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 19 atoms. PyMOL>color cyan,ss s Executive: Colored 17 atoms. PyMOL>color gray,ss ""+l Executive: Colored 1414 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: 1.11 sec. = 3231.4 frames/hour (1.11 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: 2.54 sec. = 1414.9 frames/hour (3.66 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, 3.15972900390625, 3.023855447769165, 4.2269730567932129, 3.5492086410522461, 5.0812058448791504, 3.9769895076751709, 4.1201953887939453, 2.4102611541748047, 5.6456866264343262] -> 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 = 1.951 "obj and name CA" index = 2 rmsd = 2.032 "obj and name CA" index = 3 rmsd = 1.640 "obj and name CA" index = 4 rmsd = 1.739 "obj and name CA" index = 5 rmsd = 1.686 "obj and name CA" index = 6 rmsd = 1.555 "obj and name CA" index = 7 rmsd = 1.602 "obj and name CA" index = 8 rmsd = 2.015 "obj and name CA" index = 9 rmsd = 2.763 "obj and name CA" index = 10 rmsd = 3.882 "obj and name CA" index = 11 rmsd = 3.175 "obj and name CA" index = 12 rmsd = 0.940 "obj and name CA" index = 13 rmsd = 0.759 "obj and name CA" index = 14 rmsd = 0.626 "obj and name CA" index = 15 rmsd = 0.782 "obj and name CA" index = 16 rmsd = 0.951 "obj and name CA" index = 17 rmsd = 1.164 "obj and name CA" index = 18 rmsd = 1.429 "obj and name CA" index = 19 rmsd = 1.503 "obj and name CA" index = 20 rmsd = 2.182 "obj and name CA" index = 21 rmsd = 2.462 "obj and name CA" index = 22 rmsd = 3.467 "obj and name CA" index = 23 rmsd = 4.025 "obj and name CA" index = 24 rmsd = 3.806 "obj and name CA" index = 25 rmsd = 3.769 "obj and name CA" index = 26 rmsd = 2.166 "obj and name CA" index = 27 rmsd = 2.108 "obj and name CA" index = 28 rmsd = 1.572 "obj and name CA" index = 29 rmsd = 1.356 "obj and name CA" index = 30 rmsd = 1.229 "obj and name CA" index = 31 rmsd = 1.000 "obj and name CA" index = 32 rmsd = 1.013 "obj and name CA" index = 33 rmsd = 1.291 "obj and name CA" index = 34 rmsd = 1.137 "obj and name CA" index = 35 rmsd = 1.692 "obj and name CA" index = 36 rmsd = 1.879 "obj and name CA" index = 37 rmsd = 1.997 "obj and name CA" index = 38 rmsd = 1.552 "obj and name CA" index = 39 rmsd = 1.400 "obj and name CA" index = 40 rmsd = 1.194 "obj and name CA" index = 41 rmsd = 1.439 "obj and name CA" index = 42 rmsd = 1.178 "obj and name CA" index = 43 rmsd = 0.972 "obj and name CA" index = 44 rmsd = 1.169 "obj and name CA" index = 45 rmsd = 0.977 "obj and name CA" index = 46 rmsd = 0.765 "obj and name CA" index = 47 rmsd = 1.246 "obj and name CA" index = 48 rmsd = 1.437 "obj and name CA" index = 49 rmsd = 1.728 "obj and name CA" index = 50 rmsd = 1.262 "obj and name CA" index = 51 rmsd = 0.669 "obj and name CA" index = 52 rmsd = 0.750 "obj and name CA" index = 53 rmsd = 0.734 "obj and name CA" index = 54 rmsd = 0.754 "obj and name CA" index = 55 rmsd = 0.985 "obj and name CA" index = 56 rmsd = 1.228 "obj and name CA" index = 57 rmsd = 1.469 "obj and name CA" index = 58 rmsd = 1.934 "obj and name CA" index = 59 rmsd = 1.897 "obj and name CA" index = 60 rmsd = 1.353 "obj and name CA" index = 61 rmsd = 1.025 "obj and name CA" index = 62 rmsd = 0.785 "obj and name CA" index = 63 rmsd = 0.581 "obj and name CA" index = 64 rmsd = 0.556 "obj and name CA" index = 65 rmsd = 0.759 "obj and name CA" index = 66 rmsd = 1.076 "obj and name CA" index = 67 rmsd = 1.486 "obj and name CA" index = 68 rmsd = 2.108 "obj and name CA" index = 69 rmsd = 1.355 "obj and name CA" index = 70 rmsd = 1.489 "obj and name CA" index = 71 rmsd = 1.270 "obj and name CA" index = 72 rmsd = 1.593 "obj and name CA" index = 73 rmsd = 1.566 "obj and name CA" index = 74 rmsd = 1.086 "obj and name CA" index = 75 rmsd = 1.147 "obj and name CA" index = 76 rmsd = 1.529 "obj and name CA" index = 77 rmsd = 1.213 "obj and name CA" index = 78 rmsd = 1.005 "obj and name CA" index = 79 rmsd = 1.365 "obj and name CA" index = 80 rmsd = 1.451 "obj and name CA" index = 81 rmsd = 1.363 "obj and name CA" index = 82 rmsd = 1.520 "obj and name CA" index = 83 rmsd = 1.588 "obj and name CA" index = 84 rmsd = 1.271 "obj and name CA" index = 85 rmsd = 2.421 "obj and name CA" index = 86 rmsd = 4.422 "obj and name CA" index = 87 rmsd = 5.793 "obj and name CA" index = 88 rmsd = 7.499 "obj and name CA" index = 89 rmsd = 9.354 "obj and name CA" index = 90 rmsd = 11.181 "obj and name CA" index = 91 rmsd = 12.739 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 57 atoms. PyMOL>color cyan,ss s Executive: Colored 51 atoms. PyMOL>color gray,ss ""+l Executive: Colored 2877 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: 1.55 sec. = 2318.5 frames/hour (5.21 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit