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 37 atoms.
PyMOL>color cyan,ss s
PyMOL>color gray,ss ""+l
 Executive: Colored 1304 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. = 3945.2 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 249 atoms.
PyMOL>hide everything,all
PyMOL>show lines,bb
PyMOL>color blue,bb
 Executive: Colored 249 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: 3.17 sec. = 1135.8 frames/hour (4.08 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, 8.7438421249389648, 4.3052034378051758, 4.7572054862976074, 4.6143441200256348, 6.6617317199707031, 6.488853931427002, 5.0526719093322754, 5.409947395324707, 5.2403559684753418, 6.4657511711120605, 6.5777206420898438, 4.7004027366638184, 5.9221887588500977, 2.6685166358947754, 7.3166618347167969, 3.0339024066925049, 7.5403380393981934, 7.5002756118774414, 3.840829610824585]
-> atom index_map =  [None, 2, 21, 28, 45, 62, 79, 96, 113, 130, 141, 158, 175, 194, 208, 222, 237, 254, 278, 289, 306, 320, 334, 350, 374, 388, 398, 417, 439, 451, 470, 489, 511, 523, 540, 554, 571, 582, 593, 612, 622, 644, 659, 670, 684, 703, 714, 731, 742, 759, 778, 789, 800, 819, 835, 849, 860, 874, 895, 916, 926, 940, 956, 967, 977, 987, 1009, 1020, 1037, 1052, 1072, 1079, 1103, 1127, 1148, 1170, 1187, 1207, 1229, 1251, 1265, 1287, 1299, 1316]
"obj and name CA" index = 1
rmsd = 14.903
"obj and name CA" index = 2
rmsd = 13.304
"obj and name CA" index = 3
rmsd = 11.301
"obj and name CA" index = 4
rmsd = 9.691
"obj and name CA" index = 5
rmsd = 8.119
"obj and name CA" index = 6
rmsd = 6.773
"obj and name CA" index = 7
rmsd = 5.146
"obj and name CA" index = 8
rmsd = 3.840
"obj and name CA" index = 9
rmsd = 3.427
"obj and name CA" index = 10
rmsd = 3.028
"obj and name CA" index = 11
rmsd = 2.661
"obj and name CA" index = 12
rmsd = 2.743
"obj and name CA" index = 13
rmsd = 3.042
"obj and name CA" index = 14
rmsd = 3.012
"obj and name CA" index = 15
rmsd = 3.136
"obj and name CA" index = 16
rmsd = 2.717
"obj and name CA" index = 17
rmsd = 2.271
"obj and name CA" index = 18
rmsd = 2.661
"obj and name CA" index = 19
rmsd = 2.511
"obj and name CA" index = 20
rmsd = 2.686
"obj and name CA" index = 21
rmsd = 2.343
"obj and name CA" index = 22
rmsd = 1.703
"obj and name CA" index = 23
rmsd = 1.916
"obj and name CA" index = 24
rmsd = 2.303
"obj and name CA" index = 25
rmsd = 1.838
"obj and name CA" index = 26
rmsd = 1.614
"obj and name CA" index = 27
rmsd = 2.098
"obj and name CA" index = 28
rmsd = 2.392
"obj and name CA" index = 29
rmsd = 2.129
"obj and name CA" index = 30
rmsd = 2.190
"obj and name CA" index = 31
rmsd = 2.731
"obj and name CA" index = 32
rmsd = 2.992
"obj and name CA" index = 33
rmsd = 2.615
"obj and name CA" index = 34
rmsd = 2.544
"obj and name CA" index = 35
rmsd = 2.148
"obj and name CA" index = 36
rmsd = 2.209
"obj and name CA" index = 37
rmsd = 2.452
"obj and name CA" index = 38
rmsd = 1.930
"obj and name CA" index = 39
rmsd = 1.481
"obj and name CA" index = 40
rmsd = 1.888
"obj and name CA" index = 41
rmsd = 2.148
"obj and name CA" index = 42
rmsd = 1.560
"obj and name CA" index = 43
rmsd = 1.484
"obj and name CA" index = 44
rmsd = 1.065
"obj and name CA" index = 45
rmsd = 1.265
"obj and name CA" index = 46
rmsd = 1.559
"obj and name CA" index = 47
rmsd = 1.565
"obj and name CA" index = 48
rmsd = 1.326
"obj and name CA" index = 49
rmsd = 1.318
"obj and name CA" index = 50
rmsd = 1.752
"obj and name CA" index = 51
rmsd = 1.880
"obj and name CA" index = 52
rmsd = 1.917
"obj and name CA" index = 53
rmsd = 2.261
"obj and name CA" index = 54
rmsd = 2.577
"obj and name CA" index = 55
rmsd = 2.775
"obj and name CA" index = 56
rmsd = 3.642
"obj and name CA" index = 57
rmsd = 3.920
"obj and name CA" index = 58
rmsd = 2.799
"obj and name CA" index = 59
rmsd = 3.653
"obj and name CA" index = 60
rmsd = 3.536
"obj and name CA" index = 61
rmsd = 2.509
"obj and name CA" index = 62
rmsd = 2.209
"obj and name CA" index = 63
rmsd = 2.099
"obj and name CA" index = 64
rmsd = 1.853
"obj and name CA" index = 65
rmsd = 1.709
"obj and name CA" index = 66
rmsd = 1.754
"obj and name CA" index = 67
rmsd = 1.818
"obj and name CA" index = 68
rmsd = 1.426
"obj and name CA" index = 69
rmsd = 0.988
"obj and name CA" index = 70
rmsd = 1.471
"obj and name CA" index = 71
rmsd = 1.587
"obj and name CA" index = 72
rmsd = 1.310
"obj and name CA" index = 73
rmsd = 1.590
"obj and name CA" index = 74
rmsd = 1.896
"obj and name CA" index = 75
rmsd = 1.804
"obj and name CA" index = 76
rmsd = 2.037
"obj and name CA" index = 77
rmsd = 2.572
"obj and name CA" index = 78
rmsd = 2.289
"obj and name CA" index = 79
rmsd = 3.942
"obj and name CA" index = 80
rmsd = 5.113
"obj and name CA" index = 81
rmsd = 6.288
"obj and name CA" index = 82
rmsd = 7.848
"obj and name CA" index = 83
rmsd = 9.523
PyMOL>cartoon putty, yesfit_ALL and name CA
PyMOL>show cartoon, yesfit_ALL and name CA
PyMOL>color red, ss h
 Executive: Colored 111 atoms.
PyMOL>color cyan,ss s
PyMOL>color gray,ss ""+l
 Executive: Colored 2645 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: 1.70 sec. = 2115.3 frames/hour (5.78 sec. accum.).
PyMOL>png sausage.png
 ScenePNG: wrote 600x600 pixel image to file "sausage.png".
PyMOL>quit