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 76 atoms.
PyMOL>color cyan,ss s
PyMOL>color gray,ss ""+l
 Executive: Colored 1488 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: 1.36 sec. = 2639.0 frames/hour (1.36 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 297 atoms.
PyMOL>hide everything,all
PyMOL>show lines,bb
PyMOL>color blue,bb
 Executive: Colored 297 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. = 1278.3 frames/hour (4.18 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, 2.9271371364593506, 3.1627223491668701, 3.6230361461639404, 3.3592407703399658, 3.8982639312744141, 2.4325113296508789, 4.2593073844909668, 3.2703826427459717, 3.2375349998474121, 3.5217530727386475, 2.5820965766906738, 2.9559228420257568, 2.4921588897705078, 1.6396918296813965, 1.766049861907959, 3.3574197292327881, 2.6056735515594482, 3.0251486301422119, 1.4607892036437988]
-> atom index_map =  [None, 2, 19, 31, 45, 60, 72, 86, 106, 120, 144, 165, 175, 194, 204, 221, 236, 253, 272, 294, 311, 323, 337, 347, 358, 382, 392, 411, 421, 440, 460, 475, 490, 509, 525, 540, 554, 566, 580, 592, 613, 629, 636, 650, 671, 692, 709, 728, 735, 757, 776, 797, 812, 836, 855, 867, 891, 905, 917, 929, 939, 958, 970, 984, 1005, 1015, 1032, 1039, 1058, 1073, 1089, 1099, 1123, 1138, 1153, 1160, 1174, 1191, 1213, 1225, 1244, 1255, 1270, 1289, 1306, 1318, 1328, 1350, 1369, 1391, 1401, 1416, 1423, 1442, 1457, 1474, 1491, 1508, 1525, 1542]
"obj and name CA" index = 1
rmsd = 2.258
"obj and name CA" index = 2
rmsd = 1.569
"obj and name CA" index = 3
rmsd = 1.214
"obj and name CA" index = 4
rmsd = 1.175
"obj and name CA" index = 5
rmsd = 0.907
"obj and name CA" index = 6
rmsd = 0.648
"obj and name CA" index = 7
rmsd = 0.621
"obj and name CA" index = 8
rmsd = 0.695
"obj and name CA" index = 9
rmsd = 0.566
"obj and name CA" index = 10
rmsd = 0.407
"obj and name CA" index = 11
rmsd = 0.541
"obj and name CA" index = 12
rmsd = 0.536
"obj and name CA" index = 13
rmsd = 0.355
"obj and name CA" index = 14
rmsd = 0.497
"obj and name CA" index = 15
rmsd = 0.626
"obj and name CA" index = 16
rmsd = 0.521
"obj and name CA" index = 17
rmsd = 0.552
"obj and name CA" index = 18
rmsd = 0.742
"obj and name CA" index = 19
rmsd = 0.765
"obj and name CA" index = 20
rmsd = 0.723
"obj and name CA" index = 21
rmsd = 0.567
"obj and name CA" index = 22
rmsd = 0.495
"obj and name CA" index = 23
rmsd = 0.505
"obj and name CA" index = 24
rmsd = 0.457
"obj and name CA" index = 25
rmsd = 0.323
"obj and name CA" index = 26
rmsd = 0.372
"obj and name CA" index = 27
rmsd = 0.466
"obj and name CA" index = 28
rmsd = 0.384
"obj and name CA" index = 29
rmsd = 0.298
"obj and name CA" index = 30
rmsd = 0.504
"obj and name CA" index = 31
rmsd = 0.626
"obj and name CA" index = 32
rmsd = 0.513
"obj and name CA" index = 33
rmsd = 0.545
"obj and name CA" index = 34
rmsd = 0.766
"obj and name CA" index = 35
rmsd = 0.807
"obj and name CA" index = 36
rmsd = 0.649
"obj and name CA" index = 37
rmsd = 0.617
