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 51 atoms.
PyMOL>color cyan,ss s
 Executive: Colored 39 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 3049 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: 1.42 sec. = 2526.6 frames/hour (1.42 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 606 atoms.
PyMOL>hide everything,all
PyMOL>show lines,bb
PyMOL>color blue,bb
 Executive: Colored 606 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: 5.46 sec. = 659.2 frames/hour (6.89 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, 9.1528282165527344, 9.8137073516845703, 11.343288421630859, 10.897579193115234, 8.7618703842163086, 7.4538383483886719, 9.198150634765625, 8.8041563034057617, 12.409557342529297, 8.0966196060180664, 9.8322601318359375, 10.970827102661133, 7.5568451881408691, 10.166362762451172, 8.9956130981445312, 10.829668045043945, 10.496976852416992, 9.5708513259887695, 3.9596834182739258]
-> atom index_map =  [None, 2, 21, 45, 57, 72, 96, 116, 127, 144, 155, 170, 191, 207, 228, 235, 249, 264, 278, 292, 304, 324, 343, 359, 370, 386, 396, 410, 427, 446, 460, 477, 484, 506, 525, 544, 555, 574, 584, 599, 606, 621, 628, 652, 666, 676, 687, 707, 726, 736, 747, 766, 773, 794, 809, 825, 839, 849, 865, 877, 894, 905, 916, 932, 939, 958, 968, 990, 1000, 1022, 1039, 1058, 1068, 1085, 1100, 1122, 1129, 1145, 1167, 1186, 1200, 1214, 1230, 1247, 1258, 1272, 1291, 1301, 1313, 1333, 1345, 1364, 1380, 1390, 1402, 1412, 1436, 1451, 1458, 1477, 1493, 1504, 1523, 1543, 1554, 1571, 1590, 1604, 1615, 1626, 1645, 1669, 1686, 1703, 1722, 1743, 1757, 1779, 1795, 1816, 1833, 1840, 1859, 1881, 1895, 1902, 1909, 1925, 1945, 1964, 1983, 1998, 2005, 2025, 2035, 2049, 2064, 2081, 2100, 2117, 2138, 2152, 2166, 2173, 2180, 2194, 2216, 2228, 2247, 2259, 2278, 2297, 2311, 2333, 2352, 2367, 2381, 2400, 2417, 2428, 2443, 2462, 2476, 2487, 2506, 2520, 2544, 2563, 2582, 2592, 2606, 2620, 2639, 2654, 2678, 2692, 2711, 2723, 2738, 2745, 2755, 2776, 2793, 2810, 2817, 2839, 2849, 2859, 2878, 2897, 2914, 2933, 2952, 2959, 2976, 2998, 3017, 3032, 3049, 3066, 3083, 3100, 3117]
"obj and name CA" index = 1
rmsd = 26.697
"obj and name CA" index = 2
rmsd = 24.765
"obj and name CA" index = 3
rmsd = 22.686
"obj and name CA" index = 4
rmsd = 20.731
"obj and name CA" index = 5
rmsd = 18.332
"obj and name CA" index = 6
rmsd = 16.412
"obj and name CA" index = 7
rmsd = 13.998
"obj and name CA" index = 8
rmsd = 11.962
"obj and name CA" index = 9
rmsd = 10.044
"obj and name CA" index = 10
rmsd = 8.539
"obj and name CA" index = 11
rmsd = 7.659
"obj and name CA" index = 12
rmsd = 6.619
"obj and name CA" index = 13
rmsd = 5.438
"obj and name CA" index = 14
rmsd = 5.610
"obj and name CA" index = 15
rmsd = 4.957
"obj and name CA" index = 16
rmsd = 4.860
"obj and name CA" index = 17
rmsd = 4.283
"obj and name CA" index = 18
rmsd = 4.936
"obj and name CA" index = 19
rmsd = 4.054
"obj and name CA" index = 20
rmsd = 3.657
"obj and name CA" index = 21
rmsd = 3.294
"obj and name CA" index = 22
rmsd = 3.983
"obj and name CA" index = 23
rmsd = 4.013
"obj and name CA" index = 24
rmsd = 3.337
"obj and name CA" index = 25
rmsd = 3.514
"obj and name CA" index = 26
rmsd = 4.208
"obj and name CA" index = 27
rmsd = 3.689
"obj and name CA" index = 28
rmsd = 3.197
"obj and name CA" index = 29
rmsd = 3.561
"obj and name CA" index = 30
rmsd = 3.961
"obj and name CA" index = 31
rmsd = 3.569
"obj and name CA" index = 32
rmsd = 3.081
"obj and name CA" index = 33
rmsd = 2.509
"obj and name CA" index = 34
rmsd = 1.948
"obj and name CA" index = 35
rmsd = 1.686
"obj and name CA" index = 36
rmsd = 1.408
"obj and name CA" index = 37
rmsd = 2.105
"obj and name CA" index = 38
rmsd = 2.593
