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 3 atoms.
PyMOL>color cyan,ss s
 Executive: Colored 27 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 1042 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. = 4606.1 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 198 atoms.
PyMOL>hide everything,all
PyMOL>show lines,bb
PyMOL>color blue,bb
 Executive: Colored 198 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: 2.14 sec. = 1682.5 frames/hour (2.92 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 "<string>", 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, 3.8981950283050537, 3.8920872211456299, 6.9681501388549805, 2.9829285144805908, 2.7612190246582031, 7.0948276519775391, 4.1529760360717773, 3.1539433002471924, 1.9158097505569458, 3.004486083984375, 3.0785825252532959, 7.5398654937744141, 4.3782100677490234, 5.6542854309082031, 2.2200736999511719, 3.9625065326690674, 4.2390985488891602, 6.0004839897155762, 4.6546025276184082]
-> atom index_map =  [None, 2, 21, 40, 60, 74, 81, 91, 105, 121, 145, 161, 175, 189, 205, 217, 229, 243, 264, 285, 309, 329, 344, 351, 370, 386, 403, 427, 443, 454, 466, 473, 495, 505, 515, 531, 550, 570, 585, 599, 606, 620, 644, 656, 678, 697, 713, 727, 747, 771, 790, 801, 816, 835, 850, 860, 876, 898, 912, 931, 950, 965, 982, 999, 1016, 1033, 1050]
"obj and name CA" index = 1
rmsd = 3.868
"obj and name CA" index = 2
rmsd = 2.625
"obj and name CA" index = 3
rmsd = 2.562
"obj and name CA" index = 4
rmsd = 2.301
"obj and name CA" index = 5
rmsd = 2.880
"obj and name CA" index = 6
rmsd = 2.813
"obj and name CA" index = 7
rmsd = 2.696
"obj and name CA" index = 8
rmsd = 1.986
"obj and name CA" index = 9
rmsd = 1.699
"obj and name CA" index = 10
rmsd = 0.864
"obj and name CA" index = 11
rmsd = 1.514
"obj and name CA" index = 12
rmsd = 1.698
"obj and name CA" index = 13
rmsd = 2.054
"obj and name CA" index = 14
rmsd = 2.548
"obj and name CA" index = 15
rmsd = 1.932
"obj and name CA" index = 16
rmsd = 1.917
"obj and name CA" index = 17
rmsd = 1.366
"obj and name CA" index = 18
rmsd = 1.226
"obj and name CA" index = 19
rmsd = 1.879
"obj and name CA" index = 20
rmsd = 1.896
"obj and name CA" index = 21
rmsd = 2.135
"obj and name CA" index = 22
rmsd = 2.041
"obj and name CA" index = 23
rmsd = 2.228
"obj and name CA" index = 24
rmsd = 1.651
"obj and name CA" index = 25
rmsd = 1.878
"obj and name CA" index = 26
rmsd = 1.740
"obj and name CA" index = 27
rmsd = 1.824
"obj and name CA" index = 28
rmsd = 2.361
"obj and name CA" index = 29
rmsd = 3.351
"obj and name CA" index = 30
rmsd = 2.874
"obj and name CA" index = 31
rmsd = 2.068
"obj and name CA" index = 32
rmsd = 1.322
"obj and name CA" index = 33
rmsd = 1.235
"obj and name CA" index = 34
rmsd = 1.148
"obj and name CA" index = 35
rmsd = 1.984
"obj and name CA" index = 36
rmsd = 2.381
"obj and name CA" index = 37
rmsd = 3.321
"obj and name CA" index = 38
rmsd = 4.132
"obj and name CA" index = 39
rmsd = 5.056
"obj and name CA" index = 40
rmsd = 5.181
"obj and name CA" index = 41
rmsd = 4.274
"obj and name CA" index = 42
rmsd = 3.485
"obj and name CA" index = 43
rmsd = 2.859
"obj and name CA" index = 44
rmsd = 2.211
"obj and name CA" index = 45
rmsd = 1.771
"obj and name CA" index = 46
rmsd = 1.565
"obj and name CA" index = 47
rmsd = 1.399
"obj and name CA" index = 48
rmsd = 2.023
"obj and name CA" index = 49
rmsd = 2.099
"obj and name CA" index = 50
rmsd = 2.584
"obj and name CA" index = 51
rmsd = 1.819
"obj and name CA" index = 52
rmsd = 1.505
"obj and name CA" index = 53
rmsd = 2.275
"obj and name CA" index = 54
rmsd = 2.778
"obj and name CA" index = 55
rmsd = 3.343
"obj and name CA" index = 56
rmsd = 3.759
"obj and name CA" index = 57
rmsd = 3.290
"obj and name CA" index = 58
rmsd = 3.775
"obj and name CA" index = 59
rmsd = 4.716
"obj and name CA" index = 60
rmsd = 5.338
"obj and name CA" index = 61
rmsd = 5.331
"obj and name CA" index = 62
rmsd = 5.912
"obj and name CA" index = 63
rmsd = 7.134
"obj and name CA" index = 64
rmsd = 8.896
"obj and name CA" index = 65
rmsd = 10.395
"obj and name CA" index = 66
rmsd = 12.500
PyMOL>cartoon putty, yesfit_ALL and name CA
PyMOL>show cartoon, yesfit_ALL and name CA
PyMOL>color red, ss h
 Executive: Colored 9 atoms.
PyMOL>color cyan,ss s
 Executive: Colored 81 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 2114 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: 1.08 sec. = 3321.0 frames/hour (4.01 sec. accum.).
PyMOL>png sausage.png
 ScenePNG: wrote 600x600 pixel image to file "sausage.png".
PyMOL>quit