PyMOL>load ./selSi.pdb,obj
HEADER    STRUCTURAL GENOMICS, UNKNOWN FUNCTION   29-JUN-07   2JS1
TITLE     SOLUTION NMR STRUCTURE OF THE HOMODIMER PROTEIN YVFG FROM
TITLE    2 BACILLUS SUBTILIS, NORTHEAST STRUCTURAL GENOMICS
TITLE    3 CONSORTIUM TARGET SR478
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: UNCHARACTERIZED PROTEIN YVFG;
COMPND   3 CHAIN: A, B;
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 1878 atoms.
PyMOL>color cyan,ss s
PyMOL>color gray,ss ""+l
 Executive: Colored 798 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: 1.70 sec. = 2122.0 frames/hour (1.70 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 480 atoms.
PyMOL>hide everything,all
PyMOL>show lines,bb
PyMOL>color blue,bb
 Executive: Colored 480 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: 5.56 sec. = 647.7 frames/hour (7.25 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, 2.9230070114135742, 2.2313411235809326, 2.6944894790649414, 3.1324546337127686, 2.4305477142333984, 3.2594225406646729, 2.6492674350738525, 2.9207074642181396, 2.8387210369110107, 3.3232407569885254, 3.2368834018707275, 3.2072727680206299, 2.6150412559509277, 2.7400565147399902, 4.2007031440734863, 2.8291289806365967, 2.8983252048492432, 3.1199071407318115, 3.1335320472717285]
-> atom index_map =  [None, 2, 21, 32, 47, 66, 86, 97, 113, 127, 148, 168, 187, 202, 216, 235, 257, 274, 292, 311, 326, 343, 357, 374, 385, 400, 412, 434, 453, 471, 481, 498, 512, 523, 544, 565, 589, 600, 616, 632, 643, 657, 676, 692, 709, 721, 738, 757, 771, 793, 807, 817, 833, 849, 868, 890, 914, 933, 950, 968, 987, 999, 1014, 1024, 1045, 1059, 1081, 1097, 1119, 1143, 1150, 1165, 1176, 1198, 1217, 1232, 1250, 1268, 1286, 1304, 1322, 1340, 1359, 1370, 1385, 1404, 1424, 1435, 1451, 1465, 1486, 1506, 1525, 1540, 1554, 1573, 1595, 1612, 1630, 1649, 1664, 1681, 1695, 1712, 1723, 1738, 1750, 1772, 1791, 1809, 1819, 1836, 1850, 1861, 1882, 1903, 1927, 1938, 1954, 1970, 1981, 1995, 2014, 2030, 2047, 2059, 2076, 2095, 2109, 2131, 2145, 2155, 2171, 2187, 2206, 2228, 2252, 2271, 2288, 2306, 2325, 2337, 2352, 2362, 2383, 2397, 2419, 2435, 2457, 2481, 2488, 2503, 2514, 2536, 2555, 2570, 2588, 2606, 2624, 2642, 2660]
"obj and name CA" index = 1
rmsd = 5.710
"obj and name CA" index = 2
rmsd = 4.122
"obj and name CA" index = 3
rmsd = 2.922
"obj and name CA" index = 4
rmsd = 2.000
"obj and name CA" index = 5
rmsd = 2.643
"obj and name CA" index = 6
rmsd = 1.381
"obj and name CA" index = 7
rmsd = 1.205
"obj and name CA" index = 8
rmsd = 1.069
"obj and name CA" index = 9
rmsd = 0.917
"obj and name CA" index = 10
rmsd = 0.821
"obj and name CA" index = 11
rmsd = 0.810
"obj and name CA" index = 12
rmsd = 0.903
"obj and name CA" index = 13
rmsd = 0.881
"obj and name CA" index = 14
rmsd = 0.861
"obj and name CA" index = 15
rmsd = 0.953
"obj and name CA" index = 16
rmsd = 0.959
"obj and name CA" index = 17
rmsd = 0.944
"obj and name CA" index = 18
rmsd = 1.002
"obj and name CA" index = 19
rmsd = 1.126
"obj and name CA" index = 20
rmsd = 1.287
"obj and name CA" index = 21
rmsd = 1.334
"obj and name CA" index = 22
rmsd = 1.264
"obj and name CA" index = 23
rmsd = 1.211
"obj and name CA" index = 24
rmsd = 1.103
"obj and name CA" index = 25
rmsd = 1.131
"obj and name CA" index = 26
rmsd = 1.030
"obj and name CA" index = 27
rmsd = 0.993
"obj and name CA" index = 28
rmsd = 1.065
"obj and name CA" index = 29
rmsd = 0.900
"obj and name CA" index = 30
rmsd = 0.902
"obj and name CA" index = 31
rmsd = 0.998
"obj and name CA" index = 32
rmsd = 0.987
"obj and name CA" index = 33
rmsd = 0.832
"obj and name CA" index = 34
rmsd = 0.800
"obj and name CA" index = 35
rmsd = 0.884
"obj and name CA" index = 36
rmsd = 0.894
"obj and name CA" index = 37
rmsd = 0.748
"obj and name CA" index = 38
rmsd = 0.772
"obj and name CA" index = 39
rmsd = 0.935
"obj and name CA" index = 40
rmsd = 1.034
"obj and name CA" index = 41
rmsd = 0.994
"obj and name CA" index = 42
rmsd = 1.138
"obj and name CA" index = 43
rmsd = 1.566
"obj and name CA" index = 44
rmsd = 1.794
"obj and name CA" index = 45
rmsd = 1.435
"obj and name CA" index = 46
rmsd = 1.189
"obj and name CA" index = 47
rmsd = 1.271
"obj and name CA" index = 48
rmsd = 0.921
"obj and name CA" index = 49
rmsd = 0.837
"obj and name CA" index = 50
rmsd = 0.924
"obj and name CA" index = 51
rmsd = 0.891
"obj and name CA" index = 52
rmsd = 0.682
"obj and name CA" index = 53
rmsd = 0.690
"obj and name CA" index = 54
rmsd = 0.748
"obj and name CA" index = 55
rmsd = 0.758
"obj and name CA" index = 56
rmsd = 0.697
"obj and name CA" index = 57
rmsd = 0.719
"obj and name CA" index = 58
rmsd = 0.754
"obj and name CA" index = 59
rmsd = 0.693
"obj and name CA" index = 60
rmsd = 0.775
"obj and name CA" index = 61
rmsd = 0.802
"obj and name CA" index = 62
rmsd = 0.756
"obj and name CA" index = 63
rmsd = 0.871
"obj and name CA" index = 64
rmsd = 1.013
"obj and name CA" index = 65
rmsd = 0.926
"obj and name CA" index = 66
rmsd = 0.880
"obj and name CA" index = 67
rmsd = 1.066
"obj and name CA" index = 68
rmsd = 1.171
"obj and name CA" index = 69
rmsd = 1.042
"obj and name CA" index = 70
rmsd = 1.187
"obj and name CA" index = 71
rmsd = 1.944
"obj and name CA" index = 72
rmsd = 3.384
"obj and name CA" index = 73
rmsd = 4.333
"obj and name CA" index = 74
rmsd = 4.366
"obj and name CA" index = 75
rmsd = 5.024
"obj and name CA" index = 76
rmsd = 5.182
"obj and name CA" index = 77
rmsd = 5.563
"obj and name CA" index = 78
rmsd = 5.545
"obj and name CA" index = 79
rmsd = 6.542
"obj and name CA" index = 80
rmsd = 7.206
"obj and name CA" index = 81
rmsd = 5.963
"obj and name CA" index = 82
rmsd = 4.494
"obj and name CA" index = 83
rmsd = 3.206
"obj and name CA" index = 84
rmsd = 2.324
"obj and name CA" index = 85
rmsd = 2.515
"obj and name CA" index = 86
rmsd = 1.487
"obj and name CA" index = 87
rmsd = 1.303
"obj and name CA" index = 88
rmsd = 1.193
"obj and name CA" index = 89
rmsd = 1.074
"obj and name CA" index = 90
rmsd = 0.981
"obj and name CA" index = 91
rmsd = 0.896
"obj and name CA" index = 92
rmsd = 1.010
"obj and name CA" index = 93
rmsd = 1.021
"obj and name CA" index = 94
rmsd = 0.955
"obj and name CA" index = 95
rmsd = 1.010
"obj and name CA" index = 96
rmsd = 1.083
"obj and name CA" index = 97
