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 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 16 atoms. PyMOL>color cyan,ss s Executive: Colored 17 atoms. PyMOL>color gray,ss ""+l Executive: Colored 1418 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: 1.14 sec. = 3168.1 frames/hour (1.14 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 273 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 273 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: 2.51 sec. = 1434.5 frames/hour (3.65 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 10 states [1, 10] of object "obj and name CA" (10 total states) to get new single-state object "yesfit_ALL"... -------------------------------------------------------------------------------- -> proceeding WITH FITTING to reference state... intrafit_rmsds = [-1.0, 4.6719355583190918, 5.8337817192077637, 4.0894756317138672, 3.7308669090270996, 3.2862415313720703, 3.1321535110473633, 3.8080141544342041, 3.1771082878112793, 4.4614925384521484] -> atom index_map = [None, 2, 21, 43, 62, 81, 92, 111, 122, 137, 151, 165, 179, 196, 210, 224, 241, 263, 282, 296, 315, 326, 341, 352, 376, 391, 398, 415, 429, 440, 452, 466, 487, 501, 523, 539, 551, 563, 574, 591, 605, 615, 635, 654, 668, 680, 699, 718, 740, 756, 771, 778, 794, 816, 827, 846, 866, 883, 899, 916, 928, 948, 967, 978, 994, 1006, 1028, 1043, 1057, 1069, 1079, 1093, 1117, 1132, 1146, 1162, 1181, 1195, 1217, 1233, 1248, 1258, 1274, 1294, 1309, 1328, 1343, 1360, 1377, 1394, 1411, 1428] "obj and name CA" index = 1 rmsd = 2.751 "obj and name CA" index = 2 rmsd = 2.601 "obj and name CA" index = 3 rmsd = 2.139 "obj and name CA" index = 4 rmsd = 2.353 "obj and name CA" index = 5 rmsd = 2.347 "obj and name CA" index = 6 rmsd = 1.799 "obj and name CA" index = 7 rmsd = 1.737 "obj and name CA" index = 8 rmsd = 2.436 "obj and name CA" index = 9 rmsd = 2.642 "obj and name CA" index = 10 rmsd = 3.639 "obj and name CA" index = 11 rmsd = 2.870 "obj and name CA" index = 12 rmsd = 2.006 "obj and name CA" index = 13 rmsd = 1.731 "obj and name CA" index = 14 rmsd = 1.035 "obj and name CA" index = 15 rmsd = 1.055 "obj and name CA" index = 16 rmsd = 1.168 "obj and name CA" index = 17 rmsd = 1.339 "obj and name CA" index = 18 rmsd = 1.660 "obj and name CA" index = 19 rmsd = 1.846 "obj and name CA" index = 20 rmsd = 2.429 "obj and name CA" index = 21 rmsd = 2.394 "obj and name CA" index = 22 rmsd = 2.891 "obj and name CA" index = 23 rmsd = 3.226 "obj and name CA" index = 24 rmsd = 2.983 "obj and name CA" index = 25 rmsd = 3.729 "obj and name CA" index = 26 rmsd = 2.539 "obj and name CA" index = 27 rmsd = 2.814 "obj and name CA" index = 28 rmsd = 2.103 "obj and name CA" index = 29 rmsd = 2.171 "obj and name CA" index = 30 rmsd = 1.690 "obj and name CA" index = 31 rmsd = 1.172 "obj and name CA" index = 32 rmsd = 1.123 "obj and name CA" index = 33 rmsd = 1.402 "obj and name CA" index = 34 rmsd = 1.599 "obj and name CA" index = 35 rmsd = 2.518 "obj and name CA" index = 36 rmsd = 2.785 "obj and name CA" index = 37 rmsd = 2.856 "obj and name CA" index = 38 rmsd = 2.503 "obj and name CA" index = 39 rmsd = 2.470 "obj and name CA" index = 40 rmsd = 2.681 "obj and name CA" index = 41 rmsd = 2.702 "obj and name CA" index = 42 rmsd = 2.248 "obj and name CA" index = 43 rmsd = 2.181 "obj and name CA" index = 44 rmsd = 2.221 "obj and name CA" index = 45 rmsd = 1.652 "obj and name CA" index = 46 rmsd = 1.247 "obj and name CA" index = 47 rmsd = 1.982 "obj and name CA" index = 48 rmsd = 2.096 "obj and name CA" index = 49 rmsd = 2.424 "obj and name CA" index = 50 rmsd = 2.039 "obj and name CA" index = 51 rmsd = 1.154 "obj and name CA" index = 52 rmsd = 1.142 "obj and name CA" index = 53 rmsd = 0.866 "obj and name CA" index = 54 rmsd = 0.848 "obj and name CA" index = 55 rmsd = 1.077 "obj and name CA" index = 56 rmsd = 1.169 "obj and name CA" index = 57 rmsd = 1.249 "obj and name CA" index = 58 rmsd = 1.550 "obj and name CA" index = 59 rmsd = 1.525 "obj and name CA" index = 60 rmsd = 1.259 "obj and name CA" index = 61 rmsd = 1.096 "obj and name CA" index = 62 rmsd = 0.882 "obj and name CA" index = 63 rmsd = 0.746 "obj and name CA" index = 64 rmsd = 0.978 "obj and name CA" index = 65 rmsd = 1.122 "obj and name CA" index = 66 rmsd = 1.642 "obj and name CA" index = 67 rmsd = 2.042 "obj and name CA" index = 68 rmsd = 2.670 "obj and name CA" index = 69 rmsd = 1.341 "obj and name CA" index = 70 rmsd = 1.765 "obj and name CA" index = 71 rmsd = 1.747 "obj and name CA" index = 72 rmsd = 2.305 "obj and name CA" index = 73 rmsd = 2.148 "obj and name CA" index = 74 rmsd = 1.673 "obj and name CA" index = 75 rmsd = 1.700 "obj and name CA" index = 76 rmsd = 1.944 "obj and name CA" index = 77 rmsd = 1.709 "obj and name CA" index = 78 rmsd = 1.450 "obj and name CA" index = 79 rmsd = 1.704 "obj and name CA" index = 80 rmsd = 2.105 "obj and name CA" index = 81 rmsd = 2.077 "obj and name CA" index = 82 rmsd = 2.419 "obj and name CA" index = 83 rmsd = 2.363 "obj and name CA" index = 84 rmsd = 1.705 "obj and name CA" index = 85 rmsd = 2.387 "obj and name CA" index = 86 rmsd = 4.297 "obj and name CA" index = 87 rmsd = 5.006 "obj and name CA" index = 88 rmsd = 6.864 "obj and name CA" index = 89 rmsd = 8.681 "obj and name CA" index = 90 rmsd = 10.568 "obj and name CA" index = 91 rmsd = 12.039 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 48 atoms. PyMOL>color cyan,ss s Executive: Colored 51 atoms. PyMOL>color gray,ss ""+l Executive: Colored 2887 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: 1.32 sec. = 2731.9 frames/hour (4.96 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit