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
PyMOL>color cyan,ss s
 Executive: Colored 38 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 1483 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: 1.06 sec. = 3385.6 frames/hour (1.06 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 288 atoms.
PyMOL>hide everything,all
PyMOL>show lines,bb
PyMOL>color blue,bb
 Executive: Colored 288 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: 3.33 sec. = 1080.7 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, 4.6257214546203613, 1.9405831098556519, 4.6452646255493164, 2.8229382038116455, 3.7724282741546631, 3.4120659828186035, 3.907353401184082, 4.0481228828430176, 4.9972934722900391, 4.7516322135925293, 3.9914710521697998, 4.6200313568115234, 3.1031086444854736, 3.285578727722168, 2.8177897930145264, 3.5264804363250732, 3.8633112907409668, 4.1745548248291016, 3.6625809669494629]
-> atom index_map =  [None, 2, 15, 26, 43, 57, 76, 88, 112, 124, 138, 152, 171, 185, 204, 215, 234, 253, 263, 285, 299, 313, 327, 337, 351, 362, 379, 398, 415, 429, 451, 470, 484, 495, 511, 535, 551, 573, 587, 602, 609, 630, 644, 658, 669, 688, 702, 718, 732, 747, 766, 786, 796, 817, 833, 845, 864, 875, 882, 893, 908, 922, 929, 944, 961, 973, 994, 1009, 1025, 1047, 1063, 1078, 1092, 1111, 1125, 1139, 1158, 1180, 1199, 1215, 1230, 1249, 1260, 1274, 1298, 1314, 1330, 1344, 1363, 1380, 1399, 1414, 1431, 1448, 1465, 1482, 1499]
"obj and name CA" index = 1
rmsd = 9.980
"obj and name CA" index = 2
rmsd = 8.539
"obj and name CA" index = 3
rmsd = 7.348
"obj and name CA" index = 4
rmsd = 5.842
"obj and name CA" index = 5
rmsd = 4.089
"obj and name CA" index = 6
rmsd = 2.356
"obj and name CA" index = 7
rmsd = 1.287
"obj and name CA" index = 8
rmsd = 1.419
"obj and name CA" index = 9
rmsd = 1.365
"obj and name CA" index = 10
rmsd = 1.315
"obj and name CA" index = 11
rmsd = 1.196
"obj and name CA" index = 12
rmsd = 1.195
"obj and name CA" index = 13
rmsd = 0.980
"obj and name CA" index = 14
rmsd = 0.915
"obj and name CA" index = 15
rmsd = 0.707
"obj and name CA" index = 16
rmsd = 0.691
"obj and name CA" index = 17
rmsd = 0.574
"obj and name CA" index = 18
rmsd = 0.680
"obj and name CA" index = 19
rmsd = 1.047
"obj and name CA" index = 20
rmsd = 0.853
"obj and name CA" index = 21
rmsd = 1.157
"obj and name CA" index = 22
rmsd = 1.593
"obj and name CA" index = 23
rmsd = 1.415
"obj and name CA" index = 24
rmsd = 1.107
"obj and name CA" index = 25
rmsd = 0.914
"obj and name CA" index = 26
rmsd = 0.807
"obj and name CA" index = 27
rmsd = 0.815
"obj and name CA" index = 28
rmsd = 0.789
"obj and name CA" index = 29
rmsd = 0.851
"obj and name CA" index = 30
rmsd = 0.774
"obj and name CA" index = 31
rmsd = 0.982
"obj and name CA" index = 32
rmsd = 0.953
"obj and name CA" index = 33
rmsd = 0.891
"obj and name CA" index = 34
rmsd = 1.085
"obj and name CA" index = 35
rmsd = 1.132
"obj and name CA" index = 36
rmsd = 1.224
"obj and name CA" index = 37
rmsd = 1.152
"obj and name CA" index = 38
rmsd = 1.258
"obj and name CA" index = 39
rmsd = 1.355
"obj and name CA" index = 40
rmsd = 1.461
"obj and name CA" index = 41
rmsd = 1.509
"obj and name CA" index = 42
rmsd = 1.914
"obj and name CA" index = 43
rmsd = 1.687
"obj and name CA" index = 44
rmsd = 1.383
"obj and name CA" index = 45
rmsd = 1.731
"obj and name CA" index = 46
rmsd = 1.661
"obj and name CA" index = 47
rmsd = 1.594
"obj and name CA" index = 48
rmsd = 1.407
"obj and name CA" index = 49
rmsd = 1.119
"obj and name CA" index = 50
rmsd = 0.835
"obj and name CA" index = 51
rmsd = 0.683
"obj and name CA" index = 52
rmsd = 0.616
"obj and name CA" index = 53
rmsd = 0.586
"obj and name CA" index = 54
rmsd = 0.688
"obj and name CA" index = 55
rmsd = 0.828
"obj and name CA" index = 56
rmsd = 1.474
"obj and name CA" index = 57
rmsd = 1.846
"obj and name CA" index = 58
rmsd = 1.855
"obj and name CA" index = 59
rmsd = 1.324
"obj and name CA" index = 60
rmsd = 1.145
"obj and name CA" index = 61
rmsd = 1.055
"obj and name CA" index = 62
rmsd = 0.874
"obj and name CA" index = 63
rmsd = 0.801
"obj and name CA" index = 64
rmsd = 0.756
"obj and name CA" index = 65
rmsd = 0.629
"obj and name CA" index = 66
rmsd = 0.637
"obj and name CA" index = 67
rmsd = 0.553
"obj and name CA" index = 68
rmsd = 0.602
"obj and name CA" index = 69
rmsd = 0.648
"obj and name CA" index = 70
rmsd = 0.798
"obj and name CA" index = 71
rmsd = 0.878
"obj and name CA" index = 72
rmsd = 0.985
"obj and name CA" index = 73
rmsd = 1.239
"obj and name CA" index = 74
rmsd = 1.240
"obj and name CA" index = 75
rmsd = 1.125
"obj and name CA" index = 76
rmsd = 1.070
"obj and name CA" index = 77
rmsd = 0.991
"obj and name CA" index = 78
rmsd = 1.162
"obj and name CA" index = 79
rmsd = 1.227
"obj and name CA" index = 80
rmsd = 1.041
"obj and name CA" index = 81
rmsd = 0.966
"obj and name CA" index = 82
rmsd = 0.917
"obj and name CA" index = 83
rmsd = 0.795
"obj and name CA" index = 84
rmsd = 0.711
"obj and name CA" index = 85
rmsd = 0.644
"obj and name CA" index = 86
rmsd = 0.693
"obj and name CA" index = 87
rmsd = 0.600
"obj and name CA" index = 88
rmsd = 0.692
"obj and name CA" index = 89
rmsd = 0.764
"obj and name CA" index = 90
rmsd = 0.867
"obj and name CA" index = 91
rmsd = 1.165
"obj and name CA" index = 92
rmsd = 1.409
"obj and name CA" index = 93
rmsd = 1.700
"obj and name CA" index = 94
rmsd = 3.479
"obj and name CA" index = 95
rmsd = 5.644
"obj and name CA" index = 96
rmsd = 7.596
PyMOL>cartoon putty, yesfit_ALL and name CA
PyMOL>show cartoon, yesfit_ALL and name CA
PyMOL>color red, ss h
PyMOL>color cyan,ss s
 Executive: Colored 114 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 3018 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: 1.19 sec. = 3016.3 frames/hour (5.59 sec. accum.).
PyMOL>png sausage.png
 ScenePNG: wrote 600x600 pixel image to file "sausage.png".
PyMOL>quit