rmsd = 1.061
"obj and name CA" index = 98
rmsd = 1.133
"obj and name CA" index = 99
rmsd = 1.258
"obj and name CA" index = 100
rmsd = 1.334
"obj and name CA" index = 101
rmsd = 1.595
"obj and name CA" index = 102
rmsd = 1.504
"obj and name CA" index = 103
rmsd = 1.553
"obj and name CA" index = 104
rmsd = 1.180
"obj and name CA" index = 105
rmsd = 1.193
"obj and name CA" index = 106
rmsd = 1.149
"obj and name CA" index = 107
rmsd = 1.102
"obj and name CA" index = 108
rmsd = 1.132
"obj and name CA" index = 109
rmsd = 0.940
"obj and name CA" index = 110
rmsd = 0.904
"obj and name CA" index = 111
rmsd = 1.093
"obj and name CA" index = 112
rmsd = 1.123
"obj and name CA" index = 113
rmsd = 0.914
"obj and name CA" index = 114
rmsd = 0.860
"obj and name CA" index = 115
rmsd = 1.130
"obj and name CA" index = 116
rmsd = 1.044
"obj and name CA" index = 117
rmsd = 0.850
"obj and name CA" index = 118
rmsd = 0.852
"obj and name CA" index = 119
rmsd = 1.106
"obj and name CA" index = 120
rmsd = 1.118
"obj and name CA" index = 121
rmsd = 0.955
"obj and name CA" index = 122
rmsd = 1.040
"obj and name CA" index = 123
rmsd = 1.430
"obj and name CA" index = 124
rmsd = 1.621
"obj and name CA" index = 125
rmsd = 1.720
"obj and name CA" index = 126
rmsd = 1.604
"obj and name CA" index = 127
rmsd = 1.608
"obj and name CA" index = 128
rmsd = 1.237
"obj and name CA" index = 129
rmsd = 0.951
"obj and name CA" index = 130
rmsd = 1.002
"obj and name CA" index = 131
rmsd = 1.113
"obj and name CA" index = 132
rmsd = 0.986
"obj and name CA" index = 133
rmsd = 0.907
"obj and name CA" index = 134
rmsd = 1.020
"obj and name CA" index = 135
rmsd = 0.918
"obj and name CA" index = 136
rmsd = 0.743
"obj and name CA" index = 137
rmsd = 0.877
"obj and name CA" index = 138
rmsd = 0.972
"obj and name CA" index = 139
rmsd = 0.820
"obj and name CA" index = 140
rmsd = 0.894
"obj and name CA" index = 141
rmsd = 0.974
"obj and name CA" index = 142
rmsd = 0.868
"obj and name CA" index = 143
rmsd = 0.845
"obj and name CA" index = 144
rmsd = 0.995
"obj and name CA" index = 145
rmsd = 0.996
"obj and name CA" index = 146
rmsd = 1.002
"obj and name CA" index = 147
rmsd = 1.124
"obj and name CA" index = 148
rmsd = 1.244
"obj and name CA" index = 149
rmsd = 1.678
"obj and name CA" index = 150
rmsd = 1.646
"obj and name CA" index = 151
rmsd = 2.211
"obj and name CA" index = 152
rmsd = 3.133
"obj and name CA" index = 153
rmsd = 3.403
"obj and name CA" index = 154
rmsd = 3.624
"obj and name CA" index = 155
rmsd = 3.655
"obj and name CA" index = 156
rmsd = 4.243
"obj and name CA" index = 157
rmsd = 4.314
"obj and name CA" index = 158
rmsd = 5.260
"obj and name CA" index = 159
rmsd = 5.059
"obj and name CA" index = 160
rmsd = 5.057
PyMOL>cartoon putty, yesfit_ALL and name CA
PyMOL>show cartoon, yesfit_ALL and name CA
PyMOL>color red, ss h
 Executive: Colored 3852 atoms.
PyMOL>color cyan,ss s
PyMOL>color gray,ss ""+l
 Executive: Colored 1660 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: 2.22 sec. = 1619.1 frames/hour (9.48 sec. accum.).
PyMOL>png sausage.png
 ScenePNG: wrote 600x600 pixel image to file "sausage.png".
PyMOL>quit