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 5 atoms. PyMOL>color cyan,ss s Executive: Colored 47 atoms. PyMOL>color gray,ss ""+l Executive: Colored 1751 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: 0.80 sec. = 4514.2 frames/hour (0.80 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 342 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 342 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: 3.32 sec. = 1083.6 frames/hour (4.12 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, 6.8912782669067383, 7.6049990653991699, 7.5931057929992676, 18.218044281005859, 5.4450383186340332, 11.279231071472168, 3.7114508152008057, 16.087808609008789, 7.4313440322875977, 8.6620731353759766, 6.8465790748596191, 3.6668021678924561, 7.3364744186401367, 6.2300858497619629, 14.694577217102051, 5.9816784858703613, 9.7927265167236328, 10.575614929199219, 4.2400870323181152] -> atom index_map = [None, 2, 21, 43, 57, 71, 78, 90, 105, 121, 137, 147, 166, 185, 196, 213, 227, 234, 256, 272, 291, 315, 330, 349, 363, 382, 396, 403, 420, 442, 449, 463, 478, 495, 515, 529, 548, 570, 577, 599, 606, 616, 633, 654, 668, 687, 704, 719, 735, 747, 754, 769, 793, 812, 836, 855, 877, 892, 904, 918, 929, 943, 955, 972, 988, 995, 1011, 1033, 1050, 1057, 1081, 1103, 1114, 1136, 1146, 1153, 1165, 1179, 1198, 1214, 1225, 1244, 1258, 1275, 1297, 1313, 1333, 1349, 1364, 1383, 1405, 1416, 1430, 1447, 1469, 1481, 1492, 1514, 1526, 1540, 1552, 1566, 1578, 1597, 1616, 1632, 1646, 1660, 1679, 1694, 1711, 1728, 1745, 1762, 1779] "obj and name CA" index = 1 rmsd = 7.898 "obj and name CA" index = 2 rmsd = 6.763 "obj and name CA" index = 3 rmsd = 5.164 "obj and name CA" index = 4 rmsd = 4.484 "obj and name CA" index = 5 rmsd = 4.246 "obj and name CA" index = 6 rmsd = 3.628 "obj and name CA" index = 7 rmsd = 2.867 "obj and name CA" index = 8 rmsd = 2.446 "obj and name CA" index = 9 rmsd = 2.130 "obj and name CA" index = 10 rmsd = 2.296 "obj and name CA" index = 11 rmsd = 2.792 "obj and name CA" index = 12 rmsd = 3.218 "obj and name CA" index = 13 rmsd = 4.099 "obj and name CA" index = 14 rmsd = 4.913 "obj and name CA" index = 15 rmsd = 5.793 "obj and name CA" index = 16 rmsd = 5.500 "obj and name CA" index = 17 rmsd = 5.072 "obj and name CA" index = 18 rmsd = 4.173 "obj and name CA" index = 19 rmsd = 4.074 "obj and name CA" index = 20 rmsd = 3.213 "obj and name CA" index = 21 rmsd = 2.599 "obj and name CA" index = 22 rmsd = 2.119 "obj and name CA" index = 23 rmsd = 1.953 "obj and name CA" index = 24 rmsd = 2.050 "obj and name CA" index = 25 rmsd = 2.555 "obj and name CA" index = 26 rmsd = 2.967 "obj and name CA" index = 27 rmsd = 2.560 "obj and name CA" index = 28 rmsd = 3.209 "obj and name CA" index = 29 rmsd = 3.147 "obj and name CA" index = 30 rmsd = 2.818 "obj and name CA" index = 31 rmsd = 2.750 "obj and name CA" index = 32 rmsd = 2.932 "obj and name CA" index = 33 rmsd = 3.329 "obj and name CA" index = 34 rmsd = 4.053 "obj and name CA" index = 35 rmsd = 4.545 "obj and name CA" index = 36 rmsd = 5.561 "obj and name CA" index = 37 rmsd = 6.390 "obj and name CA" index = 38 rmsd = 7.429 "obj and name CA" index = 39 rmsd = 7.919 "obj and name CA" index = 40 rmsd = 7.580 "obj and name CA" index = 41 rmsd = 6.701 "obj and name CA" index = 42 rmsd = 5.552 "obj and name CA" index = 43 rmsd = 4.595 "obj and name CA" index = 44 rmsd = 3.806 "obj and name CA" index = 45 rmsd = 3.096 "obj and name CA" index = 46 rmsd = 2.632 "obj and name CA" index = 47 rmsd = 2.201 "obj and name CA" index = 48 rmsd = 2.538 "obj and name CA" index = 49 rmsd = 2.825 "obj and name CA" index = 50 rmsd = 2.499 "obj and name CA" index = 51 rmsd = 2.372 "obj and name CA" index = 52 rmsd = 2.328 "obj and name CA" index = 53 rmsd = 2.944 "obj and name CA" index = 54 rmsd = 3.431 "obj and name CA" index = 55 rmsd = 3.439 "obj and name CA" index = 56 rmsd = 4.154 "obj and name CA" index = 57 rmsd = 5.037 "obj and name CA" index = 58 rmsd = 6.218 "obj and name CA" index = 59 rmsd = 6.554 "obj and name CA" index = 60 rmsd = 7.233 "obj and name CA" index = 61 rmsd = 6.800 "obj and name CA" index = 62 rmsd = 5.842 "obj and name CA" index = 63 rmsd = 5.855 "obj and name CA" index = 64 rmsd = 5.009 "obj and name CA" index = 65 rmsd = 4.595 "obj and name CA" index = 66 rmsd = 5.110 "obj and name CA" index = 67 rmsd = 4.763 "obj and name CA" index = 68 rmsd = 3.936 "obj and name CA" index = 69 rmsd = 3.300 "obj and name CA" index = 70 rmsd = 3.165 "obj and name CA" index = 71 rmsd = 2.837 "obj and name CA" index = 72 rmsd = 3.276 "obj and name CA" index = 73 rmsd = 3.272 "obj and name CA" index = 74 rmsd = 3.863 "obj and name CA" index = 75 rmsd = 3.693 "obj and name CA" index = 76 rmsd = 3.919 "obj and name CA" index = 77 rmsd = 3.912 "obj and name CA" index = 78 rmsd = 4.762 "obj and name CA" index = 79 rmsd = 5.112 "obj and name CA" index = 80 rmsd = 6.061 "obj and name CA" index = 81 rmsd = 6.560 "obj and name CA" index = 82 rmsd = 5.994 "obj and name CA" index = 83 rmsd = 5.754 "obj and name CA" index = 84 rmsd = 4.794 "obj and name CA" index = 85 rmsd = 4.328 "obj and name CA" index = 86 rmsd = 3.428 "obj and name CA" index = 87 rmsd = 3.351 "obj and name CA" index = 88 rmsd = 2.844 "obj and name CA" index = 89 rmsd = 2.942 "obj and name CA" index = 90 rmsd = 2.868 "obj and name CA" index = 91 rmsd = 2.922 "obj and name CA" index = 92 rmsd = 3.147 "obj and name CA" index = 93 rmsd = 3.574 "obj and name CA" index = 94 rmsd = 3.297 "obj and name CA" index = 95 rmsd = 3.632 "obj and name CA" index = 96 rmsd = 3.785 "obj and name CA" index = 97 rmsd = 5.012 "obj and name CA" index = 98 rmsd = 6.809 "obj and name CA" index = 99 rmsd = 8.004 "obj and name CA" index = 100 rmsd = 8.365 "obj and name CA" index = 101 rmsd = 9.620 "obj and name CA" index = 102 rmsd = 10.411 "obj and name CA" index = 103 rmsd = 11.584 "obj and name CA" index = 104 rmsd = 13.049 "obj and name CA" index = 105 rmsd = 14.154 "obj and name CA" index = 106 rmsd = 15.717 "obj and name CA" index = 107 rmsd = 17.334 "obj and name CA" index = 108 rmsd = 18.932 "obj and name CA" index = 109 rmsd = 19.854 "obj and name CA" index = 110 rmsd = 21.587 "obj and name CA" index = 111 rmsd = 23.659 "obj and name CA" index = 112 rmsd = 25.085 "obj and name CA" index = 113 rmsd = 26.929 "obj and name CA" index = 114 rmsd = 28.229 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 15 atoms. PyMOL>color cyan,ss s Executive: Colored 141 atoms. PyMOL>color gray,ss ""+l Executive: Colored 3556 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: 1.60 sec. = 2252.3 frames/hour (5.72 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit