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 1860 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. = 3425.6 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: 3.64 sec. = 988.2 frames/hour (4.69 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, 6.663475513458252, 4.6563858985900879, 5.2658872604370117, 4.6343731880187988, 4.5376520156860352, 2.2784256935119629, 3.7961044311523438, 2.2751469612121582, 5.6059694290161133, 6.0132579803466797, 3.416339635848999, 3.4176704883575439, 4.0350408554077148, 6.9174685478210449, 7.8998231887817383, 2.8140456676483154, 5.2161273956298828, 5.4508447647094727, 5.576664924621582] -> 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 = 16.201 "obj and name CA" index = 2 rmsd = 14.085 "obj and name CA" index = 3 rmsd = 12.710 "obj and name CA" index = 4 rmsd = 10.692 "obj and name CA" index = 5 rmsd = 8.608 "obj and name CA" index = 6 rmsd = 6.985 "obj and name CA" index = 7 rmsd = 5.574 "obj and name CA" index = 8 rmsd = 4.473 "obj and name CA" index = 9 rmsd = 4.064 "obj and name CA" index = 10 rmsd = 3.593 "obj and name CA" index = 11 rmsd = 3.212 "obj and name CA" index = 12 rmsd = 3.419 "obj and name CA" index = 13 rmsd = 3.095 "obj and name CA" index = 14 rmsd = 2.065 "obj and name CA" index = 15 rmsd = 1.536 "obj and name CA" index = 16 rmsd = 1.103 "obj and name CA" index = 17 rmsd = 0.914 "obj and name CA" index = 18 rmsd = 1.257 "obj and name CA" index = 19 rmsd = 1.308 "obj and name CA" index = 20 rmsd = 1.185 "obj and name CA" index = 21 rmsd = 1.490 "obj and name CA" index = 22 rmsd = 1.897 "obj and name CA" index = 23 rmsd = 2.275 "obj and name CA" index = 24 rmsd = 1.869 "obj and name CA" index = 25 rmsd = 1.771 "obj and name CA" index = 26 rmsd = 1.254 "obj and name CA" index = 27 rmsd = 0.853 "obj and name CA" index = 28 rmsd = 1.023 "obj and name CA" index = 29 rmsd = 0.952 "obj and name CA" index = 30 rmsd = 1.285 "obj and name CA" index = 31 rmsd = 1.644 "obj and name CA" index = 32 rmsd = 1.976 "obj and name CA" index = 33 rmsd = 2.497 "obj and name CA" index = 34 rmsd = 2.975 "obj and name CA" index = 35 rmsd = 3.150 "obj and name CA" index = 36 rmsd = 2.815 "obj and name CA" index = 37 rmsd = 2.845 "obj and name CA" index = 38 rmsd = 2.830 "obj and name CA" index = 39 rmsd = 2.537 "obj and name CA" index = 40 rmsd = 3.218 "obj and name CA" index = 41 rmsd = 2.466 "obj and name CA" index = 42 rmsd = 2.065 "obj and name CA" index = 43 rmsd = 1.908 "obj and name CA" index = 44 rmsd = 1.370 "obj and name CA" index = 45 rmsd = 1.409 "obj and name CA" index = 46 rmsd = 1.188 "obj and name CA" index = 47 rmsd = 1.509 "obj and name CA" index = 48 rmsd = 1.789 "obj and name CA" index = 49 rmsd = 2.502 "obj and name CA" index = 50 rmsd = 2.553 "obj and name CA" index = 51 rmsd = 2.164 "obj and name CA" index = 52 rmsd = 1.840 "obj and name CA" index = 53 rmsd = 1.747 "obj and name CA" index = 54 rmsd = 1.829 "obj and name CA" index = 55 rmsd = 1.835 "obj and name CA" index = 56 rmsd = 2.216 "obj and name CA" index = 57 rmsd = 2.227 "obj and name CA" index = 58 rmsd = 2.882 "obj and name CA" index = 59 rmsd = 3.027 "obj and name CA" index = 60 rmsd = 2.912 "obj and name CA" index = 61 rmsd = 2.567 "obj and name CA" index = 62 rmsd = 2.519 "obj and name CA" index = 63 rmsd = 2.079 "obj and name CA" index = 64 rmsd = 2.278 "obj and name CA" index = 65 rmsd = 2.344 "obj and name CA" index = 66 rmsd = 2.124 "obj and name CA" index = 67 rmsd = 1.870 "obj and name CA" index = 68 rmsd = 1.505 "obj and name CA" index = 69 rmsd = 1.274 "obj and name CA" index = 70 rmsd = 1.194 "obj and name CA" index = 71 rmsd = 1.162 "obj and name CA" index = 72 rmsd = 1.398 "obj and name CA" index = 73 rmsd = 1.543 "obj and name CA" index = 74 rmsd = 2.026 "obj and name CA" index = 75 rmsd = 2.207 "obj and name CA" index = 76 rmsd = 2.333 "obj and name CA" index = 77 rmsd = 3.009 "obj and name CA" index = 78 rmsd = 2.872 "obj and name CA" index = 79 rmsd = 3.440 "obj and name CA" index = 80 rmsd = 3.503 "obj and name CA" index = 81 rmsd = 3.700 "obj and name CA" index = 82 rmsd = 3.354 "obj and name CA" index = 83 rmsd = 3.222 "obj and name CA" index = 84 rmsd = 2.974 "obj and name CA" index = 85 rmsd = 2.111 "obj and name CA" index = 86 rmsd = 1.884 "obj and name CA" index = 87 rmsd = 1.912 "obj and name CA" index = 88 rmsd = 1.745 "obj and name CA" index = 89 rmsd = 2.458 "obj and name CA" index = 90 rmsd = 2.510 "obj and name CA" index = 91 rmsd = 1.946 "obj and name CA" index = 92 rmsd = 2.096 "obj and name CA" index = 93 rmsd = 1.916 "obj and name CA" index = 94 rmsd = 2.052 "obj and name CA" index = 95 rmsd = 2.298 "obj and name CA" index = 96 rmsd = 2.876 "obj and name CA" index = 97 rmsd = 2.721 "obj and name CA" index = 98 rmsd = 2.123 "obj and name CA" index = 99 rmsd = 2.121 "obj and name CA" index = 100 rmsd = 1.609 "obj and name CA" index = 101 rmsd = 1.283 "obj and name CA" index = 102 rmsd = 0.958 "obj and name CA" index = 103 rmsd = 1.222 "obj and name CA" index = 104 rmsd = 1.335 "obj and name CA" index = 105 rmsd = 1.927 "obj and name CA" index = 106 rmsd = 2.280 "obj and name CA" index = 107 rmsd = 2.772 "obj and name CA" index = 108 rmsd = 3.157 "obj and name CA" index = 109 rmsd = 2.860 "obj and name CA" index = 110 rmsd = 2.645 "obj and name CA" index = 111 rmsd = 2.212 "obj and name CA" index = 112 rmsd = 1.915 "obj and name CA" index = 113 rmsd = 1.444 "obj and name CA" index = 114 rmsd = 1.347 "obj and name CA" index = 115 rmsd = 1.270 "obj and name CA" index = 116 rmsd = 1.483 "obj and name CA" index = 117 rmsd = 1.845 "obj and name CA" index = 118 rmsd = 3.227 "obj and name CA" index = 119 rmsd = 3.962 "obj and name CA" index = 120 rmsd = 4.715 "obj and name CA" index = 121 rmsd = 5.648 "obj and name CA" index = 122 rmsd = 7.262 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 3799 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: 1.05 sec. = 3426.1 frames/hour (5.74 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit