PyMOL>load ./selSi.pdb,obj
HEADER    STRUCTURAL GENOMICS, UNKNOWN FUNCTION   19-JUN-03   1PQX
TITLE     SOLUTION NMR STRUCTURE OF STAPHYLOCOCCUS AUREUS PROTEIN
TITLE    2 SAV1430. NORTHEAST STRUCUTRAL GENOMICS CONSORTIUM TARGET
TITLE    3 ZR18.
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: CONSERVED HYPOTHETICAL PROTEIN;
COMPND   3 CHAIN: A;
COMPND   4 SYNONYM: HYPOTHETICAL PROTEIN MW1320;
COMPND   5 ENGINEERED: YES;
COMPND   6 OTHER_DETAILS: ZR18
 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
 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 373 atoms.
PyMOL>color cyan,ss s
 Executive: Colored 352 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 719 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: 1.09 sec. = 3304.8 frames/hour (1.09 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 273 atoms.
PyMOL>hide everything,all
PyMOL>show lines,bb
PyMOL>color blue,bb
 Executive: Colored 273 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: 2.19 sec. = 1646.0 frames/hour (3.28 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 10 states [1, 10] of object "obj and name CA" (10 total states) to get new single-state object "yesfit_ALL"...
--------------------------------------------------------------------------------
-> proceeding WITH FITTING to reference state...
   intrafit_rmsds =  [-1.0, 3.1764717102050781, 4.3927397727966309, 2.9135861396789551, 4.0784540176391602, 4.1207690238952637, 2.9866185188293457, 5.5846843719482422, 2.29697585105896, 4.5862441062927246]
-> atom index_map =  [None, 2, 21, 43, 62, 81, 92, 111, 122, 137, 151, 165, 179, 196, 210, 224, 241, 263, 282, 296, 315, 326, 341, 352, 376, 391, 398, 415, 429, 440, 452, 466, 487, 501, 523, 539, 551, 563, 574, 591, 605, 615, 635, 654, 668, 680, 699, 718, 740, 756, 771, 778, 794, 816, 827, 846, 866, 883, 899, 916, 928, 948, 967, 978, 994, 1006, 1028, 1043, 1057, 1069, 1079, 1093, 1117, 1132, 1146, 1162, 1181, 1195, 1217, 1233, 1248, 1258, 1274, 1294, 1309, 1328, 1343, 1360, 1377, 1394, 1411, 1428]
"obj and name CA" index = 1
rmsd = 1.699
"obj and name CA" index = 2
rmsd = 1.392
"obj and name CA" index = 3
rmsd = 1.053
"obj and name CA" index = 4
rmsd = 1.148
"obj and name CA" index = 5
rmsd = 1.179
"obj and name CA" index = 6
rmsd = 1.281
"obj and name CA" index = 7
rmsd = 1.619
"obj and name CA" index = 8
rmsd = 2.595
"obj and name CA" index = 9
rmsd = 2.847
"obj and name CA" index = 10
rmsd = 4.280
"obj and name CA" index = 11
rmsd = 3.264
"obj and name CA" index = 12
rmsd = 1.585
"obj and name CA" index = 13
rmsd = 0.968
"obj and name CA" index = 14
rmsd = 0.709
"obj and name CA" index = 15
rmsd = 0.822
"obj and name CA" index = 16
rmsd = 0.673
"obj and name CA" index = 17
rmsd = 0.638
"obj and name CA" index = 18
rmsd = 0.766
"obj and name CA" index = 19
rmsd = 0.897
"obj and name CA" index = 20
rmsd = 1.318
"obj and name CA" index = 21
rmsd = 1.317
"obj and name CA" index = 22
rmsd = 2.267
"obj and name CA" index = 23
rmsd = 2.778
"obj and name CA" index = 24
rmsd = 2.334
"obj and name CA" index = 25
rmsd = 2.421
"obj and name CA" index = 26
rmsd = 1.482
"obj and name CA" index = 27
rmsd = 1.818
"obj and name CA" index = 28
rmsd = 1.182
"obj and name CA" index = 29
rmsd = 1.065
"obj and name CA" index = 30
rmsd = 0.994
"obj and name CA" index = 31
rmsd = 0.982
"obj and name CA" index = 32
rmsd = 1.097
"obj and name CA" index = 33
rmsd = 1.245
"obj and name CA" index = 34
rmsd = 1.269
"obj and name CA" index = 35
rmsd = 1.893
"obj and name CA" index = 36
rmsd = 2.026
"obj and name CA" index = 37
rmsd = 1.846
"obj and name CA" index = 38
rmsd = 1.437
"obj and name CA" index = 39
rmsd = 1.453
"obj and name CA" index = 40
rmsd = 1.675
"obj and name CA" index = 41
rmsd = 1.447
"obj and name CA" index = 42
rmsd = 1.043
"obj and name CA" index = 43
rmsd = 1.256
"obj and name CA" index = 44
rmsd = 1.266
"obj and name CA" index = 45
rmsd = 0.883
"obj and name CA" index = 46
rmsd = 0.810
"obj and name CA" index = 47
rmsd = 1.011
"obj and name CA" index = 48
rmsd = 0.883
"obj and name CA" index = 49
rmsd = 0.799
"obj and name CA" index = 50
rmsd = 0.709
"obj and name CA" index = 51
rmsd = 0.629
"obj and name CA" index = 52
rmsd = 0.718
"obj and name CA" index = 53
rmsd = 0.767
"obj and name CA" index = 54
rmsd = 0.637
"obj and name CA" index = 55
rmsd = 0.669
"obj and name CA" index = 56
rmsd = 0.648
"obj and name CA" index = 57
rmsd = 0.680
"obj and name CA" index = 58
rmsd = 0.741
"obj and name CA" index = 59
rmsd = 0.639
"obj and name CA" index = 60
rmsd = 0.488
"obj and name CA" index = 61
rmsd = 0.405
"obj and name CA" index = 62
rmsd = 0.445
"obj and name CA" index = 63
rmsd = 0.425
"obj and name CA" index = 64
rmsd = 0.543
"obj and name CA" index = 65
rmsd = 0.688
"obj and name CA" index = 66
rmsd = 0.867
"obj and name CA" index = 67
rmsd = 1.357
"obj and name CA" index = 68
rmsd = 2.386
"obj and name CA" index = 69
rmsd = 1.168
"obj and name CA" index = 70
rmsd = 1.406
"obj and name CA" index = 71
rmsd = 1.255
"obj and name CA" index = 72
rmsd = 1.530
"obj and name CA" index = 73
rmsd = 1.405
"obj and name CA" index = 74
rmsd = 1.016
"obj and name CA" index = 75
rmsd = 1.138
"obj and name CA" index = 76
rmsd = 1.461
"obj and name CA" index = 77
rmsd = 1.256
"obj and name CA" index = 78
rmsd = 1.063
"obj and name CA" index = 79
rmsd = 1.364
"obj and name CA" index = 80
rmsd = 1.485
"obj and name CA" index = 81
rmsd = 1.278
"obj and name CA" index = 82
rmsd = 1.290
"obj and name CA" index = 83
rmsd = 1.813
"obj and name CA" index = 84
rmsd = 1.825
"obj and name CA" index = 85
rmsd = 2.710
"obj and name CA" index = 86
rmsd = 3.386
"obj and name CA" index = 87
rmsd = 3.792
"obj and name CA" index = 88
rmsd = 4.845
"obj and name CA" index = 89
rmsd = 6.921
"obj and name CA" index = 90
rmsd = 8.495
"obj and name CA" index = 91
rmsd = 9.747
PyMOL>cartoon putty, yesfit_ALL and name CA
PyMOL>show cartoon, yesfit_ALL and name CA
PyMOL>color red, ss h
 Executive: Colored 762 atoms.
PyMOL>color cyan,ss s
 Executive: Colored 723 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 1494 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: 1.24 sec. = 2909.0 frames/hour (4.51 sec. accum.).
PyMOL>png sausage.png
 ScenePNG: wrote 600x600 pixel image to file "sausage.png".
PyMOL>quit