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 1323 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. = 3400.4 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 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: 3.06 sec. = 1177.5 frames/hour (4.12 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, 4.5119762420654297, 6.4933815002441406, 4.4430255889892578, 4.9200000762939453, 3.7247130870819092, 5.5064339637756348, 4.0009403228759766, 4.5794239044189453, 2.8202626705169678, 3.2678110599517822, 5.9290142059326172, 5.526458740234375, 6.7741212844848633, 3.3313107490539551, 4.5074920654296875, 6.5835456848144531, 2.9942541122436523, 4.2561802864074707, 3.982386589050293]
-> 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 = 12.986
"obj and name CA" index = 2
rmsd = 12.072
"obj and name CA" index = 3
rmsd = 10.769
"obj and name CA" index = 4
rmsd = 9.068
"obj and name CA" index = 5
rmsd = 7.616
"obj and name CA" index = 6
rmsd = 6.299
"obj and name CA" index = 7
rmsd = 4.889
"obj and name CA" index = 8
rmsd = 3.666
"obj and name CA" index = 9
rmsd = 3.493
"obj and name CA" index = 10
rmsd = 3.123
"obj and name CA" index = 11
rmsd = 3.011
"obj and name CA" index = 12
rmsd = 3.124
"obj and name CA" index = 13
rmsd = 2.820
"obj and name CA" index = 14
rmsd = 3.023
"obj and name CA" index = 15
rmsd = 3.008
"obj and name CA" index = 16
rmsd = 2.406
"obj and name CA" index = 17
rmsd = 2.378
"obj and name CA" index = 18
rmsd = 2.696
"obj and name CA" index = 19
rmsd = 2.445
"obj and name CA" index = 20
rmsd = 1.997
"obj and name CA" index = 21
rmsd = 2.328
"obj and name CA" index = 22
rmsd = 2.560
"obj and name CA" index = 23
rmsd = 2.227
"obj and name CA" index = 24
rmsd = 2.211
"obj and name CA" index = 25
rmsd = 2.423
"obj and name CA" index = 26
rmsd = 2.114
"obj and name CA" index = 27
rmsd = 1.562
"obj and name CA" index = 28
rmsd = 1.546
"obj and name CA" index = 29
rmsd = 1.297
"obj and name CA" index = 30
rmsd = 1.541
"obj and name CA" index = 31
rmsd = 2.034
"obj and name CA" index = 32
rmsd = 2.174
"obj and name CA" index = 33
rmsd = 1.427
"obj and name CA" index = 34
rmsd = 1.607
"obj and name CA" index = 35
rmsd = 1.586
"obj and name CA" index = 36
rmsd = 2.068
"obj and name CA" index = 37
rmsd = 1.832
"obj and name CA" index = 38
rmsd = 1.414
"obj and name CA" index = 39
rmsd = 1.928
"obj and name CA" index = 40
rmsd = 2.149
"obj and name CA" index = 41
rmsd = 1.729
"obj and name CA" index = 42
rmsd = 1.828
"obj and name CA" index = 43
rmsd = 2.421
"obj and name CA" index = 44
rmsd = 2.782
"obj and name CA" index = 45
rmsd = 2.371
"obj and name CA" index = 46
rmsd = 2.705
"obj and name CA" index = 47
rmsd = 2.762
"obj and name CA" index = 48
rmsd = 2.503
"obj and name CA" index = 49
rmsd = 1.962
"obj and name CA" index = 50
rmsd = 1.790
"obj and name CA" index = 51
rmsd = 1.928
"obj and name CA" index = 52
rmsd = 1.621
"obj and name CA" index = 53
rmsd = 1.102
"obj and name CA" index = 54
rmsd = 1.098
"obj and name CA" index = 55
rmsd = 1.342
"obj and name CA" index = 56
rmsd = 1.193
"obj and name CA" index = 57
rmsd = 0.825
"obj and name CA" index = 58
rmsd = 1.146
"obj and name CA" index = 59
rmsd = 1.572
"obj and name CA" index = 60
rmsd = 1.530
"obj and name CA" index = 61
rmsd = 1.626
"obj and name CA" index = 62
rmsd = 2.094
"obj and name CA" index = 63
rmsd = 2.405
"obj and name CA" index = 64
rmsd = 2.664
"obj and name CA" index = 65
rmsd = 2.842
"obj and name CA" index = 66
rmsd = 2.400
"obj and name CA" index = 67
rmsd = 2.453
"obj and name CA" index = 68
rmsd = 1.686
"obj and name CA" index = 69
rmsd = 1.107
"obj and name CA" index = 70
rmsd = 1.143
"obj and name CA" index = 71
rmsd = 0.947
"obj and name CA" index = 72
rmsd = 1.094
"obj and name CA" index = 73
rmsd = 0.915
"obj and name CA" index = 74
rmsd = 0.533
"obj and name CA" index = 75
rmsd = 0.830
"obj and name CA" index = 76
rmsd = 1.101
"obj and name CA" index = 77
rmsd = 0.913
"obj and name CA" index = 78
rmsd = 1.056
"obj and name CA" index = 79
rmsd = 1.382
"obj and name CA" index = 80
rmsd = 1.487
"obj and name CA" index = 81
rmsd = 1.487
"obj and name CA" index = 82
rmsd = 1.662
"obj and name CA" index = 83
rmsd = 1.954
"obj and name CA" index = 84
rmsd = 2.533
"obj and name CA" index = 85
rmsd = 3.910
"obj and name CA" index = 86
rmsd = 5.945
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 2673 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: 1.60 sec. = 2248.0 frames/hour (5.72 sec. accum.).
PyMOL>png sausage.png
 ScenePNG: wrote 600x600 pixel image to file "sausage.png".
PyMOL>quit