obj and name CA" index = 32 rmsd = 1.968 "obj and name CA" index = 33 rmsd = 0.917 "obj and name CA" index = 34 rmsd = 0.689 "obj and name CA" index = 35 rmsd = 0.830 "obj and name CA" index = 36 rmsd = 0.780 "obj and name CA" index = 37 rmsd = 0.675 "obj and name CA" index = 38 rmsd = 0.825 "obj and name CA" index = 39 rmsd = 0.955 "obj and name CA" index = 40 rmsd = 0.969 "obj and name CA" index = 41 rmsd = 0.740 "obj and name CA" index = 42 rmsd = 0.747 "obj and name CA" index = 43 rmsd = 0.928 "obj and name CA" index = 44 rmsd = 0.956 "obj and name CA" index = 45 rmsd = 0.964 "obj and name CA" index = 46 rmsd = 0.932 "obj and name CA" index = 47 rmsd = 1.202 "obj and name CA" index = 48 rmsd = 1.430 "obj and name CA" index = 49 rmsd = 1.212 "obj and name CA" index = 50 rmsd = 0.961 "obj and name CA" index = 51 rmsd = 1.241 "obj and name CA" index = 52 rmsd = 1.104 "obj and name CA" index = 53 rmsd = 1.374 "obj and name CA" index = 54 rmsd = 1.298 "obj and name CA" index = 55 rmsd = 1.049 "obj and name CA" index = 56 rmsd = 0.837 "obj and name CA" index = 57 rmsd = 0.605 "obj and name CA" index = 58 rmsd = 0.561 "obj and name CA" index = 59 rmsd = 0.499 "obj and name CA" index = 60 rmsd = 0.570 "obj and name CA" index = 61 rmsd = 0.547 "obj and name CA" index = 62 rmsd = 0.689 "obj and name CA" index = 63 rmsd = 1.036 "obj and name CA" index = 64 rmsd = 1.287 "obj and name CA" index = 65 rmsd = 2.743 "obj and name CA" index = 66 rmsd = 2.284 "obj and name CA" index = 67 rmsd = 2.514 "obj and name CA" index = 68 rmsd = 1.881 "obj and name CA" index = 69 rmsd = 1.059 "obj and name CA" index = 70 rmsd = 0.698 "obj and name CA" index = 71 rmsd = 0.650 "obj and name CA" index = 72 rmsd = 0.570 "obj and name CA" index = 73 rmsd = 0.623 "obj and name CA" index = 74 rmsd = 0.963 "obj and name CA" index = 75 rmsd = 1.840 "obj and name CA" index = 76 rmsd = 2.377 "obj and name CA" index = 77 rmsd = 3.332 "obj and name CA" index = 78 rmsd = 2.212 "obj and name CA" index = 79 rmsd = 1.095 "obj and name CA" index = 80 rmsd = 0.683 "obj and name CA" index = 81 rmsd = 0.475 "obj and name CA" index = 82 rmsd = 0.495 "obj and name CA" index = 83 rmsd = 0.494 "obj and name CA" index = 84 rmsd = 0.507 "obj and name CA" index = 85 rmsd = 0.626 "obj and name CA" index = 86 rmsd = 0.885 "obj and name CA" index = 87 rmsd = 0.895 "obj and name CA" index = 88 rmsd = 0.910 "obj and name CA" index = 89 rmsd = 0.774 "obj and name CA" index = 90 rmsd = 0.628 "obj and name CA" index = 91 rmsd = 1.746 "obj and name CA" index = 92 rmsd = 0.927 "obj and name CA" index = 93 rmsd = 0.539 "obj and name CA" index = 94 rmsd = 0.623 "obj and name CA" index = 95 rmsd = 0.686 "obj and name CA" index = 96 rmsd = 0.685 "obj and name CA" index = 97 rmsd = 0.846 "obj and name CA" index = 98 rmsd = 0.843 "obj and name CA" index = 99 rmsd = 1.074 "obj and name CA" index = 100 rmsd = 1.645 "obj and name CA" index = 101 rmsd = 1.234 "obj and name CA" index = 102 rmsd = 2.018 "obj and name CA" index = 103 rmsd = 2.836 "obj and name CA" index = 104 rmsd = 1.893 "obj and name CA" index = 105 rmsd = 1.935 "obj and name CA" index = 106 rmsd = 1.329 "obj and name CA" index = 107 rmsd = 1.785 "obj and name CA" index = 108 rmsd = 1.249 "obj and name CA" index = 109 rmsd = 0.833 "obj and name CA" index = 110 rmsd = 1.400 "obj and name CA" index = 111 rmsd = 1.895 "obj and name CA" index = 112 rmsd = 1.530 "obj and name CA" index = 113 rmsd = 1.349 "obj and name CA" index = 114 rmsd = 2.436 "obj and name CA" index = 115 rmsd = 3.951 "obj and name CA" index = 116 rmsd = 5.237 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 78 atoms. PyMOL>color cyan,ss s Executive: Colored 78 atoms. PyMOL>color gray,ss ""+l Executive: Colored 3504 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: 2.44 sec. = 1478.3 frames/hour (12.73 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit