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 29 atoms.
PyMOL>color cyan,ss s
 Executive: Colored 14 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 1154 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: 1.63 sec. = 2214.4 frames/hour (1.63 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 234 atoms.
PyMOL>hide everything,all
PyMOL>show lines,bb
PyMOL>color blue,bb
 Executive: Colored 234 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: 6.35 sec. = 566.8 frames/hour (7.98 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, 0.97788596153259277, 1.356626033782959, 3.0065097808837891, 2.7810626029968262, 2.3767285346984863, 2.4697630405426025, 2.9641237258911133, 1.174715518951416, 1.1326178312301636, 2.4198908805847168, 2.6372079849243164, 1.5661702156066895, 3.0785987377166748, 1.244731068611145, 2.0911929607391357, 1.350609302520752, 2.0663938522338867, 2.1661472320556641, 3.1692187786102295]
-> atom index_map =  [None, 2, 21, 31, 50, 64, 83, 104, 121, 145, 157, 169, 180, 197, 216, 227, 239, 256, 266, 282, 297, 307, 326, 336, 353, 363, 387, 397, 404, 414, 434, 454, 465, 481, 501, 520, 532, 544, 556, 566, 576, 595, 610, 621, 631, 652, 659, 678, 702, 718, 732, 748, 767, 791, 803, 817, 834, 841, 865, 880, 899, 911, 935, 949, 969, 981, 991, 1005, 1029, 1048, 1072, 1082, 1106, 1125, 1137, 1147, 1157, 1171, 1188]
"obj and name CA" index = 1
rmsd = 1.843
"obj and name CA" index = 2
rmsd = 1.033
"obj and name CA" index = 3
rmsd = 0.676
"obj and name CA" index = 4
rmsd = 0.574
"obj and name CA" index = 5
rmsd = 0.470
"obj and name CA" index = 6
rmsd = 0.391
"obj and name CA" index = 7
rmsd = 0.486
"obj and name CA" index = 8
rmsd = 0.683
"obj and name CA" index = 9
rmsd = 1.239
"obj and name CA" index = 10
rmsd = 1.746
"obj and name CA" index = 11
rmsd = 1.555
"obj and name CA" index = 12
rmsd = 0.849
"obj and name CA" index = 13
rmsd = 0.455
"obj and name CA" index = 14
rmsd = 0.547
"obj and name CA" index = 15
rmsd = 0.501
"obj and name CA" index = 16
rmsd = 0.335
"obj and name CA" index = 17
rmsd = 0.286
"obj and name CA" index = 18
rmsd = 0.326
"obj and name CA" index = 19
rmsd = 0.336
"obj and name CA" index = 20
rmsd = 0.300
"obj and name CA" index = 21
rmsd = 0.348
"obj and name CA" index = 22
rmsd = 0.437
"obj and name CA" index = 23
rmsd = 0.450
"obj and name CA" index = 24
rmsd = 0.479
"obj and name CA" index = 25
rmsd = 0.589
"obj and name CA" index = 26
rmsd = 0.503
"obj and name CA" index = 27
rmsd = 0.627
"obj and name CA" index = 28
rmsd = 0.700
"obj and name CA" index = 29
rmsd = 0.662
"obj and name CA" index = 30
rmsd = 0.712
"obj and name CA" index = 31
rmsd = 0.646
"obj and name CA" index = 32
rmsd = 0.518
"obj and name CA" index = 33
rmsd = 0.498
"obj and name CA" index = 34
rmsd = 0.467
"obj and name CA" index = 35
rmsd = 0.765
"obj and name CA" index = 36
rmsd = 1.249
"obj and name CA" index = 37
rmsd = 0.950
"obj and name CA" index = 38
rmsd = 0.969
"obj and name CA" index = 39
rmsd = 1.164
"obj and name CA" index = 40
rmsd = 0.799
"obj and name CA" index = 41
rmsd = 0.683
"obj and name CA" index = 42
rmsd = 1.104
"obj and name CA" index = 43
rmsd = 1.083
"obj and name CA" index = 44
rmsd = 0.696
"obj and name CA" index = 45
rmsd = 0.863
"obj and name CA" index = 46
rmsd = 0.928
"obj and name CA" index = 47
rmsd = 0.576
"obj and name CA" index = 48
rmsd = 0.349
"obj and name CA" index = 49
rmsd = 0.478
"obj and name CA" index = 50
rmsd = 0.421
"obj and name CA" index = 51
rmsd = 0.422
"obj and name CA" index = 52
rmsd = 0.626
"obj and name CA" index = 53
rmsd = 0.733
"obj and name CA" index = 54
rmsd = 0.979
"obj and name CA" index = 55
rmsd = 1.123
"obj and name CA" index = 56
rmsd = 2.119
"obj and name CA" index = 57
rmsd = 0.923
"obj and name CA" index = 58
rmsd = 0.727
"obj and name CA" index = 59
rmsd = 0.512
"obj and name CA" index = 60
rmsd = 0.540
"obj and name CA" index = 61
rmsd = 0.462
"obj and name CA" index = 62
rmsd = 0.550
"obj and name CA" index = 63
rmsd = 0.443
"obj and name CA" index = 64
rmsd = 0.435
"obj and name CA" index = 65
rmsd = 0.438
"obj and name CA" index = 66
rmsd = 0.550
"obj and name CA" index = 67
rmsd = 0.494
"obj and name CA" index = 68
rmsd = 0.396
"obj and name CA" index = 69
rmsd = 0.536
"obj and name CA" index = 70
rmsd = 0.547
"obj and name CA" index = 71
rmsd = 0.448
"obj and name CA" index = 72
rmsd = 0.505
"obj and name CA" index = 73
rmsd = 0.593
"obj and name CA" index = 74
rmsd = 0.665
"obj and name CA" index = 75
rmsd = 1.079
"obj and name CA" index = 76
rmsd = 2.821
"obj and name CA" index = 77
rmsd = 5.445
"obj and name CA" index = 78
rmsd = 7.808
PyMOL>cartoon putty, yesfit_ALL and name CA
PyMOL>show cartoon, yesfit_ALL and name CA
PyMOL>color red, ss h
 Executive: Colored 87 atoms.
PyMOL>color cyan,ss s
 Executive: Colored 42 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 2343 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: 1.84 sec. = 1961.1 frames/hour (9.81 sec. accum.).
PyMOL>png sausage.png
 ScenePNG: wrote 600x600 pixel image to file "sausage.png".
PyMOL>quit