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
PyMOL>color cyan,ss s
 Executive: Colored 27 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 1045 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: 0.83 sec. = 4328.9 frames/hour (0.83 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: 2.08 sec. = 1731.0 frames/hour (2.91 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, 4.9642210006713867, 2.2093448638916016, 3.1050593852996826, 3.1353201866149902, 3.0811054706573486, 5.9168052673339844, 2.0421993732452393, 6.0174393653869629, 5.1010122299194336, 5.1227736473083496, 4.1660423278808594, 2.9570860862731934, 3.49607253074646, 3.0039918422698975, 5.6578783988952637, 3.7293877601623535, 4.0268850326538086, 5.0283260345458984, 4.4582500457763672]
-> 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 = 3.497
"obj and name CA" index = 2
rmsd = 2.484
"obj and name CA" index = 3
rmsd = 2.588
"obj and name CA" index = 4
rmsd = 2.443
"obj and name CA" index = 5
rmsd = 2.889
"obj and name CA" index = 6
rmsd = 2.706
"obj and name CA" index = 7
rmsd = 2.358
"obj and name CA" index = 8
rmsd = 1.689
"obj and name CA" index = 9
rmsd = 1.356
"obj and name CA" index = 10
rmsd = 0.807
"obj and name CA" index = 11
rmsd = 1.414
"obj and name CA" index = 12
rmsd = 1.633
"obj and name CA" index = 13
rmsd = 2.001
"obj and name CA" index = 14
rmsd = 2.382
"obj and name CA" index = 15
rmsd = 1.828
"obj and name CA" index = 16
rmsd = 1.809
"obj and name CA" index = 17
rmsd = 1.141
"obj and name CA" index = 18
rmsd = 1.249
"obj and name CA" index = 19
rmsd = 1.490
"obj and name CA" index = 20
rmsd = 1.366
"obj and name CA" index = 21
rmsd = 1.604
"obj and name CA" index = 22
rmsd = 1.575
"obj and name CA" index = 23
rmsd = 1.923
"obj and name CA" index = 24
rmsd = 1.623
"obj and name CA" index = 25
rmsd = 1.831
"obj and name CA" index = 26
rmsd = 1.761
"obj and name CA" index = 27
rmsd = 1.781
"obj and name CA" index = 28
rmsd = 2.040
"obj and name CA" index = 29
rmsd = 2.664
"obj and name CA" index = 30
rmsd = 2.308
"obj and name CA" index = 31
rmsd = 1.668
"obj and name CA" index = 32
rmsd = 1.202
"obj and name CA" index = 33
rmsd = 1.041
"obj and name CA" index = 34
rmsd = 0.925
"obj and name CA" index = 35
rmsd = 1.554
"obj and name CA" index = 36
rmsd = 1.833
"obj and name CA" index = 37
rmsd = 2.745
"obj and name CA" index = 38
rmsd = 3.393
"obj and name CA" index = 39
rmsd = 4.193
"obj and name CA" index = 40
rmsd = 4.370
"obj and name CA" index = 41
rmsd = 3.566
"obj and name CA" index = 42
rmsd = 2.804
"obj and name CA" index = 43
rmsd = 2.253
"obj and name CA" index = 44
rmsd = 1.705
"obj and name CA" index = 45
rmsd = 1.340
"obj and name CA" index = 46
rmsd = 1.190
"obj and name CA" index = 47
rmsd = 1.118
"obj and name CA" index = 48
rmsd = 1.628
"obj and name CA" index = 49
rmsd = 1.772
"obj and name CA" index = 50
rmsd = 2.167
"obj and name CA" index = 51
rmsd = 1.565
"obj and name CA" index = 52
rmsd = 1.349
"obj and name CA" index = 53
rmsd = 1.954
"obj and name CA" index = 54
rmsd = 2.430
"obj and name CA" index = 55
rmsd = 2.749
"obj and name CA" index = 56
rmsd = 3.188
"obj and name CA" index = 57
rmsd = 2.710
"obj and name CA" index = 58
rmsd = 3.305
"obj and name CA" index = 59
rmsd = 4.139
"obj and name CA" index = 60
rmsd = 4.273
"obj and name CA" index = 61
rmsd = 4.262
"obj and name CA" index = 62
rmsd = 5.172
"obj and name CA" index = 63
rmsd = 6.204
"obj and name CA" index = 64
rmsd = 8.085
"obj and name CA" index = 65
rmsd = 9.604
"obj and name CA" index = 66
rmsd = 11.717
PyMOL>cartoon putty, yesfit_ALL and name CA
PyMOL>show cartoon, yesfit_ALL and name CA
PyMOL>color red, ss h
PyMOL>color cyan,ss s
 Executive: Colored 81 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 2123 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: 1.28 sec. = 2807.9 frames/hour (4.19 sec. accum.).
PyMOL>png sausage.png
 ScenePNG: wrote 600x600 pixel image to file "sausage.png".
PyMOL>quit