"obj and name CA" index = 39
rmsd = 3.307
"obj and name CA" index = 40
rmsd = 3.259
"obj and name CA" index = 41
rmsd = 2.809
"obj and name CA" index = 42
rmsd = 3.341
"obj and name CA" index = 43
rmsd = 2.783
"obj and name CA" index = 44
rmsd = 2.666
"obj and name CA" index = 45
rmsd = 3.499
"obj and name CA" index = 46
rmsd = 3.772
"obj and name CA" index = 47
rmsd = 3.438
"obj and name CA" index = 48
rmsd = 3.810
"obj and name CA" index = 49
rmsd = 4.576
"obj and name CA" index = 50
rmsd = 4.626
"obj and name CA" index = 51
rmsd = 4.766
"obj and name CA" index = 52
rmsd = 3.981
"obj and name CA" index = 53
rmsd = 3.601
"obj and name CA" index = 54
rmsd = 2.923
"obj and name CA" index = 55
rmsd = 2.526
"obj and name CA" index = 56
rmsd = 2.217
"obj and name CA" index = 57
rmsd = 2.038
"obj and name CA" index = 58
rmsd = 2.372
"obj and name CA" index = 59
rmsd = 2.884
"obj and name CA" index = 60
rmsd = 3.328
"obj and name CA" index = 61
rmsd = 3.747
"obj and name CA" index = 62
rmsd = 3.940
"obj and name CA" index = 63
rmsd = 3.302
"obj and name CA" index = 64
rmsd = 3.374
"obj and name CA" index = 65
rmsd = 4.168
"obj and name CA" index = 66
rmsd = 4.053
"obj and name CA" index = 67
rmsd = 3.734
"obj and name CA" index = 68
rmsd = 4.403
"obj and name CA" index = 69
rmsd = 4.900
"obj and name CA" index = 70
rmsd = 4.760
"obj and name CA" index = 71
rmsd = 4.776
"obj and name CA" index = 72
rmsd = 5.496
"obj and name CA" index = 73
rmsd = 5.770
"obj and name CA" index = 74
rmsd = 5.562
"obj and name CA" index = 75
rmsd = 5.804
"obj and name CA" index = 76
rmsd = 5.054
"obj and name CA" index = 77
rmsd = 4.584
"obj and name CA" index = 78
rmsd = 3.720
"obj and name CA" index = 79
rmsd = 3.322
"obj and name CA" index = 80
rmsd = 3.092
"obj and name CA" index = 81
rmsd = 2.781
"obj and name CA" index = 82
rmsd = 3.027
"obj and name CA" index = 83
rmsd = 2.968
"obj and name CA" index = 84
rmsd = 3.095
"obj and name CA" index = 85
rmsd = 2.645
"obj and name CA" index = 86
rmsd = 3.556
"obj and name CA" index = 87
rmsd = 3.826
"obj and name CA" index = 88
rmsd = 2.981
"obj and name CA" index = 89
rmsd = 2.275
"obj and name CA" index = 90
rmsd = 2.109
"obj and name CA" index = 91
rmsd = 2.653
"obj and name CA" index = 92
rmsd = 2.815
"obj and name CA" index = 93
rmsd = 3.371
"obj and name CA" index = 94
rmsd = 3.072
"obj and name CA" index = 95
rmsd = 2.672
"obj and name CA" index = 96
rmsd = 3.040
"obj and name CA" index = 97
rmsd = 2.705
"obj and name CA" index = 98
rmsd = 1.969
"obj and name CA" index = 99
rmsd = 1.679
"obj and name CA" index = 100
rmsd = 1.015
"obj and name CA" index = 101
rmsd = 1.258
"obj and name CA" index = 102
rmsd = 1.305
"obj and name CA" index = 103
rmsd = 1.503
"obj and name CA" index = 104
rmsd = 2.078
"obj and name CA" index = 105
rmsd = 2.416
"obj and name CA" index = 106
rmsd = 3.211
"obj and name CA" index = 107
rmsd = 3.509
"obj and name CA" index = 108
rmsd = 3.999
"obj and name CA" index = 109
rmsd = 3.206
"obj and name CA" index = 110
rmsd = 2.712
"obj and name CA" index = 111
rmsd = 3.591
"obj and name CA" index = 112
rmsd = 3.569
"obj and name CA" index = 113
rmsd = 2.597
"obj and name CA" index = 114
rmsd = 2.783
"obj and name CA" index = 115
rmsd = 3.514
"obj and name CA" index = 116
rmsd = 2.961
"obj and name CA" index = 117
rmsd = 2.396
"obj and name CA" index = 118
rmsd = 3.056
"obj and name CA" index = 119
rmsd = 3.467
"obj and name CA" index = 120
rmsd = 2.848
"obj and name CA" index = 121
rmsd = 2.427
"obj and name CA" index = 122
rmsd = 3.030
"obj and name CA" index = 123
rmsd = 3.299
"obj and name CA" index = 124
rmsd = 3.138
"obj and name CA" index = 125
rmsd = 2.418
"obj and name CA" index = 126
rmsd = 2.261
"obj and name CA" index = 127
rmsd = 1.723
"obj and name CA" index = 128
rmsd = 1.720
"obj and name CA" index = 129
rmsd = 1.590
"obj and name CA" index = 130
rmsd = 1.929
"obj and name CA" index = 131
rmsd = 2.167
"obj and name CA" index = 132
rmsd = 2.225
"obj and name CA" index = 133
rmsd = 3.174
"obj and name CA" index = 134
rmsd = 3.869
"obj and name CA" index = 135
rmsd = 4.163
"obj and name CA" index = 136
rmsd = 3.704
"obj and name CA" index = 137
rmsd = 4.137
"obj and name CA" index = 138
rmsd = 4.803
"obj and name CA" index = 139
rmsd = 5.132
"obj and name CA" index = 140
rmsd = 5.390
"obj and name CA" index = 141
rmsd = 6.212
"obj and name CA" index = 142
rmsd = 6.095
"obj and name CA" index = 143
rmsd = 5.177
"obj and name CA" index = 144
rmsd = 4.844
"obj and name CA" index = 145
rmsd = 4.544
"obj and name CA" index = 146
rmsd = 4.500
"obj and name CA" index = 147
rmsd = 3.789
"obj and name CA" index = 148
rmsd = 3.968
"obj and name CA" index = 149
rmsd = 3.193
"obj and name CA" index = 150
rmsd = 2.569
"obj and name CA" index = 151
rmsd = 2.696
"obj and name CA" index = 152
rmsd = 2.762
"obj and name CA" index = 153
rmsd = 2.827
"obj and name CA" index = 154
rmsd = 3.393
"obj and name CA" index = 155
rmsd = 3.234
"obj and name CA" index = 156
rmsd = 2.642
"obj and name CA" index = 157
rmsd = 3.061
"obj and name CA" index = 158
rmsd = 3.569
"obj and name CA" index = 159
rmsd = 3.237
"obj and name CA" index = 160
rmsd = 3.046
"obj and name CA" index = 161
rmsd = 3.727
"obj and name CA" index = 162
rmsd = 3.726
"obj and name CA" index = 163
rmsd = 3.196
"obj and name CA" index = 164
rmsd = 3.593
"obj and name CA" index = 165
rmsd = 3.306
"obj and name CA" index = 166
rmsd = 3.720
"obj and name CA" index = 167
rmsd = 3.423
"obj and name CA" index = 168
rmsd = 3.314
"obj and name CA" index = 169
rmsd = 3.475
"obj and name CA" index = 170
rmsd = 3.311
"obj and name CA" index = 171
rmsd = 3.351
"obj and name CA" index = 172
rmsd = 3.522
"obj and name CA" index = 173
rmsd = 3.624
"obj and name CA" index = 174
rmsd = 4.152
"obj and name CA" index = 175
rmsd = 4.172
"obj and name CA" index = 176
rmsd = 4.809
"obj and name CA" index = 177
rmsd = 5.447
"obj and name CA" index = 178
rmsd = 6.254
"obj and name CA" index = 179
rmsd = 6.440
"obj and name CA" index = 180
rmsd = 6.692
"obj and name CA" index = 181
rmsd = 6.408
"obj and name CA" index = 182
rmsd = 5.537
"obj and name CA" index = 183
rmsd = 4.576
"obj and name CA" index = 184
rmsd = 4.037
"obj and name CA" index = 185
rmsd = 3.412
"obj and name CA" index = 186
rmsd = 3.141
"obj and name CA" index = 187
rmsd = 2.622
"obj and name CA" index = 188
rmsd = 2.556
"obj and name CA" index = 189
rmsd = 2.481
"obj and name CA" index = 190
rmsd = 2.403
"obj and name CA" index = 191
rmsd = 2.579
"obj and name CA" index = 192
rmsd = 2.694
"obj and name CA" index = 193
rmsd = 3.166
"obj and name CA" index = 194
rmsd = 3.344
"obj and name CA" index = 195
rmsd = 3.879
"obj and name CA" index = 196
rmsd = 4.397
"obj and name CA" index = 197
rmsd = 5.622
"obj and name CA" index = 198
rmsd = 6.814
"obj and name CA" index = 199
rmsd = 8.084
"obj and name CA" index = 200
rmsd = 10.405
"obj and name CA" index = 201
rmsd = 12.618
"obj and name CA" index = 202
rmsd = 14.175
PyMOL>cartoon putty, yesfit_ALL and name CA
PyMOL>show cartoon, yesfit_ALL and name CA
PyMOL>color red, ss h
 Executive: Colored 153 atoms.
PyMOL>color cyan,ss s
 Executive: Colored 117 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 6204 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: 1.30 sec. = 2761.2 frames/hour (8.19 sec. accum.).
PyMOL>png sausage.png
 ScenePNG: wrote 600x600 pixel image to file "sausage.png".
PyMOL>quit