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 11 atoms.
PyMOL>color cyan,ss s
 Executive: Colored 11 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 1158 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: 0.91 sec. = 3977.6 frames/hour (0.91 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: 3.06 sec. = 1174.6 frames/hour (3.97 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, 9.4132852554321289, 4.9170575141906738, 7.8488106727600098, 10.724580764770508, 7.9377059936523438, 9.1530818939208984, 5.4799904823303223, 10.119659423828125, 9.5130405426025391, 6.0827922821044922, 6.2604570388793945, 4.3370189666748047, 8.9537229537963867, 8.6748313903808594, 10.319679260253906, 11.113731384277344, 7.4476127624511719, 8.2649192810058594, 8.0059242248535156]
-> 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 = 3.525
"obj and name CA" index = 2
rmsd = 3.403
"obj and name CA" index = 3
rmsd = 2.831
"obj and name CA" index = 4
rmsd = 3.297
"obj and name CA" index = 5
rmsd = 3.478
"obj and name CA" index = 6
rmsd = 4.335
"obj and name CA" index = 7
rmsd = 4.658
"obj and name CA" index = 8
rmsd = 4.724
"obj and name CA" index = 9
rmsd = 4.297
"obj and name CA" index = 10
rmsd = 3.892
"obj and name CA" index = 11
rmsd = 3.832
"obj and name CA" index = 12
rmsd = 3.645
"obj and name CA" index = 13
rmsd = 4.553
"obj and name CA" index = 14
rmsd = 4.739
"obj and name CA" index = 15
rmsd = 4.165
"obj and name CA" index = 16
rmsd = 4.342
"obj and name CA" index = 17
rmsd = 3.286
"obj and name CA" index = 18
rmsd = 2.430
"obj and name CA" index = 19
rmsd = 1.758
"obj and name CA" index = 20
rmsd = 1.129
"obj and name CA" index = 21
rmsd = 1.797
"obj and name CA" index = 22
rmsd = 2.203
"obj and name CA" index = 23
rmsd = 1.857
"obj and name CA" index = 24
rmsd = 2.379
"obj and name CA" index = 25
rmsd = 2.917
"obj and name CA" index = 26
rmsd = 3.113
"obj and name CA" index = 27
rmsd = 3.429
"obj and name CA" index = 28
rmsd = 4.000
"obj and name CA" index = 29
rmsd = 3.871
"obj and name CA" index = 30
rmsd = 4.709
"obj and name CA" index = 31
rmsd = 4.486
"obj and name CA" index = 32
rmsd = 3.396
"obj and name CA" index = 33
rmsd = 3.554
"obj and name CA" index = 34
rmsd = 4.169
"obj and name CA" index = 35
rmsd = 3.624
"obj and name CA" index = 36
rmsd = 3.429
"obj and name CA" index = 37
rmsd = 2.707
"obj and name CA" index = 38
rmsd = 2.688
"obj and name CA" index = 39
rmsd = 2.109
"obj and name CA" index = 40
rmsd = 2.795
"obj and name CA" index = 41
rmsd = 3.471
"obj and name CA" index = 42
rmsd = 3.043
"obj and name CA" index = 43
rmsd = 3.085
"obj and name CA" index = 44
rmsd = 2.486
"obj and name CA" index = 45
rmsd = 2.981
"obj and name CA" index = 46
rmsd = 2.878
"obj and name CA" index = 47
rmsd = 2.820
"obj and name CA" index = 48
rmsd = 2.303
"obj and name CA" index = 49
rmsd = 1.707
"obj and name CA" index = 50
rmsd = 2.320
"obj and name CA" index = 51
rmsd = 2.714
"obj and name CA" index = 52
rmsd = 1.992
"obj and name CA" index = 53
rmsd = 2.146
"obj and name CA" index = 54
rmsd = 1.771
"obj and name CA" index = 55
rmsd = 2.707
"obj and name CA" index = 56
rmsd = 3.171
"obj and name CA" index = 57
rmsd = 3.218
"obj and name CA" index = 58
rmsd = 2.506
"obj and name CA" index = 59
rmsd = 2.643
"obj and name CA" index = 60
rmsd = 2.290
"obj and name CA" index = 61
rmsd = 3.174
"obj and name CA" index = 62
rmsd = 3.491
"obj and name CA" index = 63
rmsd = 4.291
"obj and name CA" index = 64
rmsd = 5.217
"obj and name CA" index = 65
rmsd = 4.649
"obj and name CA" index = 66
rmsd = 4.668
"obj and name CA" index = 67
rmsd = 5.001
"obj and name CA" index = 68
rmsd = 5.736
"obj and name CA" index = 69
rmsd = 6.922
"obj and name CA" index = 70
rmsd = 6.506
"obj and name CA" index = 71
rmsd = 7.307
"obj and name CA" index = 72
rmsd = 7.637
"obj and name CA" index = 73
rmsd = 8.759
"obj and name CA" index = 74
rmsd = 9.919
"obj and name CA" index = 75
rmsd = 12.045
"obj and name CA" index = 76
rmsd = 14.546
"obj and name CA" index = 77
rmsd = 16.308
"obj and name CA" index = 78
rmsd = 18.925
PyMOL>cartoon putty, yesfit_ALL and name CA
PyMOL>show cartoon, yesfit_ALL and name CA
PyMOL>color red, ss h
 Executive: Colored 33 atoms.
PyMOL>color cyan,ss s
 Executive: Colored 33 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 2366 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: 1.04 sec. = 3454.9 frames/hour (5.01 sec. accum.).
PyMOL>png sausage.png
 ScenePNG: wrote 600x600 pixel image to file "sausage.png".
PyMOL>quit