PyMOL>load ./selSi.pdb,obj
HEADER    PROTEIN BINDING                         18-DEC-09   2KRK
TITLE     SOLUTION NMR STRUCTURE OF 26S PROTEASE REGULATORY SUBUNIT 8
TITLE    2 FROM H.SAPIENS, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM
TITLE    3 TARGET TARGET HR3102A
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: 26S PROTEASE REGULATORY SUBUNIT 8;
COMPND   3 CHAIN: A;
COMPND   4 FRAGMENT: SEQUENCE DATABASE RESIDUES 320-395;
COMPND   5 SYNONYM: PROTEASOME 26S SUBUNIT ATPASE 5, PROTEASOME
COMPND   6 SUBUNIT P45, P45/SUG, THYROID HORMONE RECEPTOR-INTERACTING
COMPND   7 PROTEIN 1, TRIP1;
COMPND   8 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 827 atoms.
PyMOL>color cyan,ss s
 Executive: Colored 63 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 483 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: 1.06 sec. = 3399.9 frames/hour (1.06 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 258 atoms.
PyMOL>hide everything,all
PyMOL>show lines,bb
PyMOL>color blue,bb
 Executive: Colored 258 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: 3.09 sec. = 1165.5 frames/hour (4.15 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, 2.9215681552886963, 3.6363463401794434, 2.98917555809021, 3.2566311359405518, 3.8273334503173828, 5.0285854339599609, 4.3112168312072754, 3.2567706108093262, 3.4441688060760498, 3.1351540088653564, 4.2272982597351074, 4.3517389297485352, 2.4363038539886475, 3.5440735816955566, 5.5069236755371094, 3.2009036540985107, 5.1939425468444824, 2.7931351661682129, 5.2171363830566406]
-> atom index_map =  [None, 2, 21, 28, 46, 64, 82, 100, 118, 136, 147, 165, 179, 193, 208, 223, 233, 257, 276, 288, 307, 326, 348, 367, 385, 396, 420, 442, 459, 473, 492, 506, 530, 537, 556, 570, 589, 613, 635, 654, 664, 679, 698, 715, 729, 736, 746, 757, 764, 774, 789, 805, 827, 834, 850, 861, 875, 890, 900, 907, 924, 945, 955, 974, 998, 1013, 1037, 1061, 1077, 1095, 1111, 1125, 1142, 1157, 1169, 1189, 1204, 1221, 1231, 1247, 1257, 1279, 1295, 1312, 1329, 1351, 1363]
"obj and name CA" index = 1
rmsd = 11.162
"obj and name CA" index = 2
rmsd = 9.707
"obj and name CA" index = 3
rmsd = 8.428
"obj and name CA" index = 4
rmsd = 6.993
"obj and name CA" index = 5
rmsd = 5.866
"obj and name CA" index = 6
rmsd = 5.294
"obj and name CA" index = 7
rmsd = 4.145
"obj and name CA" index = 8
rmsd = 3.650
"obj and name CA" index = 9
rmsd = 3.521
"obj and name CA" index = 10
rmsd = 2.884
"obj and name CA" index = 11
rmsd = 2.526
"obj and name CA" index = 12
rmsd = 2.458
"obj and name CA" index = 13
rmsd = 2.005
"obj and name CA" index = 14
rmsd = 2.046
"obj and name CA" index = 15
rmsd = 2.261
"obj and name CA" index = 16
rmsd = 1.860
"obj and name CA" index = 17
rmsd = 1.495
"obj and name CA" index = 18
rmsd = 1.832
"obj and name CA" index = 19
rmsd = 1.769
"obj and name CA" index = 20
rmsd = 1.322
"obj and name CA" index = 21
rmsd = 1.507
"obj and name CA" index = 22
rmsd = 1.770
"obj and name CA" index = 23
rmsd = 1.575
"obj and name CA" index = 24
rmsd = 1.445
"obj and name CA" index = 25
rmsd = 1.675
"obj and name CA" index = 26
rmsd = 1.690
"obj and name CA" index = 27
rmsd = 1.377
"obj and name CA" index = 28
rmsd = 1.463
"obj and name CA" index = 29
rmsd = 1.370
"obj and name CA" index = 30
rmsd = 1.617
"obj and name CA" index = 31
rmsd = 2.145
"obj and name CA" index = 32
rmsd = 1.972
"obj and name CA" index = 33
rmsd = 1.281
"obj and name CA" index = 34
rmsd = 1.150
"obj and name CA" index = 35
rmsd = 1.020
"obj and name CA" index = 36
rmsd = 1.288
"obj and name CA" index = 37
rmsd = 1.097
"obj and name CA" index = 38
rmsd = 0.845
"obj and name CA" index = 39
rmsd = 1.274
"obj and name CA" index = 40
rmsd = 1.428
"obj and name CA" index = 41
rmsd = 1.202
"obj and name CA" index = 42
rmsd = 1.495
"obj and name CA" index = 43
rmsd = 2.051
"obj and name CA" index = 44
rmsd = 2.414
"obj and name CA" index = 45
rmsd = 1.996
"obj and name CA" index = 46
rmsd = 2.188
"obj and name CA" index = 47
rmsd = 2.141
"obj and name CA" index = 48
rmsd = 2.214
"obj and name CA" index = 49
rmsd = 1.737
"obj and name CA" index = 50
rmsd = 1.451
"obj and name CA" index = 51
rmsd = 1.596
"obj and name CA" index = 52
rmsd = 1.409
"obj and name CA" index = 53
rmsd = 0.959
"obj and name CA" index = 54
rmsd = 0.911
"obj and name CA" index = 55
rmsd = 1.092
"obj and name CA" index = 56
rmsd = 0.993
"obj and name CA" index = 57
rmsd = 0.709
"obj and name CA" index = 58
rmsd = 1.023
"obj and name CA" index = 59
rmsd = 1.355
"obj and name CA" index = 60
rmsd = 1.318
"obj and name CA" index = 61
rmsd = 1.397
"obj and name CA" index = 62
rmsd = 1.812
"obj and name CA" index = 63
rmsd = 2.110
"obj and name CA" index = 64
rmsd = 2.236
"obj and name CA" index = 65
rmsd = 2.360
"obj and name CA" index = 66
rmsd = 2.022
"obj and name CA" index = 67
rmsd = 1.982
"obj and name CA" index = 68
rmsd = 1.608
"obj and name CA" index = 69
rmsd = 1.069
"obj and name CA" index = 70
rmsd = 1.124
"obj and name CA" index = 71
rmsd = 0.882
"obj and name CA" index = 72
rmsd = 0.915
"obj and name CA" index = 73
rmsd = 0.722
"obj and name CA" index = 74
rmsd = 0.372
"obj and name CA" index = 75
rmsd = 0.491
"obj and name CA" index = 76
rmsd = 0.769
"obj and name CA" index = 77
rmsd = 0.779
"obj and name CA" index = 78
rmsd = 0.917
"obj and name CA" index = 79
rmsd = 1.137
"obj and name CA" index = 80
rmsd = 1.321
"obj and name CA" index = 81
rmsd = 1.466
"obj and name CA" index = 82
rmsd = 1.662
"obj and name CA" index = 83
rmsd = 1.801
"obj and name CA" index = 84
rmsd = 1.994
"obj and name CA" index = 85
rmsd = 2.708
"obj and name CA" index = 86
rmsd = 4.654
PyMOL>cartoon putty, yesfit_ALL and name CA
PyMOL>show cartoon, yesfit_ALL and name CA
PyMOL>color red, ss h
 Executive: Colored 1704 atoms.
PyMOL>color cyan,ss s
 Executive: Colored 126 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 1002 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: 1.19 sec. = 3024.4 frames/hour (5.34 sec. accum.).
PyMOL>png sausage.png
 ScenePNG: wrote 600x600 pixel image to file "sausage.png".
PyMOL>quit