PyMOL>load ./selSi.pdb,obj
HEADER    STRUCTURAL GENOMICS, UNKNOWN FUNCTION   30-JUN-09   2KL6
TITLE     SOLUTION NMR STRUCTURE OF THE CARDB DOMAIN OF PF1109 FROM
TITLE    2 PYROCOCCUS FURIOSUS. NORTHEAST STRUCTURAL GENOMICS
TITLE    3 CONSORTIUM TARGET PFR193A
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: UNCHARACTERIZED PROTEIN;
COMPND   3 CHAIN: A;
COMPND   4 FRAGMENT: SEQUENCE DATABASE RESIDUES 436-540;
COMPND   5 ENGINEERED: YES;
COMPND   6 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
PyMOL>color cyan,ss s
 Executive: Colored 61 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 1628 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: 1.44 sec. = 2497.2 frames/hour (1.44 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 324 atoms.
PyMOL>hide everything,all
PyMOL>show lines,bb
PyMOL>color blue,bb
 Executive: Colored 324 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: 4.12 sec. = 874.3 frames/hour (5.56 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, 0.45342093706130981, 0.56151676177978516, 0.51405549049377441, 0.56737989187240601, 0.56170833110809326, 0.45502296090126038, 0.53548264503479004, 0.46273007988929749, 0.443341463804245, 0.44835525751113892, 0.49042248725891113, 0.60846555233001709, 0.41107636690139771, 0.43360334634780884, 0.65307760238647461, 0.54293167591094971, 0.42650634050369263, 0.54344415664672852, 0.53962284326553345]
-> atom index_map =  [None, 2, 21, 36, 56, 70, 82, 101, 115, 131, 146, 165, 187, 194, 208, 220, 236, 252, 259, 275, 289, 311, 330, 340, 355, 376, 391, 407, 425, 441, 463, 477, 496, 503, 510, 529, 536, 552, 566, 577, 591, 613, 629, 653, 669, 690, 709, 723, 730, 744, 763, 784, 806, 820, 844, 858, 874, 885, 904, 911, 925, 947, 962, 977, 999, 1015, 1034, 1048, 1068, 1079, 1103, 1117, 1131, 1145, 1162, 1177, 1184, 1201, 1222, 1246, 1265, 1279, 1289, 1303, 1319, 1331, 1346, 1361, 1375, 1389, 1405, 1421, 1436, 1455, 1469, 1484, 1498, 1512, 1526, 1542, 1552, 1566, 1586, 1598, 1614, 1625, 1641, 1657, 1676]
"obj and name CA" index = 1
rmsd = 1.093
"obj and name CA" index = 2
rmsd = 0.637
"obj and name CA" index = 3
rmsd = 0.433
"obj and name CA" index = 4
rmsd = 0.283
"obj and name CA" index = 5
rmsd = 0.289
"obj and name CA" index = 6
rmsd = 0.227
"obj and name CA" index = 7
rmsd = 0.286
"obj and name CA" index = 8
rmsd = 0.298
"obj and name CA" index = 9
rmsd = 0.275
"obj and name CA" index = 10
rmsd = 0.258
"obj and name CA" index = 11
rmsd = 0.263
"obj and name CA" index = 12
rmsd = 0.287
"obj and name CA" index = 13
rmsd = 0.329
"obj and name CA" index = 14
rmsd = 0.398
"obj and name CA" index = 15
rmsd = 0.347
"obj and name CA" index = 16
rmsd = 0.279
"obj and name CA" index = 17
rmsd = 0.328
"obj and name CA" index = 18
rmsd = 0.294
"obj and name CA" index = 19
rmsd = 0.369
"obj and name CA" index = 20
rmsd = 0.350
"obj and name CA" index = 21
rmsd = 0.358
"obj and name CA" index = 22
rmsd = 0.324
"obj and name CA" index = 23
rmsd = 0.358
"obj and name CA" index = 24
rmsd = 0.270
"obj and name CA" index = 25
rmsd = 0.333
"obj and name CA" index = 26
rmsd = 0.356
"obj and name CA" index = 27
rmsd = 0.297
"obj and name CA" index = 28
rmsd = 0.287
"obj and name CA" index = 29
rmsd = 0.274
"obj and name CA" index = 30
rmsd = 0.243
"obj and name CA" index = 31
rmsd = 0.305
"obj and name CA" index = 32
rmsd = 0.292
"obj and name CA" index = 33
rmsd = 0.332
"obj and name CA" index = 34
rmsd = 0.289
"obj and name CA" index = 35
rmsd = 0.363
"obj and name CA" index = 36
rmsd = 0.302
"obj and name CA" index = 37
rmsd = 0.400
"obj and name CA" index = 38
rmsd = 0.535
"obj and name CA" index = 39
rmsd = 0.332
"obj and name CA" index = 40
rmsd = 0.272
"obj and name CA" index = 41
rmsd = 0.307
"obj and name CA" index = 42
rmsd = 0.311
"obj and name CA" index = 43
rmsd = 0.222
"obj and name CA" index = 44
rmsd = 0.251
"obj and name CA" index = 45
rmsd = 0.276
"obj and name CA" index = 46
rmsd = 0.450
"obj and name CA" index = 47
rmsd = 0.547
"obj and name CA" index = 48
rmsd = 0.393
"obj and name CA" index = 49
rmsd = 0.365
"obj and name CA" index = 50
rmsd = 0.307
"obj and name CA" index = 51
rmsd = 0.320
"obj and name CA" index = 52
rmsd = 0.372
"obj and name CA" index = 53
rmsd = 0.298
"obj and name CA" index = 54
rmsd = 0.331
"obj and name CA" index = 55
rmsd = 0.316
"obj and name CA" index = 56
rmsd = 0.315
"obj and name CA" index = 57
rmsd = 0.275
"obj and name CA" index = 58
rmsd = 0.322
"obj and name CA" index = 59
rmsd = 0.353
"obj and name CA" index = 60
rmsd = 0.323
"obj and name CA" index = 61
rmsd = 0.320
"obj and name CA" index = 62
rmsd = 0.284
"obj and name CA" index = 63
rmsd = 0.292
"obj and name CA" index = 64
rmsd = 0.307
"obj and name CA" index = 65
rmsd = 0.303
"obj and name CA" index = 66
rmsd = 0.324
"obj and name CA" index = 67
rmsd = 0.325
"obj and name CA" index = 68
rmsd = 0.390
"obj and name CA" index = 69
rmsd = 0.301
"obj and name CA" index = 70
rmsd = 0.273
"obj and name CA" index = 71
rmsd = 0.291
"obj and name CA" index = 72
rmsd = 0.519
"obj and name CA" index = 73
rmsd = 0.489
"obj and name CA" index = 74
rmsd = 0.455
"obj and name CA" index = 75
rmsd = 0.485
"obj and name CA" index = 76
rmsd = 0.462
"obj and name CA" index = 77
rmsd = 0.353
"obj and name CA" index = 78
rmsd = 0.346
"obj and name CA" index = 79
rmsd = 0.246
"obj and name CA" index = 80
rmsd = 0.252
"obj and name CA" index = 81
rmsd = 0.261
"obj and name CA" index = 82
rmsd = 0.285
"obj and name CA" index = 83
rmsd = 0.363
"obj and name CA" index = 84
rmsd = 0.449
"obj and name CA" index = 85
rmsd = 0.750
"obj and name CA" index = 86
rmsd = 0.803
"obj and name CA" index = 87
rmsd = 0.819
"obj and name CA" index = 88
rmsd = 0.583
"obj and name CA" index = 89
rmsd = 0.635
"obj and name CA" index = 90
rmsd = 0.708
"obj and name CA" index = 91
rmsd = 0.537
"obj and name CA" index = 92
rmsd = 0.527
"obj and name CA" index = 93
rmsd = 0.498
"obj and name CA" index = 94
rmsd = 0.785
"obj and name CA" index = 95
rmsd = 0.691
"obj and name CA" index = 96
rmsd = 0.534
"obj and name CA" index = 97
rmsd = 0.312
"obj and name CA" index = 98
rmsd = 0.281
"obj and name CA" index = 99
rmsd = 0.285
"obj and name CA" index = 100
rmsd = 0.323
"obj and name CA" index = 101
rmsd = 0.327
"obj and name CA" index = 102
rmsd = 0.365
"obj and name CA" index = 103
rmsd = 0.274
"obj and name CA" index = 104
rmsd = 0.285
"obj and name CA" index = 105
rmsd = 0.259
"obj and name CA" index = 106
rmsd = 0.355
"obj and name CA" index = 107
rmsd = 0.445
"obj and name CA" index = 108
rmsd = 0.864
PyMOL>cartoon putty, yesfit_ALL and name CA
PyMOL>show cartoon, yesfit_ALL and name CA
PyMOL>color red, ss h
PyMOL>color cyan,ss s
 Executive: Colored 183 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 3303 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: 1.68 sec. = 2139.9 frames/hour (7.24 sec. accum.).
PyMOL>png sausage.png
 ScenePNG: wrote 600x600 pixel image to file "sausage.png".
PyMOL>quit