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 16 atoms. PyMOL>color cyan,ss s Executive: Colored 27 atoms. PyMOL>color gray,ss ""+l Executive: Colored 1355 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: 0.92 sec. = 3892.3 frames/hour (0.92 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 258 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 258 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: 2.83 sec. = 1274.0 frames/hour (3.75 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, 3.4316074848175049, 1.4268629550933838, 1.719139575958252, 1.1665294170379639, 1.4509878158569336, 1.837870717048645, 1.2183773517608643, 4.45562744140625, 4.1046218872070312, 1.7722855806350708, 4.4759325981140137, 3.310197114944458, 5.6180529594421387, 1.9617218971252441, 4.425757884979248, 1.1853369474411011, 1.6061708927154541, 5.2215108871459961, 3.599076509475708] -> atom index_map = [None, 2, 21, 38, 52, 74, 85, 99, 116, 138, 152, 171, 187, 211, 227, 247, 266, 280, 294, 316, 333, 357, 371, 387, 403, 417, 427, 451, 462, 469, 485, 499, 515, 539, 551, 562, 581, 603, 625, 635, 654, 671, 688, 712, 719, 738, 757, 771, 786, 797, 808, 818, 834, 855, 879, 898, 915, 927, 934, 949, 971, 993, 1007, 1026, 1033, 1057, 1069, 1083, 1095, 1114, 1125, 1149, 1168, 1182, 1189, 1204, 1219, 1238, 1255, 1271, 1286, 1302, 1321, 1336, 1350, 1366, 1380] "obj and name CA" index = 1 rmsd = 13.044 "obj and name CA" index = 2 rmsd = 10.461 "obj and name CA" index = 3 rmsd = 8.296 "obj and name CA" index = 4 rmsd = 6.377 "obj and name CA" index = 5 rmsd = 4.159 "obj and name CA" index = 6 rmsd = 2.634 "obj and name CA" index = 7 rmsd = 1.481 "obj and name CA" index = 8 rmsd = 1.589 "obj and name CA" index = 9 rmsd = 1.554 "obj and name CA" index = 10 rmsd = 1.460 "obj and name CA" index = 11 rmsd = 1.291 "obj and name CA" index = 12 rmsd = 1.307 "obj and name CA" index = 13 rmsd = 0.964 "obj and name CA" index = 14 rmsd = 0.863 "obj and name CA" index = 15 rmsd = 0.691 "obj and name CA" index = 16 rmsd = 0.708 "obj and name CA" index = 17 rmsd = 0.921 "obj and name CA" index = 18 rmsd = 1.132 "obj and name CA" index = 19 rmsd = 1.203 "obj and name CA" index = 20 rmsd = 1.291 "obj and name CA" index = 21 rmsd = 1.330 "obj and name CA" index = 22 rmsd = 1.337 "obj and name CA" index = 23 rmsd = 1.204 "obj and name CA" index = 24 rmsd = 1.255 "obj and name CA" index = 25 rmsd = 1.232 "obj and name CA" index = 26 rmsd = 1.125 "obj and name CA" index = 27 rmsd = 1.078 "obj and name CA" index = 28 rmsd = 0.872 "obj and name CA" index = 29 rmsd = 0.734 "obj and name CA" index = 30 rmsd = 0.621 "obj and name CA" index = 31 rmsd = 0.603 "obj and name CA" index = 32 rmsd = 0.484 "obj and name CA" index = 33 rmsd = 0.608 "obj and name CA" index = 34 rmsd = 0.789 "obj and name CA" index = 35 rmsd = 0.685 "obj and name CA" index = 36 rmsd = 0.846 "obj and name CA" index = 37 rmsd = 1.020 "obj and name CA" index = 38 rmsd = 1.009 "obj and name CA" index = 39 rmsd = 0.981 "obj and name CA" index = 40 rmsd = 1.100 "obj and name CA" index = 41 rmsd = 1.408 "obj and name CA" index = 42 rmsd = 1.321 "obj and name CA" index = 43 rmsd = 1.333 "obj and name CA" index = 44 rmsd = 1.039 "obj and name CA" index = 45 rmsd = 1.039 "obj and name CA" index = 46 rmsd = 0.951 "obj and name CA" index = 47 rmsd = 1.220 "obj and name CA" index = 48 rmsd = 1.091 "obj and name CA" index = 49 rmsd = 0.708 "obj and name CA" index = 50 rmsd = 0.673 "obj and name CA" index = 51 rmsd = 0.658 "obj and name CA" index = 52 rmsd = 1.018 "obj and name CA" index = 53 rmsd = 1.315 "obj and name CA" index = 54 rmsd = 1.588 "obj and name CA" index = 55 rmsd = 2.013 "obj and name CA" index = 56 rmsd = 2.339 "obj and name CA" index = 57 rmsd = 2.106 "obj and name CA" index = 58 rmsd = 1.972 "obj and name CA" index = 59 rmsd = 1.612 "obj and name CA" index = 60 rmsd = 1.572 "obj and name CA" index = 61 rmsd = 1.281 "obj and name CA" index = 62 rmsd = 1.018 "obj and name CA" index = 63 rmsd = 0.860 "obj and name CA" index = 64 rmsd = 0.582 "obj and name CA" index = 65 rmsd = 0.654 "obj and name CA" index = 66 rmsd = 0.802 "obj and name CA" index = 67 rmsd = 0.856 "obj and name CA" index = 68 rmsd = 0.925 "obj and name CA" index = 69 rmsd = 1.196 "obj and name CA" index = 70 rmsd = 1.302 "obj and name CA" index = 71 rmsd = 1.319 "obj and name CA" index = 72 rmsd = 1.494 "obj and name CA" index = 73 rmsd = 1.708 "obj and name CA" index = 74 rmsd = 1.539 "obj and name CA" index = 75 rmsd = 1.370 "obj and name CA" index = 76 rmsd = 0.991 "obj and name CA" index = 77 rmsd = 0.763 "obj and name CA" index = 78 rmsd = 0.516 "obj and name CA" index = 79 rmsd = 0.624 "obj and name CA" index = 80 rmsd = 0.798 "obj and name CA" index = 81 rmsd = 0.938 "obj and name CA" index = 82 rmsd = 1.223 "obj and name CA" index = 83 rmsd = 1.795 "obj and name CA" index = 84 rmsd = 2.333 "obj and name CA" index = 85 rmsd = 3.781 "obj and name CA" index = 86 rmsd = 4.932 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 81 atoms. PyMOL>color gray,ss ""+l Executive: Colored 2753 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: 1.53 sec. = 2360.2 frames/hour (5.28 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit