PyMOL>load ./selSi.pdb,obj
HEADER    TRANSFERASE                             30-MAR-10   2KW2
TITLE     SOLUTION NMR OF THE SPECIALIZED ACYL CARRIER PROTEIN (RPA2022) FROM
TITLE    2 RHODOPSEUDOMONAS PALUSTRIS, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM
TITLE    3 TARGET RPR324
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: SPECIALIZED ACYL CARRIER 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 1106 atoms.
PyMOL>color cyan,ss s
PyMOL>color gray,ss ""+l
 Executive: Colored 475 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: 1.23 sec. = 2916.2 frames/hour (1.23 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 303 atoms.
PyMOL>hide everything,all
PyMOL>show lines,bb
PyMOL>color blue,bb
 Executive: Colored 303 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: 3.39 sec. = 1062.7 frames/hour (4.62 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, 1.555715799331665, 2.8010983467102051, 4.7931323051452637, 1.9620239734649658, 4.1153750419616699, 1.4049696922302246, 2.1558444499969482, 1.5731077194213867, 3.2634971141815186, 2.0234642028808594, 3.5561726093292236, 3.2959187030792236, 1.2210981845855713, 1.6698518991470337, 4.3374896049499512, 1.2645653486251831, 1.3383785486221313, 1.2442464828491211, 3.1551644802093506]
-> atom index_map =  [None, 2, 21, 35, 46, 60, 80, 92, 116, 132, 142, 156, 175, 194, 204, 219, 233, 244, 256, 275, 289, 313, 328, 342, 361, 375, 389, 404, 415, 432, 442, 461, 473, 485, 504, 511, 530, 542, 553, 572, 584, 604, 623, 635, 654, 664, 684, 694, 713, 725, 747, 757, 777, 784, 803, 825, 844, 858, 877, 892, 914, 938, 952, 969, 984, 1000, 1014, 1026, 1033, 1055, 1065, 1079, 1093, 1108, 1125, 1146, 1166, 1182, 1201, 1223, 1237, 1256, 1266, 1276, 1300, 1319, 1331, 1346, 1365, 1381, 1391, 1401, 1423, 1430, 1440, 1459, 1474, 1492, 1510, 1528, 1546, 1564]
"obj and name CA" index = 1
rmsd = 3.304
"obj and name CA" index = 2
rmsd = 2.176
"obj and name CA" index = 3
rmsd = 1.715
"obj and name CA" index = 4
rmsd = 1.360
"obj and name CA" index = 5
rmsd = 1.119
"obj and name CA" index = 6
rmsd = 1.177
"obj and name CA" index = 7
rmsd = 1.125
"obj and name CA" index = 8
rmsd = 0.776
"obj and name CA" index = 9
rmsd = 0.704
"obj and name CA" index = 10
rmsd = 0.812
"obj and name CA" index = 11
rmsd = 0.758
"obj and name CA" index = 12
rmsd = 0.562
"obj and name CA" index = 13
rmsd = 0.647
"obj and name CA" index = 14
rmsd = 0.835
"obj and name CA" index = 15
rmsd = 0.940
"obj and name CA" index = 16
rmsd = 0.904
"obj and name CA" index = 17
rmsd = 0.954
"obj and name CA" index = 18
rmsd = 0.841
"obj and name CA" index = 19
rmsd = 0.925
"obj and name CA" index = 20
rmsd = 0.977
"obj and name CA" index = 21
rmsd = 1.311
"obj and name CA" index = 22
rmsd = 1.197
"obj and name CA" index = 23
rmsd = 0.813
"obj and name CA" index = 24
rmsd = 0.944
"obj and name CA" index = 25
rmsd = 0.931
"obj and name CA" index = 26
rmsd = 0.995
"obj and name CA" index = 27
rmsd = 0.777
"obj and name CA" index = 28
rmsd = 0.559
"obj and name CA" index = 29
rmsd = 0.503
"obj and name CA" index = 30
rmsd = 0.807
"obj and name CA" index = 31
rmsd = 1.005
"obj and name CA" index = 32
rmsd = 0.966
"obj and name CA" index = 33
rmsd = 0.824
"obj and name CA" index = 34
rmsd = 0.999
"obj and name CA" index = 35
rmsd = 0.814
"obj and name CA" index = 36
rmsd = 1.006
"obj and name CA" index = 37
rmsd = 0.984
"obj and name CA" index = 38
rmsd = 1.033
"obj and name CA" index = 39
rmsd = 0.820
"obj and name CA" index = 40
rmsd = 0.640
"obj and name CA" index = 41
rmsd = 0.783
"obj and name CA" index = 42
rmsd = 0.763
"obj and name CA" index = 43
rmsd = 0.559
"obj and name CA" index = 44
rmsd = 0.628
"obj and name CA" index = 45
rmsd = 0.866
"obj and name CA" index = 46
rmsd = 0.799
"obj and name CA" index = 47
rmsd = 0.737
"obj and name CA" index = 48
rmsd = 1.044
"obj and name CA" index = 49
rmsd = 1.193
"obj and name CA" index = 50
rmsd = 1.103
"obj and name CA" index = 51
rmsd = 1.173
"obj and name CA" index = 52
rmsd = 1.409
"obj and name CA" index = 53
rmsd = 1.206
"obj and name CA" index = 54
rmsd = 1.129
"obj and name CA" index = 55
rmsd = 0.921
"obj and name CA" index = 56
rmsd = 0.970
"obj and name CA" index = 57
rmsd = 0.748
"obj and name CA" index = 58
rmsd = 1.059
"obj and name CA" index = 59
rmsd = 0.983
"obj and name CA" index = 60
rmsd = 0.721
"obj and name CA" index = 61
rmsd = 0.811
"obj and name CA" index = 62
rmsd = 0.932
"obj and name CA" index = 63
rmsd = 0.894
"obj and name CA" index = 64
rmsd = 0.935
"obj and name CA" index = 65
rmsd = 1.126
"obj and name CA" index = 66
rmsd = 1.188
"obj and name CA" index = 67
rmsd = 1.152
"obj and name CA" index = 68
rmsd = 1.092
"obj and name CA" index = 69
rmsd = 0.882
"obj and name CA" index = 70
rmsd = 0.797
"obj and name CA" index = 71
rmsd = 0.648
"obj and name CA" index = 72
rmsd = 0.637
"obj and name CA" index = 73
rmsd = 0.752
"obj and name CA" index = 74
rmsd = 0.626
"obj and name CA" index = 75
rmsd = 0.344
"obj and name CA" index = 76
rmsd = 0.431
"obj and name CA" index = 77
rmsd = 0.510
"obj and name CA" index = 78
rmsd = 0.806
"obj and name CA" index = 79
rmsd = 0.731
"obj and name CA" index = 80
rmsd = 0.599
"obj and name CA" index = 81
rmsd = 0.838
"obj and name CA" index = 82
rmsd = 0.936
"obj and name CA" index = 83
rmsd = 0.862
"obj and name CA" index = 84
rmsd = 0.891
"obj and name CA" index = 85
rmsd = 1.106
"obj and name CA" index = 86
rmsd = 1.196
"obj and name CA" index = 87
rmsd = 1.180
"obj and name CA" index = 88
rmsd = 1.265
"obj and name CA" index = 89
rmsd = 1.449
"obj and name CA" index = 90
rmsd = 1.596
"obj and name CA" index = 91
rmsd = 1.656
"obj and name CA" index = 92
rmsd = 1.679
"obj and name CA" index = 93
rmsd = 1.807
"obj and name CA" index = 94
rmsd = 1.894
"obj and name CA" index = 95
rmsd = 2.076
"obj and name CA" index = 96
rmsd = 2.313
"obj and name CA" index = 97
rmsd = 3.780
"obj and name CA" index = 98
rmsd = 5.309
"obj and name CA" index = 99
rmsd = 7.559
"obj and name CA" index = 100
rmsd = 9.336
"obj and name CA" index = 101
rmsd = 11.264
PyMOL>cartoon putty, yesfit_ALL and name CA
PyMOL>show cartoon, yesfit_ALL and name CA
PyMOL>color red, ss h
 Executive: Colored 2278 atoms.
PyMOL>color cyan,ss s
PyMOL>color gray,ss ""+l
 Executive: Colored 985 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. = 2270.4 frames/hour (6.21 sec. accum.).
PyMOL>png sausage.png
 ScenePNG: wrote 600x600 pixel image to file "sausage.png".
PyMOL>quit