PyMOL>load ./selSi.pdb,obj
HEADER    STRUCTURAL GENOMICS, UNKNOWN FUNCTION   29-DEC-08   2KCV
TITLE     SOLUTION NMR STRUCTURE OF TETRATRICOPEPTIDE REPEAT DOMAIN
TITLE    2 PROTEIN SRU_0103 FROM SALINIBACTER RUBER, NORTHEAST
TITLE    3 STRUCTURAL GENOMICS CONSORTIUM (NESG) TARGET SRR115C
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: TETRATRICOPEPTIDE REPEAT DOMAIN PROTEIN;
COMPND   3 CHAIN: A;
COMPND   4 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 1297 atoms.
PyMOL>color cyan,ss s
PyMOL>color gray,ss ""+l
 Executive: Colored 270 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: 1.29 sec. = 2792.0 frames/hour (1.29 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 297 atoms.
PyMOL>hide everything,all
PyMOL>show lines,bb
PyMOL>color blue,bb
 Executive: Colored 297 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: 3.28 sec. = 1097.4 frames/hour (4.57 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, 1.9676210880279541, 2.4997913837432861, 3.04781174659729, 2.9410364627838135, 1.6907349824905396, 3.0270910263061523, 2.7085983753204346, 4.0938234329223633, 3.6893289089202881, 1.4507583379745483, 2.4544644355773926, 2.6029231548309326, 2.5761253833770752, 1.8677933216094971, 2.9095804691314697, 3.3270077705383301, 2.8187437057495117, 3.6335029602050781, 3.1265528202056885]
-> atom index_map =  [None, 2, 19, 31, 45, 60, 72, 86, 106, 120, 144, 165, 175, 194, 204, 221, 236, 254, 273, 295, 313, 325, 339, 349, 360, 384, 394, 413, 423, 442, 462, 477, 492, 511, 527, 542, 556, 568, 582, 594, 615, 631, 638, 652, 673, 694, 712, 731, 738, 760, 779, 800, 815, 839, 858, 870, 894, 908, 920, 932, 942, 961, 973, 987, 1008, 1018, 1035, 1042, 1061, 1076, 1092, 1102, 1126, 1141, 1156, 1163, 1177, 1194, 1216, 1228, 1247, 1258, 1273, 1292, 1309, 1321, 1331, 1353, 1372, 1394, 1404, 1419, 1426, 1445, 1460, 1478, 1496, 1514, 1532, 1550]
"obj and name CA" index = 1
rmsd = 2.246
"obj and name CA" index = 2
rmsd = 1.508
"obj and name CA" index = 3
rmsd = 1.299
"obj and name CA" index = 4
rmsd = 1.159
"obj and name CA" index = 5
rmsd = 0.830
"obj and name CA" index = 6
rmsd = 0.642
"obj and name CA" index = 7
rmsd = 0.618
"obj and name CA" index = 8
rmsd = 0.707
"obj and name CA" index = 9
rmsd = 0.585
"obj and name CA" index = 10
rmsd = 0.353
"obj and name CA" index = 11
rmsd = 0.502
"obj and name CA" index = 12
rmsd = 0.583
"obj and name CA" index = 13
rmsd = 0.369
"obj and name CA" index = 14
rmsd = 0.403
"obj and name CA" index = 15
rmsd = 0.565
"obj and name CA" index = 16
rmsd = 0.464
"obj and name CA" index = 17
rmsd = 0.443
"obj and name CA" index = 18
rmsd = 0.699
"obj and name CA" index = 19
rmsd = 0.712
"obj and name CA" index = 20
rmsd = 0.733
"obj and name CA" index = 21
rmsd = 0.569
"obj and name CA" index = 22
rmsd = 0.454
"obj and name CA" index = 23
rmsd = 0.501
"obj and name CA" index = 24
rmsd = 0.497
"obj and name CA" index = 25
rmsd = 0.344
"obj and name CA" index = 26
rmsd = 0.402
"obj and name CA" index = 27
rmsd = 0.494
"obj and name CA" index = 28
rmsd = 0.393
"obj and name CA" index = 29
rmsd = 0.315
"obj and name CA" index = 30
rmsd = 0.496
"obj and name CA" index = 31
rmsd = 0.579
"obj and name CA" index = 32
rmsd = 0.453
