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 50 atoms.
PyMOL>color cyan,ss s
PyMOL>color gray,ss ""+l
 Executive: Colored 1320 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: 0.96 sec. = 3756.8 frames/hour (0.96 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 258 atoms.
PyMOL>hide everything,all
PyMOL>show lines,bb
PyMOL>color blue,bb
 Executive: Colored 258 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: 2.82 sec. = 1277.3 frames/hour (3.78 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, 4.5445671081542969, 5.8676996231079102, 6.7865500450134277, 2.8368244171142578, 6.5958251953125, 5.8152484893798828, 5.1215329170227051, 5.6290225982666016, 5.0054569244384766, 6.6933012008666992, 3.9310202598571777, 4.0017762184143066, 4.2156424522399902, 6.3545904159545898, 4.8332786560058594, 4.522911548614502, 2.80281662940979, 7.7401132583618164, 3.650684118270874]
-> atom index_map =  [None, 2, 21, 28, 45, 62, 79, 96, 113, 130, 141, 158, 172, 186, 201, 216, 226, 250, 269, 281, 300, 319, 341, 360, 377, 388, 412, 434, 451, 465, 484, 498, 522, 529, 548, 562, 581, 605, 627, 646, 656, 671, 690, 707, 721, 728, 738, 749, 756, 766, 781, 797, 819, 826, 842, 853, 867, 882, 892, 899, 916, 937, 947, 966, 990, 1005, 1029, 1053, 1069, 1086, 1102, 1116, 1133, 1148, 1160, 1180, 1195, 1212, 1222, 1238, 1248, 1270, 1286, 1303, 1320, 1342, 1354]
"obj and name CA" index = 1
rmsd = 15.190
"obj and name CA" index = 2
rmsd = 13.609
"obj and name CA" index = 3
rmsd = 11.832
"obj and name CA" index = 4
rmsd = 9.747
"obj and name CA" index = 5
rmsd = 8.521
"obj and name CA" index = 6
rmsd = 6.950
"obj and name CA" index = 7
rmsd = 5.413
"obj and name CA" index = 8
rmsd = 3.907
"obj and name CA" index = 9
rmsd = 3.118
"obj and name CA" index = 10
rmsd = 2.871
"obj and name CA" index = 11
rmsd = 2.707
"obj and name CA" index = 12
rmsd = 3.267
"obj and name CA" index = 13
rmsd = 2.990
"obj and name CA" index = 14
rmsd = 3.064
"obj and name CA" index = 15
rmsd = 2.909
"obj and name CA" index = 16
rmsd = 2.350
"obj and name CA" index = 17
rmsd = 2.228
"obj and name CA" index = 18
rmsd = 2.527
"obj and name CA" index = 19
rmsd = 2.187
"obj and name CA" index = 20
rmsd = 1.769
"obj and name CA" index = 21
rmsd = 2.077
"obj and name CA" index = 22
rmsd = 2.209
"obj and name CA" index = 23
rmsd = 1.772
"obj and name CA" index = 24
rmsd = 1.694
"obj and name CA" index = 25
rmsd = 2.162
"obj and name CA" index = 26
rmsd = 2.158
"obj and name CA" index = 27
rmsd = 1.630
"obj and name CA" index = 28
rmsd = 1.588
"obj and name CA" index = 29
rmsd = 1.362
"obj and name CA" index = 30
rmsd = 1.405
"obj and name CA" index = 31
rmsd = 1.751
"obj and name CA" index = 32
rmsd = 1.865
"obj and name CA" index = 33
rmsd = 1.370
"obj and name CA" index = 34
rmsd = 1.440
"obj and name CA" index = 35
rmsd = 1.479
"obj and name CA" index = 36
rmsd = 1.888
"obj and name CA" index = 37
rmsd = 1.672
"obj and name CA" index = 38
rmsd = 1.367
"obj and name CA" index = 39
rmsd = 1.797
"obj and name CA" index = 40
rmsd = 2.020
"obj and name CA" index = 41
rmsd = 1.730
"obj and name CA" index = 42
rmsd = 1.831
"obj and name CA" index = 43
rmsd = 2.418
"obj and name CA" index = 44
rmsd = 2.484
"obj and name CA" index = 45
rmsd = 2.059
"obj and name CA" index = 46
rmsd = 2.149
"obj and name CA" index = 47
rmsd = 2.176
"obj and name CA" index = 48
rmsd = 2.042
"obj and name CA" index = 49
rmsd = 1.623
"obj and name CA" index = 50
rmsd = 1.544
"obj and name CA" index = 51
rmsd = 1.486
"obj and name CA" index = 52
rmsd = 1.170
"obj and name CA" index = 53
rmsd = 0.958
"obj and name CA" index = 54
rmsd = 0.963
"obj and name CA" index = 55
rmsd = 0.965
"obj and name CA" index = 56
rmsd = 0.822
"obj and name CA" index = 57
rmsd = 0.658
"obj and name CA" index = 58
rmsd = 0.937
"obj and name CA" index = 59
rmsd = 1.183
"obj and name CA" index = 60
rmsd = 1.185
"obj and name CA" index = 61
rmsd = 1.239
"obj and name CA" index = 62
rmsd = 1.580
"obj and name CA" index = 63
rmsd = 1.876
"obj and name CA" index = 64
rmsd = 1.975
"obj and name CA" index = 65
rmsd = 2.055
"obj and name CA" index = 66
rmsd = 1.750
"obj and name CA" index = 67
rmsd = 1.875
"obj and name CA" index = 68
rmsd = 1.418
"obj and name CA" index = 69
rmsd = 0.996
"obj and name CA" index = 70
rmsd = 0.952
"obj and name CA" index = 71
rmsd = 0.931
"obj and name CA" index = 72
rmsd = 1.016
"obj and name CA" index = 73
rmsd = 0.777
"obj and name CA" index = 74
rmsd = 0.683
"obj and name CA" index = 75
rmsd = 1.027
"obj and name CA" index = 76
rmsd = 1.137
"obj and name CA" index = 77
rmsd = 0.898
"obj and name CA" index = 78
rmsd = 1.194
"obj and name CA" index = 79
rmsd = 1.530
"obj and name CA" index = 80
rmsd = 1.459
"obj and name CA" index = 81
rmsd = 1.390
"obj and name CA" index = 82
rmsd = 1.670
"obj and name CA" index = 83
rmsd = 1.999
"obj and name CA" index = 84
rmsd = 2.224
"obj and name CA" index = 85
rmsd = 3.333
"obj and name CA" index = 86
rmsd = 5.331
PyMOL>cartoon putty, yesfit_ALL and name CA
PyMOL>show cartoon, yesfit_ALL and name CA
PyMOL>color red, ss h
 Executive: Colored 150 atoms.
PyMOL>color cyan,ss s
PyMOL>color gray,ss ""+l
 Executive: Colored 2670 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: 1.73 sec. = 2086.7 frames/hour (5.50 sec. accum.).
PyMOL>png sausage.png
 ScenePNG: wrote 600x600 pixel image to file "sausage.png".
PyMOL>quit