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 48 atoms. PyMOL>color gray,ss ""+l Executive: Colored 1748 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: 0.78 sec. = 4607.5 frames/hour (0.78 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: 2.79 sec. = 1292.3 frames/hour (3.57 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, 6.5226759910583496, 16.202068328857422, 14.020256042480469, 5.7514324188232422, 7.9504852294921875, 6.6785531044006348, 5.3793072700500488, 6.476140022277832, 7.202115535736084, 5.4654388427734375, 9.8073043823242188, 6.1539120674133301, 4.1164803504943848, 8.1566457748413086, 5.6501212120056152, 15.385113716125488, 10.737378120422363, 4.2442703247070312, 7.0279879570007324] -> 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 = 10.575 "obj and name CA" index = 2 rmsd = 9.056 "obj and name CA" index = 3 rmsd = 6.616 "obj and name CA" index = 4 rmsd = 4.625 "obj and name CA" index = 5 rmsd = 3.912 "obj and name CA" index = 6 rmsd = 3.344 "obj and name CA" index = 7 rmsd = 2.774 "obj and name CA" index = 8 rmsd = 2.422 "obj and name CA" index = 9 rmsd = 2.479 "obj and name CA" index = 10 rmsd = 2.468 "obj and name CA" index = 11 rmsd = 3.569 "obj and name CA" index = 12 rmsd = 3.898 "obj and name CA" index = 13 rmsd = 5.018 "obj and name CA" index = 14 rmsd = 5.726 "obj and name CA" index = 15 rmsd = 6.748 "obj and name CA" index = 16 rmsd = 6.748 "obj and name CA" index = 17 rmsd = 6.660 "obj and name CA" index = 18 rmsd = 5.726 "obj and name CA" index = 19 rmsd = 5.597 "obj and name CA" index = 20 rmsd = 4.625 "obj and name CA" index = 21 rmsd = 3.991 "obj and name CA" index = 22 rmsd = 3.084 "obj and name CA" index = 23 rmsd = 2.597 "obj and name CA" index = 24 rmsd = 1.854 "obj and name CA" index = 25 rmsd = 2.193 "obj and name CA" index = 26 rmsd = 2.784 "obj and name CA" index = 27 rmsd = 2.754 "obj and name CA" index = 28 rmsd = 3.457 "obj and name CA" index = 29 rmsd = 3.948 "obj and name CA" index = 30 rmsd = 3.584 "obj and name CA" index = 31 rmsd = 3.540 "obj and name CA" index = 32 rmsd = 3.683 "obj and name CA" index = 33 rmsd = 4.207 "obj and name CA" index = 34 rmsd = 4.628 "obj and name CA" index = 35 rmsd = 4.895 "obj and name CA" index = 36 rmsd = 5.894 "obj and name CA" index = 37 rmsd = 6.288 "obj and name CA" index = 38 rmsd = 7.122 "obj and name CA" index = 39 rmsd = 7.286 "obj and name CA" index = 40 rmsd = 6.447 "obj and name CA" index = 41 rmsd = 5.753 "obj and name CA" index = 42 rmsd = 5.064 "obj and name CA" index = 43 rmsd = 4.058 "obj and name CA" index = 44 rmsd = 3.567 "obj and name CA" index = 45 rmsd = 2.918 "obj and name CA" index = 46 rmsd = 2.536 "obj and name CA" index = 47 rmsd = 2.200 "obj and name CA" index = 48 rmsd = 2.601 "obj and name CA" index = 49 rmsd = 2.731 "obj and name CA" index = 50 rmsd = 2.228 "obj and name CA" index = 51 rmsd = 1.751 "obj and name CA" index = 52 rmsd = 1.508 "obj and name CA" index = 53 rmsd = 1.798 "obj and name CA" index = 54 rmsd = 2.280 "obj and name CA" index = 55 rmsd = 2.667 "obj and name CA" index = 56 rmsd = 3.264 "obj and name CA" index = 57 rmsd = 3.824 "obj and name CA" index = 58 rmsd = 4.648 "obj and name CA" index = 59 rmsd = 4.636 "obj and name CA" index = 60 rmsd = 4.981 "obj and name CA" index = 61 rmsd = 4.627 "obj and name CA" index = 62 rmsd = 3.798 "obj and name CA" index = 63 rmsd = 3.836 "obj and name CA" index = 64 rmsd = 3.099 "obj and name CA" index = 65 rmsd = 2.886 "obj and name CA" index = 66 rmsd = 3.382 "obj and name CA" index = 67 rmsd = 3.058 "obj and name CA" index = 68 rmsd = 2.654 "obj and name CA" index = 69 rmsd = 2.258 "obj and name CA" index = 70 rmsd = 2.118 "obj and name CA" index = 71 rmsd = 2.019 "obj and name CA" index = 72 rmsd = 2.709 "obj and name CA" index = 73 rmsd = 3.095 "obj and name CA" index = 74 rmsd = 3.801 "obj and name CA" index = 75 rmsd = 3.139 "obj and name CA" index = 76 rmsd = 3.282 "obj and name CA" index = 77 rmsd = 3.090 "obj and name CA" index = 78 rmsd = 3.959 "obj and name CA" index = 79 rmsd = 4.275 "obj and name CA" index = 80 rmsd = 5.309 "obj and name CA" index = 81 rmsd = 5.554 "obj and name CA" index = 82 rmsd = 5.370 "obj and name CA" index = 83 rmsd = 5.713 "obj and name CA" index = 84 rmsd = 4.765 "obj and name CA" index = 85 rmsd = 4.329 "obj and name CA" index = 86 rmsd = 3.362 "obj and name CA" index = 87 rmsd = 3.384 "obj and name CA" index = 88 rmsd = 2.714 "obj and name CA" index = 89 rmsd = 3.327 "obj and name CA" index = 90 rmsd = 3.337 "obj and name CA" index = 91 rmsd = 3.657 "obj and name CA" index = 92 rmsd = 4.121 "obj and name CA" index = 93 rmsd = 4.527 "obj and name CA" index = 94 rmsd = 4.246 "obj and name CA" index = 95 rmsd = 4.786 "obj and name CA" index = 96 rmsd = 4.668 "obj and name CA" index = 97 rmsd = 5.381 "obj and name CA" index = 98 rmsd = 7.071 "obj and name CA" index = 99 rmsd = 7.500 "obj and name CA" index = 100 rmsd = 7.126 "obj and name CA" index = 101 rmsd = 7.724 "obj and name CA" index = 102 rmsd = 7.942 "obj and name CA" index = 103 rmsd = 9.074 "obj and name CA" index = 104 rmsd = 10.652 "obj and name CA" index = 105 rmsd = 12.556 "obj and name CA" index = 106 rmsd = 14.102 "obj and name CA" index = 107 rmsd = 16.299 "obj and name CA" index = 108 rmsd = 17.633 "obj and name CA" index = 109 rmsd = 18.661 "obj and name CA" index = 110 rmsd = 20.189 "obj and name CA" index = 111 rmsd = 22.069 "obj and name CA" index = 112 rmsd = 23.461 "obj and name CA" index = 113 rmsd = 25.200 "obj and name CA" index = 114 rmsd = 26.788 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 144 atoms. PyMOL>color gray,ss ""+l Executive: Colored 3551 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: 1.39 sec. = 2593.9 frames/hour (4.95 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit