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 13 atoms.
PyMOL>color cyan,ss s
 Executive: Colored 8 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 1159 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: 0.87 sec. = 4147.9 frames/hour (0.87 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: 3.32 sec. = 1083.3 frames/hour (4.19 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, 7.9299459457397461, 5.5783162117004395, 3.7137749195098877, 6.0682353973388672, 2.5179030895233154, 8.1092433929443359, 10.849311828613281, 3.8567194938659668, 4.9888663291931152, 7.1469302177429199, 2.9696896076202393, 10.213878631591797, 4.2567520141601562, 6.682828426361084, 7.9494242668151855, 6.5981621742248535, 4.0334987640380859, 4.9455356597900391, 6.4169769287109375]
-> atom index_map =  [None, 2, 21, 35, 54, 68, 84, 98, 105, 127, 141, 152, 166, 182, 194, 201, 211, 226, 237, 256, 270, 286, 300, 315, 334, 353, 364, 374, 393, 415, 431, 441, 458, 468, 483, 504, 520, 534, 550, 565, 584, 598, 605, 620, 636, 655, 670, 694, 709, 719, 739, 751, 761, 775, 789, 805, 827, 839, 846, 858, 868, 884, 899, 919, 938, 959, 979, 996, 1003, 1010, 1017, 1039, 1058, 1073, 1090, 1107, 1124, 1141, 1158]
"obj and name CA" index = 1
rmsd = 3.923
"obj and name CA" index = 2
rmsd = 3.928
"obj and name CA" index = 3
rmsd = 3.272
"obj and name CA" index = 4
rmsd = 3.541
"obj and name CA" index = 5
rmsd = 3.583
"obj and name CA" index = 6
rmsd = 3.886
"obj and name CA" index = 7
rmsd = 4.331
"obj and name CA" index = 8
rmsd = 4.773
"obj and name CA" index = 9
rmsd = 4.616
"obj and name CA" index = 10
rmsd = 4.728
"obj and name CA" index = 11
rmsd = 4.655
"obj and name CA" index = 12
rmsd = 4.270
"obj and name CA" index = 13
rmsd = 5.180
"obj and name CA" index = 14
rmsd = 5.297
"obj and name CA" index = 15
rmsd = 4.457
"obj and name CA" index = 16
rmsd = 3.898
"obj and name CA" index = 17
rmsd = 3.004
"obj and name CA" index = 18
rmsd = 2.544
"obj and name CA" index = 19
rmsd = 1.945
"obj and name CA" index = 20
rmsd = 1.475
"obj and name CA" index = 21
rmsd = 2.028
"obj and name CA" index = 22
rmsd = 2.513
"obj and name CA" index = 23
rmsd = 2.377
"obj and name CA" index = 24
rmsd = 2.407
"obj and name CA" index = 25
rmsd = 3.033
"obj and name CA" index = 26
rmsd = 3.431
"obj and name CA" index = 27
rmsd = 3.346
"obj and name CA" index = 28
rmsd = 3.543
"obj and name CA" index = 29
rmsd = 3.045
"obj and name CA" index = 30
rmsd = 3.303
"obj and name CA" index = 31
rmsd = 2.806
"obj and name CA" index = 32
rmsd = 2.846
"obj and name CA" index = 33
rmsd = 3.062
"obj and name CA" index = 34
rmsd = 2.694
"obj and name CA" index = 35
rmsd = 2.158
"obj and name CA" index = 36
rmsd = 1.910
"obj and name CA" index = 37
rmsd = 1.612
"obj and name CA" index = 38
rmsd = 1.829
"obj and name CA" index = 39
rmsd = 1.630
"obj and name CA" index = 40
rmsd = 2.280
"obj and name CA" index = 41
rmsd = 2.662
"obj and name CA" index = 42
rmsd = 2.292
"obj and name CA" index = 43
rmsd = 2.087
"obj and name CA" index = 44
rmsd = 1.664
"obj and name CA" index = 45
rmsd = 2.252
"obj and name CA" index = 46
rmsd = 2.387
"obj and name CA" index = 47
rmsd = 2.857
"obj and name CA" index = 48
rmsd = 2.187
"obj and name CA" index = 49
rmsd = 1.621
"obj and name CA" index = 50
rmsd = 2.331
"obj and name CA" index = 51
rmsd = 2.563
"obj and name CA" index = 52
rmsd = 1.689
"obj and name CA" index = 53
rmsd = 1.689
"obj and name CA" index = 54
rmsd = 1.703
"obj and name CA" index = 55
rmsd = 2.414
"obj and name CA" index = 56
rmsd = 3.018
"obj and name CA" index = 57
rmsd = 3.099
"obj and name CA" index = 58
rmsd = 2.394
"obj and name CA" index = 59
rmsd = 2.537
"obj and name CA" index = 60
rmsd = 2.113
"obj and name CA" index = 61
rmsd = 2.276
"obj and name CA" index = 62
rmsd = 2.392
"obj and name CA" index = 63
rmsd = 2.837
"obj and name CA" index = 64
rmsd = 3.298
"obj and name CA" index = 65
rmsd = 2.920
"obj and name CA" index = 66
rmsd = 4.387
"obj and name CA" index = 67
rmsd = 5.328
"obj and name CA" index = 68
rmsd = 6.224
"obj and name CA" index = 69
rmsd = 7.222
"obj and name CA" index = 70
rmsd = 7.362
"obj and name CA" index = 71
rmsd = 7.873
"obj and name CA" index = 72
rmsd = 8.425
"obj and name CA" index = 73
rmsd = 10.074
"obj and name CA" index = 74
rmsd = 11.100
"obj and name CA" index = 75
rmsd = 12.586
"obj and name CA" index = 76
rmsd = 14.586
"obj and name CA" index = 77
rmsd = 15.924
"obj and name CA" index = 78
rmsd = 18.314
PyMOL>cartoon putty, yesfit_ALL and name CA
PyMOL>show cartoon, yesfit_ALL and name CA
PyMOL>color red, ss h
 Executive: Colored 39 atoms.
PyMOL>color cyan,ss s
 Executive: Colored 24 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 2369 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. = 2325.6 frames/hour (5.74 sec. accum.).
PyMOL>png sausage.png
 ScenePNG: wrote 600x600 pixel image to file "sausage.png".
PyMOL>quit