PyMOL>load ./selSi.pdb,obj
HEADER    STRUCTURAL GENOMICS, UNKNOWN FUNCTION   18-OCT-09   2KPP
TITLE     SOLUTION NMR STRUCTURE OF LIN0431 PROTEIN FROM LISTERIA INNOCUA.
TITLE    2 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET LKR112
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: LIN0431 PROTEIN;
COMPND   3 CHAIN: A;
COMPND   4 FRAGMENT: SEQUENCE DATABASE RESIDUES 36-140;
COMPND   5 ENGINEERED: 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 148 atoms.
PyMOL>color cyan,ss s
 Executive: Colored 807 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 848 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: 0.88 sec. = 4068.2 frames/hour (0.88 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 342 atoms.
PyMOL>hide everything,all
PyMOL>show lines,bb
PyMOL>color blue,bb
 Executive: Colored 342 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: 2.79 sec. = 1288.4 frames/hour (3.68 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, 4.4626474380493164, 3.8969321250915527, 13.72370719909668, 2.2416524887084961, 18.830583572387695, 7.2111420631408691, 3.3977956771850586, 4.9915823936462402, 4.4276328086853027, 9.8566493988037109, 3.6076209545135498, 16.476373672485352, 14.13042163848877, 8.8861579895019531, 15.76799201965332, 8.6750335693359375, 8.0518121719360352, 5.5641875267028809, 4.5486440658569336]
-> atom index_map =  [None, 2, 21, 43, 57, 71, 78, 90, 105, 121, 137, 147, 166, 185, 196, 213, 227, 234, 256, 272, 291, 315, 330, 349, 363, 382, 396, 403, 421, 443, 450, 464, 479, 496, 516, 530, 549, 571, 578, 600, 607, 617, 634, 655, 669, 688, 705, 720, 736, 748, 755, 770, 794, 813, 837, 856, 878, 893, 905, 919, 930, 944, 956, 973, 989, 996, 1012, 1034, 1051, 1058, 1082, 1104, 1115, 1137, 1147, 1154, 1166, 1180, 1199, 1215, 1226, 1245, 1259, 1277, 1299, 1315, 1335, 1351, 1366, 1385, 1407, 1418, 1432, 1449, 1471, 1483, 1494, 1516, 1528, 1542, 1554, 1568, 1580, 1599, 1618, 1634, 1648, 1662, 1681, 1696, 1714, 1732, 1750, 1768, 1786]
"obj and name CA" index = 1
rmsd = 10.428
"obj and name CA" index = 2
rmsd = 9.618
"obj and name CA" index = 3
rmsd = 8.212
"obj and name CA" index = 4
rmsd = 7.031
"obj and name CA" index = 5
rmsd = 6.823
"obj and name CA" index = 6
rmsd = 5.596
"obj and name CA" index = 7
rmsd = 4.581
"obj and name CA" index = 8
rmsd = 3.747
"obj and name CA" index = 9
rmsd = 3.452
"obj and name CA" index = 10
rmsd = 2.987
"obj and name CA" index = 11
rmsd = 4.645
"obj and name CA" index = 12
rmsd = 4.999
"obj and name CA" index = 13
rmsd = 6.684
"obj and name CA" index = 14
rmsd = 7.646
"obj and name CA" index = 15
rmsd = 9.203
"obj and name CA" index = 16
rmsd = 9.396
"obj and name CA" index = 17
rmsd = 9.348
"obj and name CA" index = 18
rmsd = 7.955
"obj and name CA" index = 19
rmsd = 7.817
"obj and name CA" index = 20
rmsd = 6.333
"obj and name CA" index = 21
rmsd = 5.206
"obj and name CA" index = 22
rmsd = 3.880
"obj and name CA" index = 23
rmsd = 3.547
"obj and name CA" index = 24
rmsd = 2.626
"obj and name CA" index = 25
rmsd = 3.587
"obj and name CA" index = 26
rmsd = 4.366
"obj and name CA" index = 27
rmsd = 4.071
"obj and name CA" index = 28
rmsd = 5.280
"obj and name CA" index = 29
rmsd = 5.801
"obj and name CA" index = 30
rmsd = 5.328
"obj and name CA" index = 31
rmsd = 4.952
"obj and name CA" index = 32
rmsd = 5.106
"obj and name CA" index = 33
rmsd = 5.657
"obj and name CA" index = 34
rmsd = 6.310
"obj and name CA" index = 35
rmsd = 6.604
"obj and name CA" index = 36
rmsd = 8.174
"obj and name CA" index = 37
rmsd = 8.591
"obj and name CA" index = 38
rmsd = 9.912
"obj and name CA" index = 39
rmsd = 10.290
"obj and name CA" index = 40
rmsd = 9.309
"obj and name CA" index = 41
rmsd = 7.882
"obj and name CA" index = 42
rmsd = 6.929
"obj and name CA" index = 43
rmsd = 5.257
"obj and name CA" index = 44
rmsd = 4.913
"obj and name CA" index = 45
rmsd = 3.567
"obj and name CA" index = 46
rmsd = 3.494
"obj and name CA" index = 47
rmsd = 2.936
"obj and name CA" index = 48
rmsd = 4.085
"obj and name CA" index = 49
rmsd = 4.388
"obj and name CA" index = 50
rmsd = 3.483
"obj and name CA" index = 51
rmsd = 2.814
"obj and name CA" index = 52
rmsd = 1.757
"obj and name CA" index = 53
rmsd = 2.155
"obj and name CA" index = 54
rmsd = 2.842
"obj and name CA" index = 55
rmsd = 4.270
"obj and name CA" index = 56
rmsd = 4.935
"obj and name CA" index = 57
rmsd = 5.234
"obj and name CA" index = 58
rmsd = 6.397
"obj and name CA" index = 59
rmsd = 5.990
"obj and name CA" index = 60
rmsd = 6.538
"obj and name CA" index = 61
rmsd = 5.739
"obj and name CA" index = 62
rmsd = 4.895
"obj and name CA" index = 63
rmsd = 4.612
"obj and name CA" index = 64
rmsd = 3.561
"obj and name CA" index = 65
rmsd = 3.935
"obj and name CA" index = 66
rmsd = 4.715
"obj and name CA" index = 67
rmsd = 3.970
"obj and name CA" index = 68
rmsd = 3.892
"obj and name CA" index = 69
rmsd = 3.500
"obj and name CA" index = 70
rmsd = 2.822
"obj and name CA" index = 71
rmsd = 3.072
"obj and name CA" index = 72
rmsd = 4.201
"obj and name CA" index = 73
rmsd = 4.664
"obj and name CA" index = 74
rmsd = 5.161
"obj and name CA" index = 75
rmsd = 3.965
"obj and name CA" index = 76
rmsd = 3.872
"obj and name CA" index = 77
rmsd = 3.405
"obj and name CA" index = 78
rmsd = 4.680
"obj and name CA" index = 79
rmsd = 5.074
"obj and name CA" index = 80
rmsd = 6.607
"obj and name CA" index = 81
rmsd = 7.121
"obj and name CA" index = 82
rmsd = 6.941
"obj and name CA" index = 83
rmsd = 7.447
"obj and name CA" index = 84
rmsd = 6.015
"obj and name CA" index = 85
rmsd = 5.335
"obj and name CA" index = 86
rmsd = 4.035
"obj and name CA" index = 87
rmsd = 4.207
"obj and name CA" index = 88
rmsd = 3.463
"obj and name CA" index = 89
rmsd = 4.741
"obj and name CA" index = 90
rmsd = 5.100
"obj and name CA" index = 91
rmsd = 5.744
"obj and name CA" index = 92
rmsd = 6.606
"obj and name CA" index = 93
rmsd = 7.427
"obj and name CA" index = 94
rmsd = 7.039
"obj and name CA" index = 95
rmsd = 7.969
"obj and name CA" index = 96
rmsd = 7.272
"obj and name CA" index = 97
rmsd = 7.720
"obj and name CA" index = 98
rmsd = 8.495
"obj and name CA" index = 99
rmsd = 8.357
"obj and name CA" index = 100
rmsd = 7.331
"obj and name CA" index = 101
rmsd = 7.251
"obj and name CA" index = 102
rmsd = 7.521
"obj and name CA" index = 103
rmsd = 8.339
"obj and name CA" index = 104
rmsd = 9.754
"obj and name CA" index = 105
rmsd = 10.964
"obj and name CA" index = 106
rmsd = 12.317
"obj and name CA" index = 107
rmsd = 14.498
"obj and name CA" index = 108
rmsd = 15.515
"obj and name CA" index = 109
rmsd = 16.813
"obj and name CA" index = 110
rmsd = 18.344
"obj and name CA" index = 111
rmsd = 20.220
"obj and name CA" index = 112
rmsd = 21.741
"obj and name CA" index = 113
rmsd = 23.782
"obj and name CA" index = 114
rmsd = 25.483
PyMOL>cartoon putty, yesfit_ALL and name CA
PyMOL>show cartoon, yesfit_ALL and name CA
PyMOL>color red, ss h
 Executive: Colored 301 atoms.
PyMOL>color cyan,ss s
 Executive: Colored 1661 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 1758 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: 1.59 sec. = 2266.6 frames/hour (5.27 sec. accum.).
PyMOL>png sausage.png
 ScenePNG: wrote 600x600 pixel image to file "sausage.png".
PyMOL>quit