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 75 atoms.
PyMOL>color cyan,ss s
PyMOL>color gray,ss ""+l
 Executive: Colored 1491 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: 1.28 sec. = 2805.3 frames/hour (1.28 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: 3.43 sec. = 1048.1 frames/hour (4.72 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, 1.6978126764297485, 3.5470144748687744, 1.6024683713912964, 3.7577199935913086, 3.3477225303649902, 2.3634355068206787, 2.3688678741455078, 2.2693111896514893, 2.8791389465332031, 2.4127624034881592, 3.5593400001525879, 2.3162050247192383, 2.4983367919921875, 2.2223210334777832, 2.927994966506958, 1.944435715675354, 1.7788436412811279, 2.5745944976806641, 1.632001519203186]
-> 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 = 2.267
"obj and name CA" index = 2
rmsd = 1.785
"obj and name CA" index = 3
rmsd = 1.691
"obj and name CA" index = 4
rmsd = 1.696
"obj and name CA" index = 5
rmsd = 1.204
"obj and name CA" index = 6
rmsd = 0.914
"obj and name CA" index = 7
rmsd = 0.737
"obj and name CA" index = 8
rmsd = 0.878
"obj and name CA" index = 9
rmsd = 0.720
"obj and name CA" index = 10
rmsd = 0.432
"obj and name CA" index = 11
rmsd = 0.654
"obj and name CA" index = 12
rmsd = 0.657
"obj and name CA" index = 13
rmsd = 0.433
"obj and name CA" index = 14
rmsd = 0.731
"obj and name CA" index = 15
rmsd = 0.930
"obj and name CA" index = 16
rmsd = 0.708
"obj and name CA" index = 17
rmsd = 1.059
"obj and name CA" index = 18
rmsd = 1.345
"obj and name CA" index = 19
rmsd = 1.100
"obj and name CA" index = 20
rmsd = 1.236
"obj and name CA" index = 21
rmsd = 0.847
"obj and name CA" index = 22
rmsd = 1.126
"obj and name CA" index = 23
rmsd = 1.161
"obj and name CA" index = 24
rmsd = 0.764
"obj and name CA" index = 25
rmsd = 0.602
"obj and name CA" index = 26
rmsd = 0.907
"obj and name CA" index = 27
rmsd = 0.930
"obj and name CA" index = 28
rmsd = 0.630
"obj and name CA" index = 29
rmsd = 0.541
"obj and name CA" index = 30
rmsd = 0.925
"obj and name CA" index = 31
rmsd = 1.001
"obj and name CA" index = 32
rmsd = 0.690
"obj and name CA" index = 33
rmsd = 0.768
"obj and name CA" index = 34
rmsd = 1.091
"obj and name CA" index = 35
rmsd = 1.105
"obj and name CA" index = 36
rmsd = 0.822
"obj and name CA" index = 37
rmsd = 0.694
"obj and name CA" index = 38
rmsd = 0.678
"obj and name CA" index = 39
rmsd = 0.570
"obj and name CA" index = 40
rmsd = 0.510
"obj and name CA" index = 41
rmsd = 0.429
"obj and name CA" index = 42
rmsd = 0.338
"obj and name CA" index = 43
rmsd = 0.443
"obj and name CA" index = 44
rmsd = 0.474
"obj and name CA" index = 45
rmsd = 0.480
"obj and name CA" index = 46
rmsd = 0.500
"obj and name CA" index = 47
rmsd = 0.676
"obj and name CA" index = 48
rmsd = 0.747
"obj and name CA" index = 49
rmsd = 0.806
"obj and name CA" index = 50
rmsd = 0.916
"obj and name CA" index = 51
rmsd = 1.120
"obj and name CA" index = 52
rmsd = 1.269
"obj and name CA" index = 53
rmsd = 1.336
"obj and name CA" index = 54
rmsd = 1.502
"obj and name CA" index = 55
rmsd = 1.305
"obj and name CA" index = 56
rmsd = 1.372
"obj and name CA" index = 57
rmsd = 1.425
"obj and name CA" index = 58
rmsd = 1.108
"obj and name CA" index = 59
rmsd = 0.914
"obj and name CA" index = 60
rmsd = 1.021
"obj and name CA" index = 61
rmsd = 0.972
"obj and name CA" index = 62
rmsd = 0.716
"obj and name CA" index = 63
rmsd = 0.680
"obj and name CA" index = 64
rmsd = 0.864
"obj and name CA" index = 65
rmsd = 0.781
"obj and name CA" index = 66
rmsd = 0.584
"obj and name CA" index = 67
rmsd = 0.724
"obj and name CA" index = 68
rmsd = 0.893
"obj and name CA" index = 69
rmsd = 0.859
"obj and name CA" index = 70
rmsd = 0.719
"obj and name CA" index = 71
rmsd = 1.011
"obj and name CA" index = 72
rmsd = 1.252
"obj and name CA" index = 73
rmsd = 1.193
"obj and name CA" index = 74
rmsd = 0.992
"obj and name CA" index = 75
rmsd = 1.000
"obj and name CA" index = 76
rmsd = 0.941
"obj and name CA" index = 77
rmsd = 0.917
"obj and name CA" index = 78
rmsd = 0.696
"obj and name CA" index = 79
rmsd = 0.710
"obj and name CA" index = 80
rmsd = 0.815
"obj and name CA" index = 81
rmsd = 0.771
"obj and name CA" index = 82
rmsd = 0.643
"obj and name CA" index = 83
rmsd = 0.853
"obj and name CA" index = 84
rmsd = 1.011
"obj and name CA" index = 85
rmsd = 0.872
"obj and name CA" index = 86
rmsd = 1.011
"obj and name CA" index = 87
rmsd = 1.267
"obj and name CA" index = 88
rmsd = 1.311
"obj and name CA" index = 89
rmsd = 1.261
"obj and name CA" index = 90
rmsd = 1.464
"obj and name CA" index = 91
rmsd = 1.620
"obj and name CA" index = 92
rmsd = 1.718
"obj and name CA" index = 93
rmsd = 2.141
"obj and name CA" index = 94
rmsd = 2.461
"obj and name CA" index = 95
rmsd = 3.355
"obj and name CA" index = 96
rmsd = 4.795
"obj and name CA" index = 97
rmsd = 6.850
"obj and name CA" index = 98
rmsd = 8.300
"obj and name CA" index = 99
rmsd = 10.068
PyMOL>cartoon putty, yesfit_ALL and name CA
PyMOL>show cartoon, yesfit_ALL and name CA
PyMOL>color red, ss h
 Executive: Colored 225 atoms.
PyMOL>color cyan,ss s
PyMOL>color gray,ss ""+l
 Executive: Colored 2998 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. = 2114.6 frames/hour (6.42 sec. accum.).
PyMOL>png sausage.png
 ScenePNG: wrote 600x600 pixel image to file "sausage.png".
PyMOL>quit