PyMOL>load ./selSi.pdb,obj
HEADER    STRUCTURAL GENOMICS, UNKNOWN FUNCTION   09-OCT-04   1XPV
TITLE     SOLUTION STRUCTURE OF NORTHEAST STRUCTURAL GENOMICS TARGET
TITLE    2 PROTEIN XCR50 FROM X. CAMPESTRIS
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: HYPOTHETICAL PROTEIN XCC2852;
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 551 atoms.
PyMOL>color cyan,ss s
 Executive: Colored 205 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 438 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: 1.36 sec. = 2648.7 frames/hour (1.36 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 234 atoms.
PyMOL>hide everything,all
PyMOL>show lines,bb
PyMOL>color blue,bb
 Executive: Colored 234 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: 5.13 sec. = 702.3 frames/hour (6.48 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, 2.9352827072143555, 0.6814877986907959, 1.6309783458709717, 0.77990156412124634, 2.5574147701263428, 3.064523458480835, 0.80638206005096436, 2.2740862369537354, 2.1971428394317627, 2.0989143848419189, 0.99402803182601929, 2.9408986568450928, 2.4527819156646729, 2.9341874122619629, 2.2345681190490723, 2.892970085144043, 2.3333344459533691, 0.94199228286743164, 2.5670497417449951]
-> atom index_map =  [None, 2, 19, 29, 48, 62, 81, 102, 119, 143, 155, 167, 178, 195, 214, 225, 237, 254, 264, 280, 295, 305, 324, 334, 351, 361, 385, 395, 402, 412, 432, 452, 463, 479, 499, 518, 530, 542, 554, 564, 574, 593, 608, 619, 629, 650, 657, 676, 700, 716, 730, 746, 765, 789, 801, 815, 832, 839, 863, 878, 897, 909, 933, 947, 967, 979, 989, 1003, 1027, 1046, 1070, 1080, 1104, 1123, 1135, 1145, 1155, 1169, 1186]
"obj and name CA" index = 1
rmsd = 2.992
"obj and name CA" index = 2
rmsd = 1.273
"obj and name CA" index = 3
rmsd = 0.834
"obj and name CA" index = 4
rmsd = 0.620
"obj and name CA" index = 5
rmsd = 0.427
"obj and name CA" index = 6
rmsd = 0.327
"obj and name CA" index = 7
rmsd = 0.353
"obj and name CA" index = 8
rmsd = 0.657
"obj and name CA" index = 9
rmsd = 1.112
"obj and name CA" index = 10
rmsd = 2.037
"obj and name CA" index = 11
rmsd = 1.243
"obj and name CA" index = 12
rmsd = 0.859
"obj and name CA" index = 13
rmsd = 0.758
"obj and name CA" index = 14
rmsd = 0.568
"obj and name CA" index = 15
rmsd = 0.580
"obj and name CA" index = 16
rmsd = 0.476
"obj and name CA" index = 17
rmsd = 0.334
"obj and name CA" index = 18
rmsd = 0.395
"obj and name CA" index = 19
rmsd = 0.394
"obj and name CA" index = 20
rmsd = 0.264
"obj and name CA" index = 21
rmsd = 0.349
"obj and name CA" index = 22
rmsd = 0.484
"obj and name CA" index = 23
rmsd = 0.418
"obj and name CA" index = 24
rmsd = 0.420
"obj and name CA" index = 25
rmsd = 0.581
"obj and name CA" index = 26
rmsd = 0.586
"obj and name CA" index = 27
rmsd = 0.725
"obj and name CA" index = 28
rmsd = 0.826
"obj and name CA" index = 29
rmsd = 0.816
"obj and name CA" index = 30
rmsd = 0.824
"obj and name CA" index = 31
rmsd = 0.692
"obj and name CA" index = 32
rmsd = 0.452
"obj and name CA" index = 33
rmsd = 0.395
"obj and name CA" index = 34
rmsd = 0.409
"obj and name CA" index = 35
rmsd = 0.642
"obj and name CA" index = 36
rmsd = 1.142
"obj and name CA" index = 37
rmsd = 0.918
"obj and name CA" index = 38
rmsd = 0.885
"obj and name CA" index = 39
rmsd = 0.868
"obj and name CA" index = 40
rmsd = 0.603
"obj and name CA" index = 41
rmsd = 0.603
"obj and name CA" index = 42
rmsd = 0.759
"obj and name CA" index = 43
rmsd = 0.659
"obj and name CA" index = 44
rmsd = 0.419
"obj and name CA" index = 45
rmsd = 0.503
"obj and name CA" index = 46
rmsd = 0.492
"obj and name CA" index = 47
rmsd = 0.359
"obj and name CA" index = 48
rmsd = 0.283
"obj and name CA" index = 49
rmsd = 0.291
"obj and name CA" index = 50
rmsd = 0.294
"obj and name CA" index = 51
rmsd = 0.465
"obj and name CA" index = 52
rmsd = 0.612
"obj and name CA" index = 53
rmsd = 0.762
"obj and name CA" index = 54
rmsd = 0.981
"obj and name CA" index = 55
rmsd = 1.028
"obj and name CA" index = 56
rmsd = 2.312
"obj and name CA" index = 57
rmsd = 0.937
"obj and name CA" index = 58
rmsd = 0.674
"obj and name CA" index = 59
rmsd = 0.587
"obj and name CA" index = 60
rmsd = 0.586
"obj and name CA" index = 61
rmsd = 0.465
"obj and name CA" index = 62
rmsd = 0.527
"obj and name CA" index = 63
rmsd = 0.411
"obj and name CA" index = 64
rmsd = 0.400
"obj and name CA" index = 65
rmsd = 0.408
"obj and name CA" index = 66
rmsd = 0.468
"obj and name CA" index = 67
rmsd = 0.445
"obj and name CA" index = 68
rmsd = 0.377
"obj and name CA" index = 69
rmsd = 0.472
"obj and name CA" index = 70
rmsd = 0.594
"obj and name CA" index = 71
rmsd = 0.521
"obj and name CA" index = 72
rmsd = 0.525
"obj and name CA" index = 73
rmsd = 0.667
"obj and name CA" index = 74
rmsd = 0.803
"obj and name CA" index = 75
rmsd = 1.082
"obj and name CA" index = 76
rmsd = 2.710
"obj and name CA" index = 77
rmsd = 5.315
"obj and name CA" index = 78
rmsd = 7.896
PyMOL>cartoon putty, yesfit_ALL and name CA
PyMOL>show cartoon, yesfit_ALL and name CA
PyMOL>color red, ss h
 Executive: Colored 1131 atoms.
PyMOL>color cyan,ss s
 Executive: Colored 412 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 923 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. = 2260.2 frames/hour (8.08 sec. accum.).
PyMOL>png sausage.png
 ScenePNG: wrote 600x600 pixel image to file "sausage.png".
PyMOL>quit