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 27 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 1494 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: 1.10 sec. = 3265.8 frames/hour (1.10 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: 4.07 sec. = 884.2 frames/hour (5.17 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, 2.80611252784729, 3.1296343803405762, 2.6949319839477539, 5.4103913307189941, 3.207404613494873, 3.5376436710357666, 3.0813355445861816, 2.7189357280731201, 1.7577013969421387, 3.7031548023223877, 4.4013943672180176, 3.4425404071807861, 1.8550950288772583, 3.020878791809082, 2.4731247425079346, 4.2858371734619141, 1.8422589302062988, 4.2867755889892578, 3.1412169933319092]
-> 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 = 9.403
"obj and name CA" index = 2
rmsd = 8.031
"obj and name CA" index = 3
rmsd = 6.910
"obj and name CA" index = 4
rmsd = 5.173
"obj and name CA" index = 5
rmsd = 3.289
"obj and name CA" index = 6
rmsd = 2.884
"obj and name CA" index = 7
rmsd = 2.363
"obj and name CA" index = 8
rmsd = 1.761
"obj and name CA" index = 9
rmsd = 1.423
"obj and name CA" index = 10
rmsd = 1.259
"obj and name CA" index = 11
rmsd = 1.085
"obj and name CA" index = 12
rmsd = 1.129
"obj and name CA" index = 13
rmsd = 1.029
"obj and name CA" index = 14
rmsd = 1.047
"obj and name CA" index = 15
rmsd = 0.852
"obj and name CA" index = 16
rmsd = 0.858
"obj and name CA" index = 17
rmsd = 0.708
"obj and name CA" index = 18
rmsd = 1.009
"obj and name CA" index = 19
rmsd = 1.211
"obj and name CA" index = 20
rmsd = 0.844
"obj and name CA" index = 21
rmsd = 1.410
"obj and name CA" index = 22
rmsd = 2.094
"obj and name CA" index = 23
rmsd = 2.090
"obj and name CA" index = 24
rmsd = 1.585
"obj and name CA" index = 25
rmsd = 1.248
"obj and name CA" index = 26
rmsd = 0.985
"obj and name CA" index = 27
rmsd = 0.882
"obj and name CA" index = 28
rmsd = 0.894
"obj and name CA" index = 29
rmsd = 0.925
"obj and name CA" index = 30
rmsd = 0.827
"obj and name CA" index = 31
rmsd = 0.934
"obj and name CA" index = 32
rmsd = 0.943
"obj and name CA" index = 33
rmsd = 0.904
"obj and name CA" index = 34
rmsd = 1.007
"obj and name CA" index = 35
rmsd = 0.871
"obj and name CA" index = 36
rmsd = 0.943
"obj and name CA" index = 37
rmsd = 0.892
"obj and name CA" index = 38
rmsd = 1.119
"obj and name CA" index = 39
rmsd = 1.446
"obj and name CA" index = 40
rmsd = 1.874
"obj and name CA" index = 41
rmsd = 1.657
"obj and name CA" index = 42
rmsd = 2.197
"obj and name CA" index = 43
rmsd = 1.829
"obj and name CA" index = 44
rmsd = 1.550
"obj and name CA" index = 45
rmsd = 2.124
"obj and name CA" index = 46
rmsd = 2.182
"obj and name CA" index = 47
rmsd = 2.232
"obj and name CA" index = 48
rmsd = 1.779
"obj and name CA" index = 49
rmsd = 1.214
"obj and name CA" index = 50
rmsd = 0.927
"obj and name CA" index = 51
rmsd = 0.782
"obj and name CA" index = 52
rmsd = 0.846
"obj and name CA" index = 53
rmsd = 0.662
"obj and name CA" index = 54
rmsd = 0.886
"obj and name CA" index = 55
rmsd = 1.085
"obj and name CA" index = 56
rmsd = 1.991
"obj and name CA" index = 57
rmsd = 2.137
"obj and name CA" index = 58
rmsd = 1.964
"obj and name CA" index = 59
rmsd = 1.585
"obj and name CA" index = 60
rmsd = 1.527
"obj and name CA" index = 61
rmsd = 1.426
"obj and name CA" index = 62
rmsd = 1.231
"obj and name CA" index = 63
rmsd = 1.041
"obj and name CA" index = 64
rmsd = 0.830
"obj and name CA" index = 65
rmsd = 0.769
"obj and name CA" index = 66
rmsd = 0.793
"obj and name CA" index = 67
rmsd = 0.697
"obj and name CA" index = 68
rmsd = 0.636
"obj and name CA" index = 69
rmsd = 0.664
"obj and name CA" index = 70
rmsd = 0.739
"obj and name CA" index = 71
rmsd = 0.795
"obj and name CA" index = 72
rmsd = 0.885
"obj and name CA" index = 73
rmsd = 1.291
"obj and name CA" index = 74
rmsd = 1.245
"obj and name CA" index = 75
rmsd = 1.020
"obj and name CA" index = 76
rmsd = 1.030
"obj and name CA" index = 77
rmsd = 0.864
"obj and name CA" index = 78
rmsd = 0.946
"obj and name CA" index = 79
rmsd = 1.018
"obj and name CA" index = 80
rmsd = 0.965
"obj and name CA" index = 81
rmsd = 1.017
"obj and name CA" index = 82
rmsd = 1.016
"obj and name CA" index = 83
rmsd = 0.943
"obj and name CA" index = 84
rmsd = 0.814
"obj and name CA" index = 85
rmsd = 0.817
"obj and name CA" index = 86
rmsd = 0.988
"obj and name CA" index = 87
rmsd = 0.961
"obj and name CA" index = 88
rmsd = 1.091
"obj and name CA" index = 89
rmsd = 1.065
"obj and name CA" index = 90
rmsd = 1.084
"obj and name CA" index = 91
rmsd = 1.271
"obj and name CA" index = 92
rmsd = 1.489
"obj and name CA" index = 93
rmsd = 2.097
"obj and name CA" index = 94
rmsd = 4.254
"obj and name CA" index = 95
rmsd = 6.439
"obj and name CA" index = 96
rmsd = 8.400
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 81 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 3051 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: 1.29 sec. = 2785.9 frames/hour (6.47 sec. accum.).
PyMOL>png sausage.png
 ScenePNG: wrote 600x600 pixel image to file "sausage.png".
PyMOL>quit