"obj and name CA" index = 33
rmsd = 0.527
"obj and name CA" index = 34
rmsd = 0.736
"obj and name CA" index = 35
rmsd = 0.729
"obj and name CA" index = 36
rmsd = 0.612
"obj and name CA" index = 37
rmsd = 0.608
"obj and name CA" index = 38
rmsd = 0.585
"obj and name CA" index = 39
rmsd = 0.424
"obj and name CA" index = 40
rmsd = 0.400
"obj and name CA" index = 41
rmsd = 0.352
"obj and name CA" index = 42
rmsd = 0.290
"obj and name CA" index = 43
rmsd = 0.425
"obj and name CA" index = 44
rmsd = 0.430
"obj and name CA" index = 45
rmsd = 0.345
"obj and name CA" index = 46
rmsd = 0.382
"obj and name CA" index = 47
rmsd = 0.559
"obj and name CA" index = 48
rmsd = 0.583
"obj and name CA" index = 49
rmsd = 0.498
"obj and name CA" index = 50
rmsd = 0.634
"obj and name CA" index = 51
rmsd = 0.805
"obj and name CA" index = 52
rmsd = 0.753
"obj and name CA" index = 53
rmsd = 0.763
"obj and name CA" index = 54
rmsd = 0.968
"obj and name CA" index = 55
rmsd = 0.892
"obj and name CA" index = 56
rmsd = 1.086
"obj and name CA" index = 57
rmsd = 1.208
"obj and name CA" index = 58
rmsd = 0.904
"obj and name CA" index = 59
rmsd = 0.740
"obj and name CA" index = 60
rmsd = 0.879
"obj and name CA" index = 61
rmsd = 0.877
"obj and name CA" index = 62
rmsd = 0.685
"obj and name CA" index = 63
rmsd = 0.721
"obj and name CA" index = 64
rmsd = 0.892
"obj and name CA" index = 65
rmsd = 0.861
"obj and name CA" index = 66
rmsd = 0.661
"obj and name CA" index = 67
rmsd = 0.769
"obj and name CA" index = 68
rmsd = 0.847
"obj and name CA" index = 69
rmsd = 0.688
"obj and name CA" index = 70
rmsd = 0.640
"obj and name CA" index = 71
rmsd = 0.833
"obj and name CA" index = 72
rmsd = 0.936
"obj and name CA" index = 73
rmsd = 0.801
"obj and name CA" index = 74
rmsd = 0.726
"obj and name CA" index = 75
rmsd = 0.826
"obj and name CA" index = 76
rmsd = 0.929
"obj and name CA" index = 77
rmsd = 0.981
"obj and name CA" index = 78
rmsd = 0.715
"obj and name CA" index = 79
rmsd = 0.778
"obj and name CA" index = 80
rmsd = 0.868
"obj and name CA" index = 81
rmsd = 0.704
"obj and name CA" index = 82
rmsd = 0.608
"obj and name CA" index = 83
rmsd = 0.817
"obj and name CA" index = 84
rmsd = 0.826
"obj and name CA" index = 85
rmsd = 0.721
"obj and name CA" index = 86
rmsd = 0.821
"obj and name CA" index = 87
rmsd = 1.008
"obj and name CA" index = 88
rmsd = 1.018
"obj and name CA" index = 89
rmsd = 0.985
"obj and name CA" index = 90
rmsd = 1.189
"obj and name CA" index = 91
rmsd = 1.336
"obj and name CA" index = 92
rmsd = 1.336
"obj and name CA" index = 93
rmsd = 1.698
"obj and name CA" index = 94
rmsd = 2.518
"obj and name CA" index = 95
rmsd = 2.927
"obj and name CA" index = 96
rmsd = 4.382
"obj and name CA" index = 97
rmsd = 6.432
"obj and name CA" index = 98
rmsd = 7.847
"obj and name CA" index = 99
rmsd = 9.977
PyMOL>cartoon putty, yesfit_ALL and name CA
PyMOL>show cartoon, yesfit_ALL and name CA
PyMOL>color red, ss h
 Executive: Colored 2670 atoms.
PyMOL>color cyan,ss s
PyMOL>color gray,ss ""+l
 Executive: Colored 563 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: 1.96 sec. = 1838.9 frames/hour (6.53 sec. accum.).
PyMOL>png sausage.png
 ScenePNG: wrote 600x600 pixel image to file "sausage.png".
PyMOL>quit