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 37 atoms. PyMOL>color gray,ss ""+l Executive: Colored 1861 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: 1.05 sec. = 3413.3 frames/hour (1.05 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 366 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 366 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: 3.83 sec. = 940.3 frames/hour (4.88 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, 5.073786735534668, 4.0001034736633301, 5.0526013374328613, 6.4831829071044922, 3.7649180889129639, 4.9824881553649902, 3.8508815765380859, 5.3572616577148438, 6.151613712310791, 4.4131956100463867, 5.230750560760498, 3.1093266010284424, 6.5970020294189453, 5.8401632308959961, 4.9912662506103516, 4.9977679252624512, 5.2053537368774414, 4.6888461112976074, 3.3136136531829834] -> atom index_map = [None, 2, 21, 28, 45, 62, 79, 96, 113, 130, 141, 158, 175, 189, 196, 210, 226, 237, 256, 271, 286, 305, 317, 333, 345, 352, 374, 394, 413, 437, 456, 478, 492, 506, 517, 532, 549, 561, 578, 592, 609, 616, 623, 647, 662, 679, 698, 722, 744, 763, 770, 782, 796, 807, 823, 834, 855, 877, 898, 912, 923, 947, 968, 984, 1003, 1025, 1035, 1042, 1059, 1073, 1089, 1103, 1122, 1146, 1156, 1166, 1180, 1190, 1197, 1213, 1227, 1237, 1248, 1262, 1276, 1290, 1302, 1321, 1340, 1364, 1386, 1400, 1417, 1431, 1442, 1466, 1473, 1487, 1494, 1509, 1521, 1537, 1559, 1575, 1594, 1613, 1635, 1649, 1660, 1677, 1684, 1699, 1714, 1730, 1740, 1757, 1781, 1792, 1806, 1822, 1842, 1864, 1878] "obj and name CA" index = 1 rmsd = 17.407 "obj and name CA" index = 2 rmsd = 15.267 "obj and name CA" index = 3 rmsd = 14.241 "obj and name CA" index = 4 rmsd = 12.023 "obj and name CA" index = 5 rmsd = 10.204 "obj and name CA" index = 6 rmsd = 8.586 "obj and name CA" index = 7 rmsd = 6.901 "obj and name CA" index = 8 rmsd = 5.597 "obj and name CA" index = 9 rmsd = 4.496 "obj and name CA" index = 10 rmsd = 4.322 "obj and name CA" index = 11 rmsd = 3.429 "obj and name CA" index = 12 rmsd = 3.100 "obj and name CA" index = 13 rmsd = 3.081 "obj and name CA" index = 14 rmsd = 2.279 "obj and name CA" index = 15 rmsd = 1.831 "obj and name CA" index = 16 rmsd = 1.449 "obj and name CA" index = 17 rmsd = 1.014 "obj and name CA" index = 18 rmsd = 1.114 "obj and name CA" index = 19 rmsd = 1.193 "obj and name CA" index = 20 rmsd = 1.106 "obj and name CA" index = 21 rmsd = 1.497 "obj and name CA" index = 22 rmsd = 2.076 "obj and name CA" index = 23 rmsd = 2.658 "obj and name CA" index = 24 rmsd = 2.038 "obj and name CA" index = 25 rmsd = 1.822 "obj and name CA" index = 26 rmsd = 1.175 "obj and name CA" index = 27 rmsd = 0.785 "obj and name CA" index = 28 rmsd = 0.983 "obj and name CA" index = 29 rmsd = 1.152 "obj and name CA" index = 30 rmsd = 1.461 "obj and name CA" index = 31 rmsd = 1.910 "obj and name CA" index = 32 rmsd = 1.997 "obj and name CA" index = 33 rmsd = 2.571 "obj and name CA" index = 34 rmsd = 3.028 "obj and name CA" index = 35 rmsd = 3.392 "obj and name CA" index = 36 rmsd = 3.335 "obj and name CA" index = 37 rmsd = 3.255 "obj and name CA" index = 38 rmsd = 3.317 "obj and name CA" index = 39 rmsd = 2.896 "obj and name CA" index = 40 rmsd = 3.652 "obj and name CA" index = 41 rmsd = 3.016 "obj and name CA" index = 42 rmsd = 2.448 "obj and name CA" index = 43 rmsd = 2.108 "obj and name CA" index = 44 rmsd = 1.541 "obj and name CA" index = 45 rmsd = 1.516 "obj and name CA" index = 46 rmsd = 1.327 "obj and