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 27 atoms.
PyMOL>color cyan,ss s
 Executive: Colored 8 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 1164 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: 1.69 sec. = 2132.0 frames/hour (1.69 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 234 atoms.
PyMOL>hide everything,all
PyMOL>show lines,bb
PyMOL>color blue,bb
 Executive: Colored 234 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: 7.80 sec. = 461.5 frames/hour (9.49 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, 3.429706335067749, 3.2452502250671387, 1.5023080110549927, 2.0962057113647461, 2.1266200542449951, 3.7646110057830811, 3.2990975379943848, 3.5363168716430664, 3.4461987018585205, 1.460419774055481, 3.6353104114532471, 3.9150445461273193, 2.7475125789642334, 3.7893226146697998, 2.7671380043029785, 3.1272053718566895, 2.0169236660003662, 1.7633401155471802, 2.6009078025817871]
-> atom index_map =  [None, 2, 21, 31, 50, 64, 83, 104, 121, 145, 157, 169, 180, 197, 216, 227, 239, 256, 266, 282, 297, 307, 326, 336, 353, 363, 387, 397, 404, 414, 434, 454, 465, 481, 501, 520, 532, 544, 556, 566, 576, 595, 610, 621, 631, 652, 659, 678, 702, 718, 732, 748, 767, 791, 803, 817, 834, 841, 865, 880, 899, 911, 935, 949, 969, 981, 991, 1005, 1029, 1048, 1072, 1082, 1106, 1125, 1137, 1147, 1157, 1171, 1188]
"obj and name CA" index = 1
rmsd = 2.581
"obj and name CA" index = 2
rmsd = 1.322
"obj and name CA" index = 3
rmsd = 0.912
"obj and name CA" index = 4
rmsd = 0.775
"obj and name CA" index = 5
rmsd = 0.637
"obj and name CA" index = 6
rmsd = 0.513
"obj and name CA" index = 7
rmsd = 0.724
"obj and name CA" index = 8
rmsd = 0.898
"obj and name CA" index = 9
rmsd = 1.481
"obj and name CA" index = 10
rmsd = 1.921
"obj and name CA" index = 11
rmsd = 1.713
"obj and name CA" index = 12
rmsd = 1.170
"obj and name CA" index = 13
rmsd = 1.045
"obj and name CA" index = 14
rmsd = 0.951
"obj and name CA" index = 15
rmsd = 0.847
"obj and name CA" index = 16
rmsd = 0.740
"obj and name CA" index = 17
rmsd = 0.608
"obj and name CA" index = 18
rmsd = 0.576
"obj and name CA" index = 19
rmsd = 0.680
"obj and name CA" index = 20
rmsd = 0.634
"obj and name CA" index = 21
rmsd = 0.552
"obj and name CA" index = 22
rmsd = 0.658
"obj and name CA" index = 23
rmsd = 0.799
"obj and name CA" index = 24
rmsd = 0.765
"obj and name CA" index = 25
rmsd = 0.796
"obj and name CA" index = 26
rmsd = 0.827
"obj and name CA" index = 27
rmsd = 1.065
"obj and name CA" index = 28
rmsd = 0.944
"obj and name CA" index = 29
rmsd = 0.796
"obj and name CA" index = 30
rmsd = 0.980
"obj and name CA" index = 31
rmsd = 0.871
"obj and name CA" index = 32
rmsd = 0.720
"obj and name CA" index = 33
rmsd = 0.724
"obj and name CA" index = 34
rmsd = 0.761
"obj and name CA" index = 35
rmsd = 1.193
"obj and name CA" index = 36
rmsd = 1.489
"obj and name CA" index = 37
rmsd = 1.211
"obj and name CA" index = 38
rmsd = 1.363
"obj and name CA" index = 39
rmsd = 1.431
"obj and name CA" index = 40
rmsd = 0.788
"obj and name CA" index = 41
rmsd = 0.940
"obj and name CA" index = 42
rmsd = 1.502
"obj and name CA" index = 43
rmsd = 1.297
"obj and name CA" index = 44
rmsd = 1.015
"obj and name CA" index = 45
rmsd = 1.394
"obj and name CA" index = 46
rmsd = 1.609
"obj and name CA" index = 47
rmsd = 1.205
"obj and name CA" index = 48
rmsd = 0.945
"obj and name CA" index = 49
rmsd = 1.024
"obj and name CA" index = 50
rmsd = 0.659
"obj and name CA" index = 51
rmsd = 0.667
"obj and name CA" index = 52
rmsd = 0.813
"obj and name CA" index = 53
rmsd = 0.975
"obj and name CA" index = 54
rmsd = 1.465
"obj and name CA" index = 55
rmsd = 1.267
"obj and name CA" index = 56
rmsd = 2.042
"obj and name CA" index = 57
rmsd = 1.089
"obj and name CA" index = 58
rmsd = 1.010
"obj and name CA" index = 59
rmsd = 0.760
"obj and name CA" index = 60
rmsd = 1.310
"obj and name CA" index = 61
rmsd = 1.227
"obj and name CA" index = 62
rmsd = 1.314
"obj and name CA" index = 63
rmsd = 1.153
"obj and name CA" index = 64
rmsd = 1.471
"obj and name CA" index = 65
rmsd = 1.560
"obj and name CA" index = 66
rmsd = 1.509
"obj and name CA" index = 67
rmsd = 1.120
"obj and name CA" index = 68
rmsd = 0.897
"obj and name CA" index = 69
rmsd = 1.005
"obj and name CA" index = 70
rmsd = 1.011
"obj and name CA" index = 71
rmsd = 0.847
"obj and name CA" index = 72
rmsd = 0.870
"obj and name CA" index = 73
rmsd = 1.052
"obj and name CA" index = 74
rmsd = 1.258
"obj and name CA" index = 75
rmsd = 1.490
"obj and name CA" index = 76
rmsd = 3.254
"obj and name CA" index = 77
rmsd = 5.761
"obj and name CA" index = 78
rmsd = 8.106
PyMOL>cartoon putty, yesfit_ALL and name CA
PyMOL>show cartoon, yesfit_ALL and name CA
PyMOL>color red, ss h
 Executive: Colored 81 atoms.
PyMOL>color cyan,ss s
 Executive: Colored 24 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 2369 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: 1.93 sec. = 1869.2 frames/hour (11.41 sec. accum.).
PyMOL>png sausage.png
 ScenePNG: wrote 600x600 pixel image to file "sausage.png".
PyMOL>quit