PyMOL>load ./selSi.pdb,obj
HEADER    DNA BINDING PROTEIN                     30-JUN-08   2K5V
TITLE     SOLUTION NMR STRUCTURE OF THE SECOND OB-FOLD DOMAIN OF
TITLE    2 REPLICATION PROTEIN A FROM METHANOCOCCUS MARIPALUDIS.
TITLE    3 NORTHEAST STRUCTURAL GENOMICS TARGET MRR110B.
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: REPLICATION PROTEIN A;
COMPND   3 CHAIN: A;
COMPND   4 ENGINEERED: YES;
COMPND   5 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 3 atoms.
PyMOL>color cyan,ss s
 Executive: Colored 43 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 1481 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: 1.30 sec. = 2761.5 frames/hour (1.30 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: 5.30 sec. = 679.4 frames/hour (6.60 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, 2.3736231327056885, 1.8945177793502808, 2.3448295593261719, 2.3326244354248047, 1.9076961278915405, 2.6517837047576904, 2.3794047832489014, 1.8562726974487305, 1.9896001815795898, 2.0825185775756836, 1.9229974746704102, 2.1862766742706299, 1.571901798248291, 1.8254526853561401, 1.7058628797531128, 1.8725861310958862, 2.5209040641784668, 1.696000337600708, 1.617117166519165]
-> 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 = 1.437
"obj and name CA" index = 2
rmsd = 0.741
"obj and name CA" index = 3
rmsd = 0.448
"obj and name CA" index = 4
rmsd = 0.512
"obj and name CA" index = 5
rmsd = 0.428
"obj and name CA" index = 6
rmsd = 0.608
"obj and name CA" index = 7
rmsd = 0.701
"obj and name CA" index = 8
rmsd = 0.663
"obj and name CA" index = 9
rmsd = 0.633
"obj and name CA" index = 10
rmsd = 0.605
"obj and name CA" index = 11
rmsd = 0.629
"obj and name CA" index = 12
rmsd = 0.557
"obj and name CA" index = 13
rmsd = 0.594
"obj and name CA" index = 14
rmsd = 0.522
"obj and name CA" index = 15
rmsd = 0.421
"obj and name CA" index = 16
rmsd = 0.412
"obj and name CA" index = 17
rmsd = 0.517
"obj and name CA" index = 18
rmsd = 0.493
"obj and name CA" index = 19
rmsd = 0.608
"obj and name CA" index = 20
rmsd = 0.491
"obj and name CA" index = 21
rmsd = 0.611
"obj and name CA" index = 22
rmsd = 0.557
"obj and name CA" index = 23
rmsd = 0.623
"obj and name CA" index = 24
rmsd = 0.766
"obj and name CA" index = 25
rmsd = 0.987
"obj and name CA" index = 26
rmsd = 0.868
"obj and name CA" index = 27
rmsd = 0.812
"obj and name CA" index = 28
rmsd = 0.814
"obj and name CA" index = 29
rmsd = 0.776
"obj and name CA" index = 30
rmsd = 0.930
"obj and name CA" index = 31
rmsd = 1.019
"obj and name CA" index = 32
rmsd = 1.801
"obj and name CA" index = 33
rmsd = 1.973
"obj and name CA" index = 34
rmsd = 2.365
"obj and name CA" index = 35
rmsd = 1.545
"obj and name CA" index = 36
rmsd = 1.436
"obj and name CA" index = 37
rmsd = 0.890
"obj and name CA" index = 38
rmsd = 0.614
"obj and name CA" index = 39
rmsd = 0.562
"obj and name CA" index = 40
rmsd = 0.475
"obj and name CA" index = 41
rmsd = 0.628
"obj and name CA" index = 42
rmsd = 0.497
"obj and name CA" index = 43
rmsd = 0.491
"obj and name CA" index = 44
rmsd = 0.451
"obj and name CA" index = 45
rmsd = 0.553
"obj and name CA" index = 46
rmsd = 0.608
"obj and name CA" index = 47
rmsd = 0.803
"obj and name CA" index = 48
rmsd = 0.714
"obj and name CA" index = 49
rmsd = 0.585
"obj and name CA" index = 50
rmsd = 0.509
"obj and name CA" index = 51
rmsd = 0.433
"obj and name CA" index = 52
rmsd = 0.596
"obj and name CA" index = 53
rmsd = 0.574
"obj and name CA" index = 54
rmsd = 0.484
"obj and name CA" index = 55
rmsd = 0.419
"obj and name CA" index = 56
rmsd = 0.492
"obj and name CA" index = 57
rmsd = 0.700
"obj and name CA" index = 58
rmsd = 0.788
"obj and name CA" index = 59
rmsd = 0.591
"obj and name CA" index = 60
rmsd = 0.641
"obj and name CA" index = 61
rmsd = 0.749
"obj and name CA" index = 62
rmsd = 0.687
"obj and name CA" index = 63
rmsd = 1.045
"obj and name CA" index = 64
rmsd = 0.716
"obj and name CA" index = 65
rmsd = 0.906
"obj and name CA" index = 66
rmsd = 0.785
"obj and name CA" index = 67
rmsd = 0.900
"obj and name CA" index = 68
rmsd = 0.852
"obj and name CA" index = 69
rmsd = 0.631
"obj and name CA" index = 70
rmsd = 0.589
"obj and name CA" index = 71
rmsd = 0.551
"obj and name CA" index = 72
rmsd = 0.398
"obj and name CA" index = 73
rmsd = 0.390
"obj and name CA" index = 74
rmsd = 0.495
"obj and name CA" index = 75
rmsd = 0.433
"obj and name CA" index = 76
rmsd = 0.428
"obj and name CA" index = 77
rmsd = 0.543
"obj and name CA" index = 78
rmsd = 0.785
"obj and name CA" index = 79
rmsd = 1.367
"obj and name CA" index = 80
rmsd = 2.192
"obj and name CA" index = 81
rmsd = 2.394
"obj and name CA" index = 82
rmsd = 1.352
"obj and name CA" index = 83
rmsd = 0.707
"obj and name CA" index = 84
rmsd = 0.660
"obj and name CA" index = 85
rmsd = 0.463
"obj and name CA" index = 86
rmsd = 0.439
"obj and name CA" index = 87
rmsd = 0.404
"obj and name CA" index = 88
rmsd = 0.568
"obj and name CA" index = 89
rmsd = 0.597
"obj and name CA" index = 90
rmsd = 0.533
"obj and name CA" index = 91
rmsd = 0.739
"obj and name CA" index = 92
rmsd = 0.718
"obj and name CA" index = 93
rmsd = 0.598
"obj and name CA" index = 94
rmsd = 0.768
"obj and name CA" index = 95
rmsd = 1.380
"obj and name CA" index = 96
rmsd = 2.651
"obj and name CA" index = 97
rmsd = 3.382
"obj and name CA" index = 98
rmsd = 4.693
PyMOL>cartoon putty, yesfit_ALL and name CA
PyMOL>show cartoon, yesfit_ALL and name CA
PyMOL>color red, ss h
 Executive: Colored 9 atoms.
PyMOL>color cyan,ss s
 Executive: Colored 129 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 3014 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: 1.70 sec. = 2123.2 frames/hour (8.30 sec. accum.).
PyMOL>png sausage.png
 ScenePNG: wrote 600x600 pixel image to file "sausage.png".
PyMOL>quit