name CA" index = 47 rmsd = 1.640 "obj and name CA" index = 48 rmsd = 1.976 "obj and name CA" index = 49 rmsd = 2.941 "obj and name CA" index = 50 rmsd = 2.838 "obj and name CA" index = 51 rmsd = 2.431 "obj and name CA" index = 52 rmsd = 1.854 "obj and name CA" index = 53 rmsd = 1.813 "obj and name CA" index = 54 rmsd = 1.923 "obj and name CA" index = 55 rmsd = 1.910 "obj and name CA" index = 56 rmsd = 2.333 "obj and name CA" index = 57 rmsd = 2.599 "obj and name CA" index = 58 rmsd = 3.502 "obj and name CA" index = 59 rmsd = 3.614 "obj and name CA" index = 60 rmsd = 3.608 "obj and name CA" index = 61 rmsd = 3.285 "obj and name CA" index = 62 rmsd = 3.244 "obj and name CA" index = 63 rmsd = 2.658 "obj and name CA" index = 64 rmsd = 2.851 "obj and name CA" index = 65 rmsd = 2.687 "obj and name CA" index = 66 rmsd = 2.265 "obj and name CA" index = 67 rmsd = 2.170 "obj and name CA" index = 68 rmsd = 1.662 "obj and name CA" index = 69 rmsd = 1.533 "obj and name CA" index = 70 rmsd = 1.273 "obj and name CA" index = 71 rmsd = 1.209 "obj and name CA" index = 72 rmsd = 1.380 "obj and name CA" index = 73 rmsd = 1.483 "obj and name CA" index = 74 rmsd = 1.863 "obj and name CA" index = 75 rmsd = 2.114 "obj and name CA" index = 76 rmsd = 2.188 "obj and name CA" index = 77 rmsd = 2.912 "obj and name CA" index = 78 rmsd = 2.962 "obj and name CA" index = 79 rmsd = 3.540 "obj and name CA" index = 80 rmsd = 3.949 "obj and name CA" index = 81 rmsd = 3.897 "obj and name CA" index = 82 rmsd = 3.848 "obj and name CA" index = 83 rmsd = 3.633 "obj and name CA" index = 84 rmsd = 3.078 "obj and name CA" index = 85 rmsd = 2.159 "obj and name CA" index = 86 rmsd = 1.969 "obj and name CA" index = 87 rmsd = 1.961 "obj and name CA" index = 88 rmsd = 1.708 "obj and name CA" index = 89 rmsd = 2.264 "obj and name CA" index = 90 rmsd = 2.320 "obj and name CA" index = 91 rmsd = 1.791 "obj and name CA" index = 92 rmsd = 1.906 "obj and name CA" index = 93 rmsd = 2.008 "obj and name CA" index = 94 rmsd = 2.293 "obj and name CA" index = 95 rmsd = 2.708 "obj and name CA" index = 96 rmsd = 3.415 "obj and name CA" index = 97 rmsd = 3.386 "obj and name CA" index = 98 rmsd = 2.817 "obj and name CA" index = 99 rmsd = 2.347 "obj and name CA" index = 100 rmsd = 1.765 "obj and name CA" index = 101 rmsd = 1.530 "obj and name CA" index = 102 rmsd = 1.171 "obj and name CA" index = 103 rmsd = 1.418 "obj and name CA" index = 104 rmsd = 1.515 "obj and name CA" index = 105 rmsd = 2.132 "obj and name CA" index = 106 rmsd = 2.647 "obj and name CA" index = 107 rmsd = 3.194 "obj and name CA" index = 108 rmsd = 3.593 "obj and name CA" index = 109 rmsd = 3.171 "obj and name CA" index = 110 rmsd = 2.892 "obj and name CA" index = 111 rmsd = 2.422 "obj and name CA" index = 112 rmsd = 2.125 "obj and name CA" index = 113 rmsd = 1.671 "obj and name CA" index = 114 rmsd = 1.571 "obj and name CA" index = 115 rmsd = 1.465 "obj and name CA" index = 116 rmsd = 1.720 "obj and name CA" index = 117 rmsd = 2.009 "obj and name CA" index = 118 rmsd = 3.280 "obj and name CA" index = 119 rmsd = 4.133 "obj and name CA" index = 120 rmsd = 5.181 "obj and name CA" index = 121 rmsd = 6.392 "obj and name CA" index = 122 rmsd = 7.872 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 111 atoms. PyMOL>color gray,ss ""+l Executive: Colored 3800 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: 1.68 sec. = 2141.4 frames/hour (6.56 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit