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 24 atoms.
PyMOL>color cyan,ss s
 Executive: Colored 20 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 1392 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: 1.14 sec. = 3155.1 frames/hour (1.14 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 273 atoms.
PyMOL>hide everything,all
PyMOL>show lines,bb
PyMOL>color blue,bb
 Executive: Colored 273 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: 3.25 sec. = 1109.0 frames/hour (4.39 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, 5.0216794013977051, 7.7547845840454102, 9.181788444519043, 6.4978199005126953, 6.1280403137207031, 5.309481143951416, 8.4342555999755859, 4.370448112487793, 6.4459662437438965, 7.0048961639404297, 4.7476253509521484, 4.0550384521484375, 7.7422542572021484, 4.7792110443115234, 4.7940006256103516, 5.05010986328125, 5.7657527923583984, 9.053624153137207, 7.8834528923034668]
-> atom index_map =  [None, 2, 21, 28, 45, 62, 79, 96, 113, 130, 141, 158, 175, 194, 208, 230, 247, 254, 276, 290, 304, 320, 337, 352, 371, 385, 400, 422, 446, 470, 477, 496, 518, 539, 554, 573, 592, 603, 618, 632, 639, 646, 657, 674, 686, 708, 732, 752, 768, 785, 800, 816, 831, 847, 859, 866, 883, 905, 925, 942, 949, 959, 966, 977, 991, 1013, 1035, 1051, 1061, 1083, 1093, 1114, 1124, 1134, 1153, 1163, 1173, 1192, 1207, 1229, 1248, 1268, 1282, 1294, 1308, 1322, 1341, 1351, 1370, 1382, 1392, 1406]
"obj and name CA" index = 1
rmsd = 15.216
"obj and name CA" index = 2
rmsd = 12.880
"obj and name CA" index = 3
rmsd = 11.639
"obj and name CA" index = 4
rmsd = 9.971
"obj and name CA" index = 5
rmsd = 8.149
"obj and name CA" index = 6
rmsd = 6.936
"obj and name CA" index = 7
rmsd = 5.508
"obj and name CA" index = 8
rmsd = 4.507
"obj and name CA" index = 9
rmsd = 3.205
"obj and name CA" index = 10
rmsd = 2.665
"obj and name CA" index = 11
rmsd = 2.110
"obj and name CA" index = 12
rmsd = 2.024
"obj and name CA" index = 13
rmsd = 2.098
"obj and name CA" index = 14
rmsd = 3.082
"obj and name CA" index = 15
rmsd = 3.415
"obj and name CA" index = 16
rmsd = 3.015
"obj and name CA" index = 17
rmsd = 2.491
"obj and name CA" index = 18
rmsd = 2.173
"obj and name CA" index = 19
rmsd = 1.643
"obj and name CA" index = 20
rmsd = 1.606
"obj and name CA" index = 21
rmsd = 2.128
"obj and name CA" index = 22
rmsd = 2.007
"obj and name CA" index = 23
rmsd = 1.727
"obj and name CA" index = 24
rmsd = 2.118
"obj and name CA" index = 25
rmsd = 2.461
"obj and name CA" index = 26
rmsd = 2.382
"obj and name CA" index = 27
rmsd = 2.451
"obj and name CA" index = 28
rmsd = 2.617
"obj and name CA" index = 29
rmsd = 2.573
"obj and name CA" index = 30
rmsd = 2.094
"obj and name CA" index = 31
rmsd = 2.044
"obj and name CA" index = 32
rmsd = 1.595
"obj and name CA" index = 33
rmsd = 1.651
"obj and name CA" index = 34
rmsd = 1.764
"obj and name CA" index = 35
rmsd = 2.034
"obj and name CA" index = 36
rmsd = 2.498
"obj and name CA" index = 37
rmsd = 2.901
"obj and name CA" index = 38
rmsd = 3.744
"obj and name CA" index = 39
rmsd = 4.763
"obj and name CA" index = 40
rmsd = 5.558
"obj and name CA" index = 41
rmsd = 5.515
"obj and name CA" index = 42
rmsd = 5.166
"obj and name CA" index = 43
rmsd = 4.610
"obj and name CA" index = 44
rmsd = 3.761
"obj and name CA" index = 45
rmsd = 3.222
"obj and name CA" index = 46
rmsd = 2.567
"obj and name CA" index = 47
rmsd = 2.116
"obj and name CA" index = 48
rmsd = 1.583
"obj and name CA" index = 49
rmsd = 1.485
"obj and name CA" index = 50
rmsd = 1.463
"obj and name CA" index = 51
rmsd = 1.946
"obj and name CA" index = 52
rmsd = 2.090
"obj and name CA" index = 53
rmsd = 2.871
"obj and name CA" index = 54
rmsd = 3.034
"obj and name CA" index = 55
rmsd = 2.669
"obj and name CA" index = 56
rmsd = 2.243
"obj and name CA" index = 57
rmsd = 1.925
"obj and name CA" index = 58
rmsd = 1.846
"obj and name CA" index = 59
rmsd = 1.859
"obj and name CA" index = 60
rmsd = 2.225
"obj and name CA" index = 61
rmsd = 2.625
"obj and name CA" index = 62
rmsd = 3.284
"obj and name CA" index = 63
rmsd = 3.010
"obj and name CA" index = 64
rmsd = 2.433
"obj and name CA" index = 65
rmsd = 2.453
"obj and name CA" index = 66
rmsd = 2.309
"obj and name CA" index = 67
rmsd = 1.865
"obj and name CA" index = 68
rmsd = 1.524
"obj and name CA" index = 69
rmsd = 1.605
"obj and name CA" index = 70
rmsd = 1.672
"obj and name CA" index = 71
rmsd = 1.362
"obj and name CA" index = 72
rmsd = 1.219
"obj and name CA" index = 73
rmsd = 1.532
"obj and name CA" index = 74
rmsd = 1.791
"obj and name CA" index = 75
rmsd = 1.759
"obj and name CA" index = 76
rmsd = 1.778
"obj and name CA" index = 77
rmsd = 2.179
"obj and name CA" index = 78
rmsd = 2.514
"obj and name CA" index = 79
rmsd = 2.505
"obj and name CA" index = 80
rmsd = 2.470
"obj and name CA" index = 81
rmsd = 2.767
"obj and name CA" index = 82
rmsd = 3.139
"obj and name CA" index = 83
rmsd = 3.530
"obj and name CA" index = 84
rmsd = 3.616
"obj and name CA" index = 85
rmsd = 4.153
"obj and name CA" index = 86
rmsd = 5.448
"obj and name CA" index = 87
rmsd = 7.215
"obj and name CA" index = 88
rmsd = 8.232
"obj and name CA" index = 89
rmsd = 9.033
"obj and name CA" index = 90
rmsd = 10.727
"obj and name CA" index = 91
rmsd = 12.615
PyMOL>cartoon putty, yesfit_ALL and name CA
PyMOL>show cartoon, yesfit_ALL and name CA
PyMOL>color red, ss h
 Executive: Colored 72 atoms.
PyMOL>color cyan,ss s
 Executive: Colored 60 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 2822 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: 1.06 sec. = 3401.6 frames/hour (5.45 sec. accum.).
PyMOL>png sausage.png
 ScenePNG: wrote 600x600 pixel image to file "sausage.png".
PyMOL>quit