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 7 atoms.
PyMOL>color cyan,ss s
 Executive: Colored 52 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 1469 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: 1.32 sec. = 2727.3 frames/hour (1.32 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 294 atoms.
PyMOL>hide everything,all
PyMOL>show lines,bb
PyMOL>color blue,bb
 Executive: Colored 294 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: 4.45 sec. = 809.7 frames/hour (5.77 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, 2.7814960479736328, 2.7284731864929199, 2.5850379467010498, 2.7330288887023926, 2.1940150260925293, 2.6220829486846924, 2.679307222366333, 2.6143269538879395, 2.4664828777313232, 2.410947322845459, 2.9928762912750244, 2.8663456439971924, 2.7905447483062744, 2.6998054981231689, 2.2878563404083252, 3.2534482479095459, 3.0511701107025146, 2.6412272453308105, 2.6559276580810547]
-> atom index_map =  [None, 2, 21, 35, 56, 78, 97, 108, 123, 142, 159, 173, 187, 206, 217, 224, 238, 257, 271, 281, 296, 312, 328, 338, 348, 369, 383, 405, 427, 442, 462, 473, 497, 519, 531, 538, 552, 574, 581, 598, 617, 639, 650, 669, 689, 708, 730, 742, 754, 768, 775, 786, 805, 829, 836, 850, 869, 893, 907, 922, 941, 951, 963, 983, 998, 1014, 1036, 1058, 1065, 1077, 1096, 1106, 1121, 1137, 1148, 1155, 1176, 1192, 1214, 1231, 1238, 1259, 1270, 1277, 1296, 1311, 1330, 1341, 1357, 1369, 1383, 1402, 1409, 1428, 1447, 1462, 1484, 1495, 1514]
"obj and name CA" index = 1
rmsd = 1.977
"obj and name CA" index = 2
rmsd = 0.668
"obj and name CA" index = 3
rmsd = 0.333
"obj and name CA" index = 4
rmsd = 0.334
"obj and name CA" index = 5
rmsd = 0.368
"obj and name CA" index = 6
rmsd = 0.462
"obj and name CA" index = 7
rmsd = 0.359
"obj and name CA" index = 8
rmsd = 0.327
"obj and name CA" index = 9
rmsd = 0.397
"obj and name CA" index = 10
rmsd = 0.468
"obj and name CA" index = 11
rmsd = 0.432
"obj and name CA" index = 12
rmsd = 0.358
"obj and name CA" index = 13
rmsd = 0.412
"obj and name CA" index = 14
rmsd = 0.353
"obj and name CA" index = 15
rmsd = 0.338
"obj and name CA" index = 16
rmsd = 0.338
"obj and name CA" index = 17
rmsd = 0.388
"obj and name CA" index = 18
rmsd = 0.368
"obj and name CA" index = 19
rmsd = 0.440
"obj and name CA" index = 20
rmsd = 0.435
"obj and name CA" index = 21
rmsd = 0.490
"obj and name CA" index = 22
rmsd = 0.450
"obj and name CA" index = 23
rmsd = 0.453
"obj and name CA" index = 24
rmsd = 0.593
"obj and name CA" index = 25
rmsd = 0.806
"obj and name CA" index = 26
rmsd = 0.784
"obj and name CA" index = 27
rmsd = 0.694
"obj and name CA" index = 28
rmsd = 0.692
"obj and name CA" index = 29
rmsd = 0.699
"obj and name CA" index = 30
rmsd = 0.752
"obj and name CA" index = 31
rmsd = 0.843
"obj and name CA" index = 32
rmsd = 1.373
"obj and name CA" index = 33
rmsd = 1.299
"obj and name CA" index = 34
rmsd = 1.750
"obj and name CA" index = 35
rmsd = 1.200
"obj and name CA" index = 36
rmsd = 1.173
"obj and name CA" index = 37
rmsd = 0.412
"obj and name CA" index = 38
rmsd = 0.342
"obj and name CA" index = 39
rmsd = 0.344
"obj and name CA" index = 40
rmsd = 0.357
"obj and name CA" index = 41
rmsd = 0.371
"obj and name CA" index = 42
rmsd = 0.337
"obj and name CA" index = 43
rmsd = 0.355
"obj and name CA" index = 44
rmsd = 0.337
"obj and name CA" index = 45
rmsd = 0.436
"obj and name CA" index = 46
rmsd = 0.495
"obj and name CA" index = 47
rmsd = 0.564
"obj and name CA" index = 48
rmsd = 0.536
"obj and name CA" index = 49
rmsd = 0.394
"obj and name CA" index = 50
rmsd = 0.340
"obj and name CA" index = 51
rmsd = 0.309
"obj and name CA" index = 52
rmsd = 0.314
"obj and name CA" index = 53
rmsd = 0.312
"obj and name CA" index = 54
rmsd = 0.281
"obj and name CA" index = 55
rmsd = 0.289
"obj and name CA" index = 56
rmsd = 0.335
"obj and name CA" index = 57
rmsd = 0.411
"obj and name CA" index = 58
rmsd = 0.493
"obj and name CA" index = 59
rmsd = 0.397
"obj and name CA" index = 60
rmsd = 0.415
"obj and name CA" index = 61
rmsd = 0.524
"obj and name CA" index = 62
rmsd = 0.482
"obj and name CA" index = 63
rmsd = 0.693
"obj and name CA" index = 64
rmsd = 0.550
"obj and name CA" index = 65
rmsd = 0.595
"obj and name CA" index = 66
rmsd = 0.576
"obj and name CA" index = 67
rmsd = 0.673
"obj and name CA" index = 68
rmsd = 0.659
"obj and name CA" index = 69
rmsd = 0.531
"obj and name CA" index = 70
rmsd = 0.501
"obj and name CA" index = 71
rmsd = 0.433
"obj and name CA" index = 72
rmsd = 0.292
"obj and name CA" index = 73
rmsd = 0.296
"obj and name CA" index = 74
rmsd = 0.261
"obj and name CA" index = 75
rmsd = 0.262
"obj and name CA" index = 76
rmsd = 0.255
"obj and name CA" index = 77
rmsd = 0.439
"obj and name CA" index = 78
rmsd = 0.813
"obj and name CA" index = 79
rmsd = 1.421
"obj and name CA" index = 80
rmsd = 2.342
"obj and name CA" index = 81
rmsd = 2.234
"obj and name CA" index = 82
rmsd = 1.465
"obj and name CA" index = 83
rmsd = 0.640
"obj and name CA" index = 84
rmsd = 0.420
"obj and name CA" index = 85
rmsd = 0.213
"obj and name CA" index = 86
rmsd = 0.263
"obj and name CA" index = 87
rmsd = 0.251
"obj and name CA" index = 88
rmsd = 0.340
"obj and name CA" index = 89
rmsd = 0.386
"obj and name CA" index = 90
rmsd = 0.364
"obj and name CA" index = 91
rmsd = 0.479
"obj and name CA" index = 92
rmsd = 0.549
"obj and name CA" index = 93
rmsd = 0.580
"obj and name CA" index = 94
rmsd = 0.588
"obj and name CA" index = 95
rmsd = 1.151
"obj and name CA" index = 96
rmsd = 2.494
"obj and name CA" index = 97
rmsd = 3.544
"obj and name CA" index = 98
rmsd = 5.102
PyMOL>cartoon putty, yesfit_ALL and name CA
PyMOL>show cartoon, yesfit_ALL and name CA
PyMOL>color red, ss h
 Executive: Colored 21 atoms.
PyMOL>color cyan,ss s
 Executive: Colored 156 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 2977 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. = 2233.8 frames/hour (7.38 sec. accum.).
PyMOL>png sausage.png
 ScenePNG: wrote 600x600 pixel image to file "sausage.png".
PyMOL>quit