"obj and name CA" index = 38
rmsd = 0.569
"obj and name CA" index = 39
rmsd = 0.470
"obj and name CA" index = 40
rmsd = 0.466
"obj and name CA" index = 41
rmsd = 0.433
"obj and name CA" index = 42
rmsd = 0.355
"obj and name CA" index = 43
rmsd = 0.477
"obj and name CA" index = 44
rmsd = 0.554
"obj and name CA" index = 45
rmsd = 0.444
"obj and name CA" index = 46
rmsd = 0.424
"obj and name CA" index = 47
rmsd = 0.610
"obj and name CA" index = 48
rmsd = 0.646
"obj and name CA" index = 49
rmsd = 0.529
"obj and name CA" index = 50
rmsd = 0.635
"obj and name CA" index = 51
rmsd = 0.802
"obj and name CA" index = 52
rmsd = 0.818
"obj and name CA" index = 53
rmsd = 0.811
"obj and name CA" index = 54
rmsd = 0.993
"obj and name CA" index = 55
rmsd = 0.896
"obj and name CA" index = 56
rmsd = 1.020
"obj and name CA" index = 57
rmsd = 1.053
"obj and name CA" index = 58
rmsd = 0.829
"obj and name CA" index = 59
rmsd = 0.746
"obj and name CA" index = 60
rmsd = 0.873
"obj and name CA" index = 61
rmsd = 0.815
"obj and name CA" index = 62
rmsd = 0.650
"obj and name CA" index = 63
rmsd = 0.726
"obj and name CA" index = 64
rmsd = 0.830
"obj and name CA" index = 65
rmsd = 0.703
"obj and name CA" index = 66
rmsd = 0.625
"obj and name CA" index = 67
rmsd = 0.800
"obj and name CA" index = 68
rmsd = 0.820
"obj and name CA" index = 69
rmsd = 0.668
"obj and name CA" index = 70
rmsd = 0.696
"obj and name CA" index = 71
rmsd = 0.843
"obj and name CA" index = 72
rmsd = 0.813
"obj and name CA" index = 73
rmsd = 0.707
"obj and name CA" index = 74
rmsd = 0.686
"obj and name CA" index = 75
rmsd = 0.828
"obj and name CA" index = 76
rmsd = 0.962
"obj and name CA" index = 77
rmsd = 0.907
"obj and name CA" index = 78
rmsd = 0.736
"obj and name CA" index = 79
rmsd = 0.836
"obj and name CA" index = 80
rmsd = 0.972
"obj and name CA" index = 81
rmsd = 0.862
"obj and name CA" index = 82
rmsd = 0.778
"obj and name CA" index = 83
rmsd = 0.940
"obj and name CA" index = 84
rmsd = 0.997
"obj and name CA" index = 85
rmsd = 0.892
"obj and name CA" index = 86
rmsd = 0.946
"obj and name CA" index = 87
rmsd = 1.103
"obj and name CA" index = 88
rmsd = 1.108
"obj and name CA" index = 89
rmsd = 1.042
"obj and name CA" index = 90
rmsd = 1.132
"obj and name CA" index = 91
rmsd = 1.283
"obj and name CA" index = 92
rmsd = 1.264
"obj and name CA" index = 93
rmsd = 1.500
"obj and name CA" index = 94
rmsd = 2.670
"obj and name CA" index = 95
rmsd = 3.783
"obj and name CA" index = 96
rmsd = 4.943
"obj and name CA" index = 97
rmsd = 6.961
"obj and name CA" index = 98
rmsd = 8.392
"obj and name CA" index = 99
rmsd = 10.350
PyMOL>cartoon putty, yesfit_ALL and name CA
PyMOL>show cartoon, yesfit_ALL and name CA
PyMOL>color red, ss h
 Executive: Colored 228 atoms.
PyMOL>color cyan,ss s
PyMOL>color gray,ss ""+l
 Executive: Colored 2993 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: 1.61 sec. = 2238.7 frames/hour (5.79 sec. accum.).
PyMOL>png sausage.png
 ScenePNG: wrote 600x600 pixel image to file "sausage.png".
PyMOL>quit