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 61 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 1520 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: 1.23 sec. = 2921.1 frames/hour (1.23 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 303 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 303 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: 3.51 sec. = 1024.9 frames/hour (4.74 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, 1.8548778295516968, 2.0550017356872559, 4.2501115798950195, 2.199857234954834, 3.8430266380310059, 1.9209779500961304, 2.5850942134857178, 1.3647156953811646, 3.2149231433868408, 2.6080803871154785, 2.7037191390991211, 4.5184674263000488, 3.710230827331543, 1.2150282859802246, 3.3245487213134766, 1.7243648767471313, 3.0506341457366943, 3.691401481628418, 1.7173742055892944] -> atom index_map = [None, 2, 21, 35, 46, 60, 80, 92, 116, 132, 142, 156, 175, 194, 204, 219, 233, 244, 256, 275, 289, 313, 328, 342, 361, 375, 389, 404, 415, 432, 442, 461, 473, 485, 504, 511, 530, 542, 553, 572, 584, 604, 623, 635, 654, 664, 684, 694, 713, 725, 747, 757, 777, 784, 803, 825, 844, 858, 877, 892, 914, 938, 952, 969, 984, 1000, 1014, 1026, 1033, 1055, 1065, 1079, 1093, 1108, 1125, 1146, 1166, 1182, 1201, 1223, 1237, 1256, 1266, 1276, 1300, 1319, 1331, 1346, 1365, 1381, 1391, 1401, 1423, 1430, 1440, 1459, 1474, 1491, 1508, 1525, 1542, 1559] "obj and name CA" index = 1 rmsd = 2.588 "obj and name CA" index = 2 rmsd = 1.468 "obj and name CA" index = 3 rmsd = 1.356 "obj and name CA" index = 4 rmsd = 1.143 "obj and name CA" index = 5 rmsd = 1.080 "obj and name CA" index = 6 rmsd = 1.114 "obj and name CA" index = 7 rmsd = 1.022 "obj and name CA" index = 8 rmsd = 0.934 "obj and name CA" index = 9 rmsd = 0.938 "obj and name CA" index = 10 rmsd = 0.960 "obj and name CA" index = 11 rmsd = 0.908 "obj and name CA" index = 12 rmsd = 0.885 "obj and name CA" index = 13 rmsd = 0.983 "obj and name CA" index = 14 rmsd = 1.035 "obj and name CA" index = 15 rmsd = 1.029 "obj and name CA" index = 16 rmsd = 1.052 "obj and name CA" index = 17 rmsd = 1.054 "obj and name CA" index = 18 rmsd = 1.007 "obj and name CA" index = 19 rmsd = 1.225 "obj and name CA" index = 20 rmsd = 1.257 "obj and name CA" index = 21 rmsd = 1.624 "obj and name CA" index = 22 rmsd = 1.297 "obj and name CA" index = 23 rmsd = 0.795 "obj and name CA" index = 24 rmsd = 0.806 "obj and name CA" index = 25 rmsd = 0.804 "obj and name CA" index = 26 rmsd = 0.808 "obj and name CA" index = 27 rmsd = 0.746 "obj and name CA" index = 28 rmsd = 0.589 "obj and name CA" index = 29 rmsd = 0.480 "obj and name CA" index = 30 rmsd = 0.720 "obj and name CA" index = 31 rmsd = 0.905 "obj and name CA" index = 32 rmsd = 0.891 "obj and name CA" index = 33 rmsd = 0.766 "obj and name CA" index = 34 rmsd = 0.946 "obj and name CA" index = 35 rmsd = 0.754 "obj and name CA" index = 36 rmsd = 0.933 "obj and name CA" index = 37 rmsd = 0.941 "obj and name CA" index = 38 rmsd = 0.898 "obj and name CA" index = 39 rmsd = 0.745 "obj and name CA" index = 40 rmsd = 0.563 "obj and name CA" index = 41 rmsd = 0.788 "obj and name CA" index = 42 rmsd = 0.806 "obj and name CA" index = 43 rmsd = 0.550 "obj and name CA" index = 44 rmsd = 0.621 "obj and name CA" index = 45 rmsd = 0.891 "obj and name CA" index = 46 rmsd = 0.853 "obj and name CA" index = 47 rmsd = 0.723 "obj and name CA" index = 48 rmsd = 1.005 "obj and name CA" index = 49 rmsd = 1.203 "obj and name CA" index = 50 rmsd = 1.063 "obj and name CA" index = 51 rmsd = 1.190 "obj and name CA" index = 52 rmsd = 1.414 "obj and name CA" index = 53 rmsd = 1.266 "obj and name CA" index = 54 rmsd = 1.220 "obj and name CA" index = 55 rmsd = 0.949 "obj and name CA" index = 56 rmsd = 1.164 "obj and name CA" index = 57 rmsd = 0.788 "obj and name CA" index = 58 rmsd = 0.987 "obj and name CA" index = 59 rmsd = 1.144 "obj and name CA" index = 60 rmsd = 0.957 "obj and name CA" index = 61 rmsd = 0.863 "obj and name CA" index = 62 rmsd = 1.225 "obj and name CA" index = 63 rmsd = 1.188 "obj and name CA" index = 64 rmsd = 0.967 "obj and name CA" index = 65 rmsd = 1.267 "obj and name CA" index = 66 rmsd = 1.494 "obj and name CA" index = 67 rmsd = 1.491 "obj and name CA" index = 68 rmsd = 1.515 "obj and name CA" index = 69 rmsd = 1.297 "obj and name CA" index = 70 rmsd = 1.066 "obj and name CA" index = 71 rmsd = 0.768 "obj and name CA" index = 72 rmsd = 0.798 "obj and name CA" index = 73 rmsd = 0.973 "obj and name CA" index = 74 rmsd = 0.862 "obj and name CA" index = 75 rmsd = 0.555 "obj and name CA" index = 76 rmsd = 0.600 "obj and name CA" index = 77 rmsd = 0.585 "obj and name CA" index = 78 rmsd = 0.748 "obj and name CA" index = 79 rmsd = 0.794 "obj and name CA" index = 80 rmsd = 0.639 "obj and name CA" index = 81 rmsd = 0.779 "obj and name CA" index = 82 rmsd = 0.978 "obj and name CA" index = 83 rmsd = 0.948 "obj and name CA" index = 84 rmsd = 0.930 "obj and name CA" index = 85 rmsd = 1.127 "obj and name CA" index = 86 rmsd = 1.261 "obj and name CA" index = 87 rmsd = 1.181 "obj and name CA" index = 88 rmsd = 1.256 "obj and name CA" index = 89 rmsd = 1.460 "obj and name CA" index = 90 rmsd = 1.469 "obj and name CA" index = 91 rmsd = 1.478 "obj and name CA" index = 92 rmsd = 1.721 "obj and name CA" index = 93 rmsd = 1.862 "obj and name CA" index = 94 rmsd = 1.785 "obj and name CA" index = 95 rmsd = 2.054 "obj and name CA" index = 96 rmsd = 2.115 "obj and name CA" index = 97 rmsd = 3.498 "obj and name CA" index = 98 rmsd = 5.509 "obj and name CA" index = 99 rmsd = 7.671 "obj and name CA" index = 100 rmsd = 9.513 "obj and name CA" index = 101 rmsd = 11.590 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 183 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 3074 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: 1.29 sec. = 2780.3 frames/hour (6.04 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit