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 59 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 1644 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: 1.43 sec. = 2509.7 frames/hour (1.43 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 327 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 327 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: 4.81 sec. = 749.2 frames/hour (6.24 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, 4.9200291633605957, 7.5961732864379883, 3.0992362499237061, 3.209254264831543, 3.5973834991455078, 4.2261080741882324, 6.745415210723877, 4.8886942863464355, 6.1116247177124023, 7.9425334930419922, 6.712890625, 3.7133731842041016, 3.8548872470855713, 3.4546382427215576, 4.4454154968261719, 7.1260895729064941, 5.8802666664123535, 4.0192441940307617, 8.4183111190795898] -> atom index_map = [None, 2, 20, 34, 54, 76, 88, 110, 121, 138, 152, 166, 176, 195, 210, 232, 242, 261, 273, 293, 312, 319, 326, 343, 357, 371, 382, 392, 403, 419, 433, 450, 461, 478, 490, 505, 516, 530, 540, 562, 569, 588, 607, 629, 650, 669, 686, 698, 717, 724, 740, 754, 770, 781, 795, 810, 826, 842, 858, 868, 892, 899, 914, 931, 946, 953, 977, 991, 1005, 1020, 1040, 1054, 1076, 1098, 1114, 1124, 1131, 1155, 1165, 1180, 1202, 1218, 1228, 1239, 1246, 1260, 1284, 1303, 1322, 1341, 1363, 1377, 1391, 1406, 1427, 1447, 1458, 1472, 1493, 1510, 1527, 1542, 1559, 1578, 1600, 1615, 1634, 1650, 1669, 1684] "obj and name CA" index = 1 rmsd = 14.727 "obj and name CA" index = 2 rmsd = 12.787 "obj and name CA" index = 3 rmsd = 11.669 "obj and name CA" index = 4 rmsd = 9.524 "obj and name CA" index = 5 rmsd = 7.953 "obj and name CA" index = 6 rmsd = 6.508 "obj and name CA" index = 7 rmsd = 4.711 "obj and name CA" index = 8 rmsd = 3.076 "obj and name CA" index = 9 rmsd = 3.086 "obj and name CA" index = 10 rmsd = 2.626 "obj and name CA" index = 11 rmsd = 2.191 "obj and name CA" index = 12 rmsd = 1.802 "obj and name CA" index = 13 rmsd = 2.122 "obj and name CA" index = 14 rmsd = 2.005 "obj and name CA" index = 15 rmsd = 1.518 "obj and name CA" index = 16 rmsd = 1.609 "obj and name CA" index = 17 rmsd = 1.847 "obj and name CA" index = 18 rmsd = 1.507 "obj and name CA" index = 19 rmsd = 1.378 "obj and name CA" index = 20 rmsd = 1.872 "obj and name CA" index = 21 rmsd = 2.334 "obj and name CA" index = 22 rmsd = 3.083 "obj and name CA" index = 23 rmsd = 3.562 "obj and name CA" index = 24 rmsd = 3.726 "obj and name CA" index = 25 rmsd = 3.606 "obj and name CA" index = 26 rmsd = 2.948 "obj and name CA" index = 27 rmsd = 2.556 "obj and name CA" index = 28 rmsd = 3.652 "obj and name CA" index = 29 rmsd = 3.871 "obj and name CA" index = 30 rmsd = 2.227 "obj and name CA" index = 31 rmsd = 2.336 "obj and name CA" index = 32 rmsd = 2.147 "obj and name CA" index = 33 rmsd = 1.874 "obj and name CA" index = 34 rmsd = 1.641 "obj and name CA" index = 35 rmsd = 1.432 "obj and name CA" index = 36 rmsd = 1.037 "obj and name CA" index = 37 rmsd = 0.854 "obj and name CA" index = 38 rmsd = 0.803 "obj and name CA" index = 39 rmsd = 0.834 "obj and name CA" index = 40 rmsd = 0.919 "obj and name CA" index = 41 rmsd = 0.910 "obj and name CA" index = 42 rmsd = 1.187 "obj and name CA" index = 43 rmsd = 1.374 "obj and name CA" index = 44 rmsd = 1.488 "obj and name CA" index = 45 rmsd = 1.589 "obj and name CA" index = 46 rmsd = 1.720 "obj and name CA" index = 47 rmsd = 1.983 "obj and name CA" index = 48 rmsd = 2.138 "obj and name CA" index = 49 rmsd = 1.953 "obj and name CA" index = 50 rmsd = 2.028 "obj and name CA" index = 51 rmsd = 1.712 "obj and name CA" index = 52 rmsd = 1.988 "obj and name CA" index = 53 rmsd = 1.796 "obj and name CA" index = 54 rmsd = 2.146 "obj and name CA" index = 55 rmsd = 1.992 "obj and name CA" index = 56 rmsd = 1.534 "obj and name CA" index = 57 rmsd = 1.807 "obj and name CA" index = 58 rmsd = 2.151 "obj and name CA" index = 59 rmsd = 1.980 "obj and name CA" index = 60 rmsd = 1.826 "obj and name CA" index = 61 rmsd = 2.115 "obj and name CA" index = 62 rmsd = 2.340 "obj and name CA" index = 63 rmsd = 2.281 "obj and name CA" index = 64 rmsd = 2.151 "obj and name CA" index = 65 rmsd = 1.797 "obj and name CA" index = 66 rmsd = 1.865 "obj and name CA" index = 67 rmsd = 2.003 "obj and name CA" index = 68 rmsd = 1.879 "obj and name CA" index = 69 rmsd = 1.336 "obj and name CA" index = 70 rmsd = 1.401 "obj and name CA" index = 71 rmsd = 1.686 "obj and name CA" index = 72 rmsd = 1.473 "obj and name CA" index = 73 rmsd = 1.079 "obj and name CA" index = 74 rmsd = 1.353 "obj and name CA" index = 75 rmsd = 1.565 "obj and name CA" index = 76 rmsd = 1.232 "obj and name CA" index = 77 rmsd = 1.246 "obj and name CA" index = 78 rmsd = 1.680 "obj and name CA" index = 79 rmsd = 1.788 "obj and name CA" index = 80 rmsd = 1.758 "obj and name CA" index = 81 rmsd = 1.993 "obj and name CA" index = 82 rmsd = 2.226 "obj and name CA" index = 83 rmsd = 2.442 "obj and name CA" index = 84 rmsd = 2.422 "obj and name CA" index = 85 rmsd = 2.313 "obj and name CA" index = 86 rmsd = 1.880 "obj and name CA" index = 87 rmsd = 2.190 "obj and name CA" index = 88 rmsd = 1.854 "obj and name CA" index = 89 rmsd = 2.779 "obj and name CA" index = 90 rmsd = 2.467 "obj and name CA" index = 91 rmsd = 2.644 "obj and name CA" index = 92 rmsd = 2.973 "obj and name CA" index = 93 rmsd = 3.254 "obj and name CA" index = 94 rmsd = 1.620 "obj and name CA" index = 95 rmsd = 2.000 "obj and name CA" index = 96 rmsd = 2.119 "obj and name CA" index = 97 rmsd = 2.229 "obj and name CA" index = 98 rmsd = 1.955 "obj and name CA" index = 99 rmsd = 1.918 "obj and name CA" index = 100 rmsd = 2.215 "obj and name CA" index = 101 rmsd = 2.284 "obj and name CA" index = 102 rmsd = 1.960 "obj and name CA" index = 103 rmsd = 2.183 "obj and name CA" index = 104 rmsd = 2.587 "obj and name CA" index = 105 rmsd = 2.479 "obj and name CA" index = 106 rmsd = 2.312 "obj and name CA" index = 107 rmsd = 2.741 "obj and name CA" index = 108 rmsd = 3.197 "obj and name CA" index = 109 rmsd = 3.307 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 177 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 3335 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: 1.77 sec. = 2028.3 frames/hour (8.01 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit