PyMOL>load ./selSi.pdb,obj
HEADER    TRANSFERASE                             08-SEP-09   2KO1
TITLE     SOLUTION NMR STRUCTURE OF THE ACT DOMAIN FROM GTP
TITLE    2 PYROPHOSPHOKINASE OF CHLOROBIUM TEPIDUM. NORTHEAST
TITLE    3 STRUCTURAL GENOMICS CONSORTIUM TARGET CTR148A
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: GTP PYROPHOSPHOKINASE;
COMPND   3 CHAIN: A, B;
COMPND   4 SYNONYM: CTR148A;
COMPND   5 EC: 2.7.6.5;
COMPND   6 ENGINEERED: YES;
COMPND   7 MUTATION: YES
 ObjectMolecule: Read secondary structure assignments.
 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 775 atoms.
PyMOL>color cyan,ss s
 Executive: Colored 1183 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 900 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: 1.85 sec. = 1950.6 frames/hour (1.85 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 528 atoms.
PyMOL>hide everything,all
PyMOL>show lines,bb
PyMOL>color blue,bb
 Executive: Colored 528 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: 6.86 sec. = 524.6 frames/hour (8.71 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, 2.3478667736053467, 1.5867233276367188, 2.9066617488861084, 2.226588249206543, 2.0488741397857666, 3.0310800075531006, 2.0954735279083252, 2.5667135715484619, 1.5492608547210693, 2.0777513980865479, 1.9790867567062378, 2.0651645660400391, 2.6185224056243896, 2.3301403522491455, 2.1208324432373047, 2.0620079040527344, 2.0762310028076172, 2.1914317607879639, 2.5039951801300049]
-> atom index_map =  [None, 2, 21, 35, 47, 67, 86, 96, 103, 122, 146, 165, 181, 188, 203, 215, 237, 251, 258, 275, 289, 303, 320, 339, 353, 360, 376, 395, 406, 428, 448, 460, 474, 488, 507, 531, 545, 564, 580, 599, 613, 623, 645, 657, 664, 683, 703, 717, 728, 742, 761, 778, 797, 817, 833, 855, 869, 883, 895, 917, 936, 950, 964, 983, 1000, 1012, 1034, 1053, 1077, 1099, 1115, 1132, 1139, 1155, 1175, 1189, 1205, 1220, 1244, 1263, 1274, 1288, 1307, 1322, 1340, 1358, 1376, 1394, 1412, 1431, 1450, 1464, 1476, 1496, 1515, 1525, 1532, 1551, 1575, 1594, 1610, 1617, 1632, 1644, 1666, 1680, 1687, 1704, 1718, 1732, 1749, 1768, 1782, 1789, 1805, 1824, 1835, 1857, 1877, 1889, 1903, 1917, 1936, 1960, 1974, 1993, 2009, 2028, 2042, 2052, 2074, 2086, 2093, 2112, 2132, 2146, 2157, 2171, 2190, 2207, 2226, 2246, 2262, 2284, 2298, 2312, 2324, 2346, 2365, 2379, 2393, 2412, 2429, 2441, 2463, 2482, 2506, 2528, 2544, 2561, 2568, 2584, 2604, 2618, 2634, 2649, 2673, 2692, 2703, 2717, 2736, 2751, 2769, 2787, 2805, 2823, 2841]
"obj and name CA" index = 1
rmsd = 3.059
"obj and name CA" index = 2
rmsd = 1.331
"obj and name CA" index = 3
rmsd = 0.876
"obj and name CA" index = 4
rmsd = 0.704
"obj and name CA" index = 5
rmsd = 0.565
"obj and name CA" index = 6
rmsd = 0.469
"obj and name CA" index = 7
rmsd = 0.403
"obj and name CA" index = 8
rmsd = 0.370
"obj and name CA" index = 9
rmsd = 0.429
"obj and name CA" index = 10
rmsd = 0.369
"obj and name CA" index = 11
rmsd = 0.428
"obj and name CA" index = 12
rmsd = 0.486
"obj and name CA" index = 13
rmsd = 0.579
"obj and name CA" index = 14
rmsd = 0.642
"obj and name CA" index = 15
rmsd = 0.788
"obj and name CA" index = 16
rmsd = 1.288
"obj and name CA" index = 17
rmsd = 0.791
"obj and name CA" index = 18
rmsd = 0.411
"obj and name CA" index = 19
rmsd = 0.364
"obj and name CA" index = 20
rmsd = 0.384
"obj and name CA" index = 21
rmsd = 0.358
"obj and name CA" index = 22
rmsd = 0.279
"obj and name CA" index = 23
rmsd = 0.301
"obj and name CA" index = 24
rmsd = 0.378
"obj and name CA" index = 25
rmsd = 0.400
"obj and name CA" index = 26
rmsd = 0.325
"obj and name CA" index = 27
rmsd = 0.520
"obj and name CA" index = 28
rmsd = 0.708
"obj and name CA" index = 29
rmsd = 0.590
"obj and name CA" index = 30
rmsd = 0.774
"obj and name CA" index = 31
rmsd = 0.502
"obj and name CA" index = 32
rmsd = 0.499
"obj and name CA" index = 33
rmsd = 0.428
"obj and name CA" index = 34
rmsd = 0.478
"obj and name CA" index = 35
rmsd = 0.414
"obj and name CA" index = 36
rmsd = 0.443
"obj and name CA" index = 37
rmsd = 0.403
"obj and name CA" index = 38
rmsd = 0.357
"obj and name CA" index = 39
rmsd = 0.431
"obj and name CA" index = 40
rmsd = 0.487
"obj and name CA" index = 41
rmsd = 0.704
"obj and name CA" index = 42
rmsd = 1.041
"obj and name CA" index = 43
rmsd = 0.750
"obj and name CA" index = 44
rmsd = 0.541
"obj and name CA" index = 45
rmsd = 0.429
"obj and name CA" index = 46
rmsd = 0.414
"obj and name CA" index = 47
rmsd = 0.382
"obj and name CA" index = 48
rmsd = 0.353
"obj and name CA" index = 49
rmsd = 0.322
"obj and name CA" index = 50
rmsd = 0.391
"obj and name CA" index = 51
rmsd = 0.416
"obj and name CA" index = 52
rmsd = 0.489
"obj and name CA" index = 53
rmsd = 0.540
"obj and name CA" index = 54
rmsd = 0.746
"obj and name CA" index = 55
rmsd = 0.628
"obj and name CA" index = 56
rmsd = 0.573
"obj and name CA" index = 57
rmsd = 0.606
"obj and name CA" index = 58
rmsd = 0.510
"obj and name CA" index = 59
rmsd = 0.386
"obj and name CA" index = 60
rmsd = 0.443
"obj and name CA" index = 61
rmsd = 0.492
"obj and name CA" index = 62
rmsd = 0.397
"obj and name CA" index = 63
rmsd = 0.442
"obj and name CA" index = 64
rmsd = 0.480
"obj and name CA" index = 65
rmsd = 0.415
"obj and name CA" index = 66
rmsd = 0.358
"obj and name CA" index = 67
rmsd = 0.456
"obj and name CA" index = 68
rmsd = 0.566
"obj and name CA" index = 69
rmsd = 0.498
"obj and name CA" index = 70
rmsd = 0.734
"obj and name CA" index = 71
rmsd = 0.588
"obj and name CA" index = 72
rmsd = 0.455
"obj and name CA" index = 73
rmsd = 0.508
"obj and name CA" index = 74
rmsd = 0.453
"obj and name CA" index = 75
rmsd = 0.416
"obj and name CA" index = 76
rmsd = 0.516
"obj and name CA" index = 77
rmsd = 0.453
"obj and name CA" index = 78
rmsd = 0.508
"obj and name CA" index = 79
rmsd = 0.763
"obj and name CA" index = 80
rmsd = 0.889
"obj and name CA" index = 81
rmsd = 0.822
"obj and name CA" index = 82
rmsd = 1.207
"obj and name CA" index = 83
rmsd = 0.897
"obj and name CA" index = 84
rmsd = 1.840
"obj and name CA" index = 85
rmsd = 2.697
"obj and name CA" index = 86
rmsd = 4.234
"obj and name CA" index = 87
rmsd = 5.885
"obj and name CA" index = 88
rmsd = 6.926
"obj and name CA" index = 89
rmsd = 3.270
"obj and name CA" index = 90
rmsd = 1.161
"obj and name CA" index = 91
rmsd = 0.704
"obj and name CA" index = 92
rmsd = 0.509
"obj and name CA" index = 93
rmsd = 0.393
"obj and name CA" index = 94
rmsd = 0.356
"obj and name CA" index = 95
rmsd = 0.360
"obj and name CA" index = 96
rmsd = 0.302
"obj and name CA" index = 97
rmsd = 0.356
"obj and name CA" index = 98
rmsd = 0.326
"obj and name CA" index = 99
rmsd = 0.386
"obj and name CA" index = 100
rmsd = 0.451
"obj and name CA" index = 101
rmsd = 0.558
"obj and name CA" index = 102
rmsd = 0.704
"obj and name CA" index = 103
rmsd = 0.788
"obj and name CA" index = 104
rmsd = 1.024
"obj and name CA" index = 105
rmsd = 0.604
"obj and name CA" index = 106
rmsd = 0.412
"obj and name CA" index = 107
rmsd = 0.414
"obj and name CA" index = 108
rmsd = 0.459
"obj and name CA" index = 109
rmsd = 0.389
"obj and name CA" index = 110
rmsd = 0.336
"obj and name CA" index = 111
rmsd = 0.376
"obj and name CA" index = 112
rmsd = 0.390
"obj and name CA" index = 113
rmsd = 0.391
"obj and name CA" index = 114
rmsd = 0.398
"obj and name CA" index = 115
rmsd = 0.509
"obj and name CA" index = 116
rmsd = 0.613
"obj and name CA" index = 117
rmsd = 0.494
"obj and name CA" index = 118
rmsd = 0.664
"obj and name CA" index = 119
rmsd = 0.445
"obj and name CA" index = 120
rmsd = 0.448
"obj and name CA" index = 121
rmsd = 0.413
"obj and name CA" index = 122
rmsd = 0.381
"obj and name CA" index = 123
rmsd = 0.321
"obj and name CA" index = 124
rmsd = 0.402
"obj and name CA" index = 125
rmsd = 0.408
"obj and name CA" index = 126
rmsd = 0.377
"obj and name CA" index = 127
rmsd = 0.488
"obj and name CA" index = 128
rmsd = 0.567
"obj and name CA" index = 129
rmsd = 0.740
"obj and name CA" index = 130
rmsd = 0.942
"obj and name CA" index = 131
rmsd = 0.684
"obj and name CA" index = 132
rmsd = 0.496
"obj and name CA" index = 133
rmsd = 0.442
"obj and name CA" index = 134
rmsd = 0.432
"obj and name CA" index = 135
rmsd = 0.412
"obj and name CA" index = 136
rmsd = 0.397
"obj and name CA" index = 137
rmsd = 0.305
"obj and name CA" index = 138
rmsd = 0.308
"obj and name CA" index = 139
rmsd = 0.315
"obj and name CA" index = 140
rmsd = 0.348
"obj and name CA" index = 141
rmsd = 0.410
"obj and name CA" index = 142
rmsd = 0.583
"obj and name CA" index = 143
rmsd = 0.573
"obj and name CA" index = 144
rmsd = 0.471
"obj and name CA" index = 145
rmsd = 0.491
"obj and name CA" index = 146
rmsd = 0.469
"obj and name CA" index = 147
rmsd = 0.361
"obj and name CA" index = 148
rmsd = 0.424
"obj and name CA" index = 149
rmsd = 0.446
"obj and name CA" index = 150
rmsd = 0.347
"obj and name CA" index = 151
rmsd = 0.348
"obj and name CA" index = 152
rmsd = 0.383
"obj and name CA" index = 153
rmsd = 0.373
"obj and name CA" index = 154
rmsd = 0.343
"obj and name CA" index = 155
rmsd = 0.386
"obj and name CA" index = 156
rmsd = 0.443
"obj and name CA" index = 157
rmsd = 0.459
"obj and name CA" index = 158
rmsd = 0.715
"obj and name CA" index = 159
rmsd = 0.595
"obj and name CA" index = 160
rmsd = 0.416
"obj and name CA" index = 161
rmsd = 0.488
"obj and name CA" index = 162
rmsd = 0.421
"obj and name CA" index = 163
rmsd = 0.343
"obj and name CA" index = 164
rmsd = 0.481
"obj and name CA" index = 165
rmsd = 0.452
"obj and name CA" index = 166
rmsd = 0.550
"obj and name CA" index = 167
rmsd = 0.905
"obj and name CA" index = 168
rmsd = 0.798
"obj and name CA" index = 169
rmsd = 0.773
"obj and name CA" index = 170
rmsd = 1.340
"obj and name CA" index = 171
rmsd = 0.775
"obj and name CA" index = 172
rmsd = 1.617
"obj and name CA" index = 173
rmsd = 2.853
"obj and name CA" index = 174
rmsd = 4.194
"obj and name CA" index = 175
rmsd = 6.349
"obj and name CA" index = 176
rmsd = 8.619
PyMOL>cartoon putty, yesfit_ALL and name CA
PyMOL>show cartoon, yesfit_ALL and name CA
PyMOL>color red, ss h
 Executive: Colored 1598 atoms.
PyMOL>color cyan,ss s
 Executive: Colored 2430 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 1864 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: 2.36 sec. = 1522.2 frames/hour (11.07 sec. accum.).
PyMOL>png sausage.png
 ScenePNG: wrote 600x600 pixel image to file "sausage.png".
PyMOL>quit