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 21 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 1388 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: 1.02 sec. = 3544.6 frames/hour (1.02 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: 3.15 sec. = 1143.6 frames/hour (4.16 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, 7.782163143157959, 5.837531566619873, 8.7380905151367188, 8.1373233795166016, 7.7290282249450684, 7.8429555892944336, 7.4185185432434082, 7.9623332023620605, 8.9228553771972656, 7.4365630149841309, 7.3855562210083008, 9.2279548645019531, 7.9896883964538574, 8.4204616546630859, 6.8292760848999023, 7.8315930366516113, 8.2964630126953125, 7.8501176834106445, 5.6898612976074219]
-> 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 = 13.322
"obj and name CA" index = 2
rmsd = 12.834
"obj and name CA" index = 3
rmsd = 11.803
"obj and name CA" index = 4
rmsd = 10.603
"obj and name CA" index = 5
rmsd = 9.319
"obj and name CA" index = 6
rmsd = 7.915
"obj and name CA" index = 7
rmsd = 6.097
"obj and name CA" index = 8
rmsd = 4.817
"obj and name CA" index = 9
rmsd = 3.688
"obj and name CA" index = 10
rmsd = 2.770
"obj and name CA" index = 11
rmsd = 2.006
"obj and name CA" index = 12
rmsd = 1.765
"obj and name CA" index = 13
rmsd = 1.912
"obj and name CA" index = 14
rmsd = 2.593
"obj and name CA" index = 15
rmsd = 2.738
"obj and name CA" index = 16
rmsd = 2.364
"obj and name CA" index = 17
rmsd = 2.005
"obj and name CA" index = 18
rmsd = 1.391
"obj and name CA" index = 19
rmsd = 1.343
"obj and name CA" index = 20
rmsd = 1.078
"obj and name CA" index = 21
rmsd = 1.385
"obj and name CA" index = 22
rmsd = 1.633
"obj and name CA" index = 23
rmsd = 1.460
"obj and name CA" index = 24
rmsd = 1.464
"obj and name CA" index = 25
rmsd = 1.858
"obj and name CA" index = 26
rmsd = 1.922
"obj and name CA" index = 27
rmsd = 1.769
"obj and name CA" index = 28
rmsd = 1.774
"obj and name CA" index = 29
rmsd = 1.676
"obj and name CA" index = 30
rmsd = 1.262
"obj and name CA" index = 31
rmsd = 1.085
"obj and name CA" index = 32
rmsd = 0.898
"obj and name CA" index = 33
rmsd = 1.110
"obj and name CA" index = 34
rmsd = 1.349
"obj and name CA" index = 35
rmsd = 1.649
"obj and name CA" index = 36
rmsd = 1.967
"obj and name CA" index = 37
rmsd = 2.108
"obj and name CA" index = 38
rmsd = 2.690
"obj and name CA" index = 39
rmsd = 3.452
"obj and name CA" index = 40
rmsd = 4.263
"obj and name CA" index = 41
rmsd = 4.252
"obj and name CA" index = 42
rmsd = 3.585
"obj and name CA" index = 43
rmsd = 3.184
"obj and name CA" index = 44
rmsd = 2.520
"obj and name CA" index = 45
rmsd = 2.197
"obj and name CA" index = 46
rmsd = 1.735
"obj and name CA" index = 47
rmsd = 1.594
"obj and name CA" index = 48
rmsd = 1.195
"obj and name CA" index = 49
rmsd = 1.162
"obj and name CA" index = 50
rmsd = 1.037
"obj and name CA" index = 51
rmsd = 1.299
"obj and name CA" index = 52
rmsd = 1.494
"obj and name CA" index = 53
rmsd = 1.915
"obj and name CA" index = 54
rmsd = 1.809
"obj and name CA" index = 55
rmsd = 1.771
"obj and name CA" index = 56
rmsd = 1.548
"obj and name CA" index = 57
rmsd = 1.507
"obj and name CA" index = 58
rmsd = 1.518
"obj and name CA" index = 59
rmsd = 1.550
"obj and name CA" index = 60
rmsd = 1.692
"obj and name CA" index = 61
rmsd = 1.669
"obj and name CA" index = 62
rmsd = 1.786
"obj and name CA" index = 63
rmsd = 1.459
"obj and name CA" index = 64
rmsd = 1.184
"obj and name CA" index = 65
rmsd = 0.997
"obj and name CA" index = 66
rmsd = 1.177
"obj and name CA" index = 67
rmsd = 1.196
"obj and name CA" index = 68
rmsd = 0.880
"obj and name CA" index = 69
rmsd = 1.071
"obj and name CA" index = 70
rmsd = 1.398
"obj and name CA" index = 71
rmsd = 1.214
"obj and name CA" index = 72
rmsd = 1.188
"obj and name CA" index = 73
rmsd = 1.563
"obj and name CA" index = 74
rmsd = 1.670
"obj and name CA" index = 75
rmsd = 1.576
"obj and name CA" index = 76
rmsd = 1.773
"obj and name CA" index = 77
rmsd = 2.103
"obj and name CA" index = 78
rmsd = 2.219
"obj and name CA" index = 79
rmsd = 2.192
"obj and name CA" index = 80
rmsd = 2.363
"obj and name CA" index = 81
rmsd = 2.685
"obj and name CA" index = 82
rmsd = 2.912
"obj and name CA" index = 83
rmsd = 3.358
"obj and name CA" index = 84
rmsd = 3.421
"obj and name CA" index = 85
rmsd = 4.274
"obj and name CA" index = 86
rmsd = 5.265
"obj and name CA" index = 87
rmsd = 7.454
"obj and name CA" index = 88
rmsd = 7.939
"obj and name CA" index = 89
rmsd = 8.935
"obj and name CA" index = 90
rmsd = 10.567
"obj and name CA" index = 91
rmsd = 12.335
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 63 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 2816 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: 1.07 sec. = 3361.7 frames/hour (5.23 sec. accum.).
PyMOL>png sausage.png
 ScenePNG: wrote 600x600 pixel image to file "sausage.png".
PyMOL>quit