PyMOL>load ./selSi.pdb,obj
HEADER    STRUCTURAL GENOMICS, UNKNOWN FUNCTION   22-DEC-07   2JZ2
TITLE     SOLUTION NMR STRUCTURE OF SSL0352 PROTEIN FROM SYNECHOCYSTIS SP. PCC
TITLE    2 6803. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET SGR42
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: SSL0352 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
PyMOL>color cyan,ss s
 Executive: Colored 475 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 597 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: 0.73 sec. = 4904.2 frames/hour (0.73 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 198 atoms.
PyMOL>hide everything,all
PyMOL>show lines,bb
PyMOL>color blue,bb
 Executive: Colored 198 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: 2.03 sec. = 1769.7 frames/hour (2.77 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, 2.3395321369171143, 3.7265374660491943, 5.902864933013916, 2.1856963634490967, 4.3173089027404785, 4.4949760437011719, 5.3026885986328125, 6.1179900169372559, 4.6658143997192383, 2.1187758445739746, 2.7547464370727539, 3.8154215812683105, 4.6170597076416016, 1.7772420644760132, 3.0474984645843506, 6.063572883605957, 2.7369494438171387, 4.0305814743041992, 4.7343683242797852]
-> atom index_map =  [None, 2, 21, 40, 60, 74, 81, 91, 105, 121, 145, 161, 175, 189, 205, 217, 229, 243, 264, 285, 309, 329, 344, 351, 370, 386, 403, 427, 443, 454, 466, 473, 495, 505, 515, 531, 550, 570, 585, 599, 606, 620, 644, 656, 678, 697, 713, 727, 747, 771, 790, 801, 816, 835, 850, 860, 876, 898, 912, 931, 950, 965, 983, 1001, 1019, 1037, 1055]
"obj and name CA" index = 1
rmsd = 3.057
"obj and name CA" index = 2
rmsd = 2.454
"obj and name CA" index = 3
rmsd = 2.660
"obj and name CA" index = 4
rmsd = 2.336
"obj and name CA" index = 5
rmsd = 2.524
"obj and name CA" index = 6
rmsd = 2.470
"obj and name CA" index = 7
rmsd = 2.134
"obj and name CA" index = 8
rmsd = 1.612
"obj and name CA" index = 9
rmsd = 1.484
"obj and name CA" index = 10
rmsd = 1.103
"obj and name CA" index = 11
rmsd = 1.748
"obj and name CA" index = 12
rmsd = 1.858
"obj and name CA" index = 13
rmsd = 2.456
"obj and name CA" index = 14
rmsd = 2.853
"obj and name CA" index = 15
rmsd = 2.306
"obj and name CA" index = 16
rmsd = 2.306
"obj and name CA" index = 17
rmsd = 1.609
"obj and name CA" index = 18
rmsd = 1.675
"obj and name CA" index = 19
rmsd = 1.927
"obj and name CA" index = 20
rmsd = 1.624
"obj and name CA" index = 21
rmsd = 1.620
"obj and name CA" index = 22
rmsd = 1.236
"obj and name CA" index = 23
rmsd = 1.427
"obj and name CA" index = 24
rmsd = 1.368
"obj and name CA" index = 25
rmsd = 1.551
"obj and name CA" index = 26
rmsd = 1.903
"obj and name CA" index = 27
rmsd = 2.023
"obj and name CA" index = 28
rmsd = 2.439
"obj and name CA" index = 29
rmsd = 3.074
"obj and name CA" index = 30
rmsd = 2.434
"obj and name CA" index = 31
rmsd = 1.793
"obj and name CA" index = 32
rmsd = 1.342
"obj and name CA" index = 33
rmsd = 1.064
"obj and name CA" index = 34
rmsd = 0.553
"obj and name CA" index = 35
rmsd = 0.923
"obj and name CA" index = 36
rmsd = 1.255
"obj and name CA" index = 37
rmsd = 1.893
"obj and name CA" index = 38
rmsd = 2.700
"obj and name CA" index = 39
rmsd = 3.119
"obj and name CA" index = 40
rmsd = 3.047
"obj and name CA" index = 41
rmsd = 2.576
"obj and name CA" index = 42
rmsd = 1.866
"obj and name CA" index = 43
rmsd = 1.649
"obj and name CA" index = 44
rmsd = 1.264
"obj and name CA" index = 45
rmsd = 1.269
"obj and name CA" index = 46
rmsd = 1.296
"obj and name CA" index = 47
rmsd = 1.124
"obj and name CA" index = 48
rmsd = 1.429
"obj and name CA" index = 49
rmsd = 1.604
"obj and name CA" index = 50
rmsd = 1.775
"obj and name CA" index = 51
rmsd = 1.357
"obj and name CA" index = 52
rmsd = 1.273
"obj and name CA" index = 53
rmsd = 2.108
"obj and name CA" index = 54
rmsd = 2.412
"obj and name CA" index = 55
rmsd = 2.636
"obj and name CA" index = 56
rmsd = 3.258
"obj and name CA" index = 57
rmsd = 2.922
"obj and name CA" index = 58
rmsd = 3.267
"obj and name CA" index = 59
rmsd = 3.853
"obj and name CA" index = 60
rmsd = 3.449
"obj and name CA" index = 61
rmsd = 3.374
"obj and name CA" index = 62
rmsd = 3.874
"obj and name CA" index = 63
rmsd = 5.051
"obj and name CA" index = 64
rmsd = 6.594
"obj and name CA" index = 65
rmsd = 7.903
"obj and name CA" index = 66
rmsd = 9.983
PyMOL>cartoon putty, yesfit_ALL and name CA
PyMOL>show cartoon, yesfit_ALL and name CA
PyMOL>color red, ss h
PyMOL>color cyan,ss s
 Executive: Colored 976 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 1234 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: 0.84 sec. = 4280.1 frames/hour (3.61 sec. accum.).
PyMOL>png sausage.png
 ScenePNG: wrote 600x600 pixel image to file "sausage.png".
PyMOL>quit