PyMOL>load ./selSi.pdb,obj
HEADER    STRUCTURAL GENOMICS, UNKNOWN FUNCTION   29-DEC-06   2JN8
TITLE     SOLUTION NMR STRUCTURE OF Q8ZRJ2 FROM SALMONELLA
TITLE    2 TYPHIMURIUM. NORTHEAST STRUCTURAL GENOMICS TARGET STR65.
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: PUTATIVE CYTOPLASMIC 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 1187 atoms.
PyMOL>color cyan,ss s
PyMOL>color gray,ss ""+l
 Executive: Colored 513 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: 1.13 sec. = 3184.6 frames/hour (1.13 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 327 atoms.
PyMOL>hide everything,all
PyMOL>show lines,bb
PyMOL>color blue,bb
 Executive: Colored 327 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: 4.51 sec. = 797.7 frames/hour (5.64 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, 2.2031619548797607, 4.5440521240234375, 2.9861559867858887, 2.5619115829467773, 5.1076765060424805, 2.7503211498260498, 2.8263871669769287, 5.2118563652038574, 2.6403400897979736, 3.3555915355682373, 3.6519927978515625, 2.8222923278808594, 3.425410270690918, 2.7480146884918213, 2.2416882514953613, 2.8534228801727295, 3.1558818817138672, 3.5372910499572754, 4.7818059921264648]
-> atom index_map =  [None, 2, 18, 32, 52, 74, 86, 108, 119, 136, 150, 164, 174, 193, 208, 230, 240, 259, 271, 291, 310, 317, 324, 341, 355, 369, 380, 390, 401, 417, 431, 449, 460, 477, 489, 504, 515, 529, 539, 561, 568, 587, 606, 628, 649, 668, 686, 698, 717, 724, 740, 754, 770, 781, 795, 810, 826, 842, 858, 868, 892, 899, 914, 931, 946, 953, 977, 991, 1005, 1020, 1040, 1054, 1076, 1098, 1114, 1124, 1131, 1155, 1165, 1180, 1202, 1218, 1228, 1239, 1246, 1260, 1284, 1303, 1322, 1341, 1363, 1377, 1391, 1406, 1427, 1447, 1458, 1472, 1493, 1510, 1527, 1542, 1559, 1578, 1600, 1615, 1634, 1650, 1669, 1684]
"obj and name CA" index = 1
rmsd = 12.553
"obj and name CA" index = 2
rmsd = 10.497
"obj and name CA" index = 3
rmsd = 9.366
"obj and name CA" index = 4
rmsd = 7.517
"obj and name CA" index = 5
rmsd = 6.227
"obj and name CA" index = 6
rmsd = 5.615
"obj and name CA" index = 7
rmsd = 4.659
"obj and name CA" index = 8
rmsd = 3.264
"obj and name CA" index = 9
rmsd = 2.879
"obj and name CA" index = 10
rmsd = 2.767
"obj and name CA" index = 11
rmsd = 2.276
"obj and name CA" index = 12
rmsd = 2.100
"obj and name CA" index = 13
rmsd = 2.190
"obj and name CA" index = 14
rmsd = 1.947
"obj and name CA" index = 15
rmsd = 1.488
"obj and name CA" index = 16
rmsd = 1.569
"obj and name CA" index = 17
rmsd = 1.749
"obj and name CA" index = 18
rmsd = 1.345
"obj and name CA" index = 19
rmsd = 1.087
"obj and name CA" index = 20
rmsd = 1.461
"obj and name CA" index = 21
rmsd = 2.068
"obj and name CA" index = 22
rmsd = 2.654
"obj and name CA" index = 23
rmsd = 2.999
"obj and name CA" index = 24
rmsd = 3.024
"obj and name CA" index = 25
rmsd = 2.895
"obj and name CA" index = 26
rmsd = 2.100
"obj and name CA" index = 27
rmsd = 1.514
"obj and name CA" index = 28
rmsd = 3.088
"obj and name CA" index = 29
rmsd = 3.221
"obj and name CA" index = 30
rmsd = 1.606
"obj and name CA" index = 31
rmsd = 2.006
"obj and name CA" index = 32
rmsd = 1.926
"obj and name CA" index = 33
rmsd = 1.530
"obj and name CA" index = 34
rmsd = 1.231
"obj and name CA" index = 35
rmsd = 1.310
"obj and name CA" index = 36
rmsd = 1.150
"obj and name CA" index = 37
rmsd = 0.736
"obj and name CA" index = 38
rmsd = 0.559
"obj and name CA" index = 39
rmsd = 0.690
"obj and name CA" index = 40
rmsd = 0.724
"obj and name CA" index = 41
rmsd = 0.677
"obj and name CA" index = 42
rmsd = 0.698
"obj and name CA" index = 43
rmsd = 0.791
"obj and name CA" index = 44
rmsd = 1.068
"obj and name CA" index = 45
rmsd = 1.132
"obj and name CA" index = 46
rmsd = 1.201
"obj and name CA" index = 47
rmsd = 1.444
"obj and name CA" index = 48
rmsd = 1.720
"obj and name CA" index = 49
rmsd = 1.756
"obj and name CA" index = 50
rmsd = 1.717
"obj and name CA" index = 51
rmsd = 1.572
"obj and name CA" index = 52
rmsd = 1.707
"obj and name CA" index = 53
rmsd = 1.490
"obj and name CA" index = 54
rmsd = 1.899
"obj and name CA" index = 55
rmsd = 1.899
"obj and name CA" index = 56
rmsd = 1.388
"obj and name CA" index = 57
rmsd = 1.606
"obj and name CA" index = 58
rmsd = 2.073
"obj and name CA" index = 59
rmsd = 1.880
"obj and name CA" index = 60
rmsd = 1.554
"obj and name CA" index = 61
rmsd = 2.036
"obj and name CA" index = 62
rmsd = 2.276
"obj and name CA" index = 63
rmsd = 1.989
"obj and name CA" index = 64
rmsd = 1.920
"obj and name CA" index = 65
rmsd = 1.337
"obj and name CA" index = 66
rmsd = 1.352
"obj and name CA" index = 67
rmsd = 1.418
"obj and name CA" index = 68
rmsd = 1.270
"obj and name CA" index = 69
rmsd = 1.101
"obj and name CA" index = 70
rmsd = 1.185
"obj and name CA" index = 71
rmsd = 1.381
"obj and name CA" index = 72
rmsd = 1.260
"obj and name CA" index = 73
rmsd = 0.973
"obj and name CA" index = 74
rmsd = 1.330
"obj and name CA" index = 75
rmsd = 1.419
"obj and name CA" index = 76
rmsd = 1.014
"obj and name CA" index = 77
rmsd = 1.147
"obj and name CA" index = 78
rmsd = 1.569
"obj and name CA" index = 79
rmsd = 1.566
"obj and name CA" index = 80
rmsd = 1.379
"obj and name CA" index = 81
rmsd = 1.800
"obj and name CA" index = 82
rmsd = 2.150
"obj and name CA" index = 83
rmsd = 2.080
"obj and name CA" index = 84
rmsd = 2.056
"obj and name CA" index = 85
rmsd = 2.063
"obj and name CA" index = 86
rmsd = 1.825
"obj and name CA" index = 87
rmsd = 2.585
"obj and name CA" index = 88
rmsd = 2.148
"obj and name CA" index = 89
rmsd = 2.974
"obj and name CA" index = 90
rmsd = 2.284
"obj and name CA" index = 91
rmsd = 2.413
"obj and name CA" index = 92
rmsd = 2.848
"obj and name CA" index = 93
rmsd = 3.036
"obj and name CA" index = 94
rmsd = 1.517
"obj and name CA" index = 95
rmsd = 1.880
"obj and name CA" index = 96
rmsd = 1.973
"obj and name CA" index = 97
rmsd = 2.064
"obj and name CA" index = 98
rmsd = 1.722
"obj and name CA" index = 99
rmsd = 1.638
"obj and name CA" index = 100
rmsd = 2.085
"obj and name CA" index = 101
rmsd = 2.140
"obj and name CA" index = 102
rmsd = 1.841
"obj and name CA" index = 103
rmsd = 1.952
"obj and name CA" index = 104
rmsd = 2.383
"obj and name CA" index = 105
rmsd = 2.472
"obj and name CA" index = 106
rmsd = 2.446
"obj and name CA" index = 107
rmsd = 2.728
"obj and name CA" index = 108
rmsd = 3.510
"obj and name CA" index = 109
rmsd = 3.979
PyMOL>cartoon putty, yesfit_ALL and name CA
PyMOL>show cartoon, yesfit_ALL and name CA
PyMOL>color red, ss h
 Executive: Colored 2435 atoms.
PyMOL>color cyan,ss s
PyMOL>color gray,ss ""+l
 Executive: Colored 1074 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: 1.28 sec. = 2807.7 frames/hour (6.93 sec. accum.).
PyMOL>png sausage.png
 ScenePNG: wrote 600x600 pixel image to file "sausage.png".
PyMOL>quit