PyMOL>load ./selSi.pdb,obj
HEADER    TRANSFERASE                             30-JUN-10   2L05
TITLE     SOLUTION NMR STRUCTURE OF THE RAS-BINDING DOMAIN OF SERINE/THREONINE-
TITLE    2 PROTEIN KINASE B-RAF FROM HOMO SAPIENS, NORTHEAST STRUCTURAL GENOMICS
TITLE    3 CONSORTIUM TARGET HR4694F
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE B-RAF;
COMPND   3 CHAIN: A;
COMPND   4 FRAGMENT: RBD DOMAIN RESIDUES 149-232;
COMPND   5 SYNONYM: PROTO-ONCOGENE B-RAF, P94, V-RAF MURINE SARCOMA VIRAL
COMPND   6 ONCOGENE HOMOLOG B1;
COMPND   7 EC: 2.7.11.1;
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 15 atoms.
PyMOL>color cyan,ss s
 Executive: Colored 29 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 1354 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: 0.98 sec. = 3669.7 frames/hour (0.98 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: 3.02 sec. = 1193.4 frames/hour (4.00 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, 2.7763946056365967, 1.5407685041427612, 1.5859711170196533, 1.4429323673248291, 2.5387451648712158, 2.2409341335296631, 2.1080865859985352, 1.6620910167694092, 1.6817002296447754, 1.9217100143432617, 1.3587263822555542, 2.9235365390777588, 1.3587414026260376, 2.4301648139953613, 1.128517746925354, 2.5078890323638916, 1.4371594190597534, 1.9774073362350464, 2.3372642993927002]
-> atom index_map =  [None, 2, 20, 37, 51, 73, 84, 98, 115, 137, 151, 170, 186, 210, 226, 246, 265, 279, 293, 315, 332, 356, 370, 386, 402, 416, 426, 450, 461, 468, 484, 498, 514, 538, 550, 561, 580, 602, 624, 634, 653, 670, 687, 711, 718, 737, 756, 770, 785, 796, 807, 817, 833, 854, 878, 897, 914, 926, 933, 948, 970, 992, 1006, 1025, 1032, 1056, 1068, 1082, 1094, 1113, 1124, 1148, 1167, 1181, 1188, 1203, 1218, 1237, 1255, 1271, 1286, 1302, 1321, 1336, 1350, 1366, 1380]
"obj and name CA" index = 1
rmsd = 7.029
"obj and name CA" index = 2
rmsd = 5.420
"obj and name CA" index = 3
rmsd = 4.177
"obj and name CA" index = 4
rmsd = 3.324
"obj and name CA" index = 5
rmsd = 2.415
"obj and name CA" index = 6
rmsd = 2.359
"obj and name CA" index = 7
rmsd = 1.417
"obj and name CA" index = 8
rmsd = 1.110
"obj and name CA" index = 9
rmsd = 0.958
"obj and name CA" index = 10
rmsd = 0.795
"obj and name CA" index = 11
rmsd = 0.631
"obj and name CA" index = 12
rmsd = 0.658
"obj and name CA" index = 13
rmsd = 0.574
"obj and name CA" index = 14
rmsd = 0.618
"obj and name CA" index = 15
rmsd = 0.806
"obj and name CA" index = 16
rmsd = 0.992
"obj and name CA" index = 17
rmsd = 1.028
"obj and name CA" index = 18
rmsd = 1.057
"obj and name CA" index = 19
rmsd = 0.839
"obj and name CA" index = 20
rmsd = 0.874
"obj and name CA" index = 21
rmsd = 0.781
"obj and name CA" index = 22
rmsd = 0.744
"obj and name CA" index = 23
rmsd = 0.748
"obj and name CA" index = 24
rmsd = 0.863
"obj and name CA" index = 25
rmsd = 0.866
"obj and name CA" index = 26
rmsd = 0.929
"obj and name CA" index = 27
rmsd = 0.919
"obj and name CA" index = 28
rmsd = 0.928
"obj and name CA" index = 29
rmsd = 0.809
"obj and name CA" index = 30
rmsd = 0.593
"obj and name CA" index = 31
rmsd = 0.492
"obj and name CA" index = 32
rmsd = 0.651
"obj and name CA" index = 33
rmsd = 0.828
"obj and name CA" index = 34
rmsd = 0.815
"obj and name CA" index = 35
rmsd = 0.720
"obj and name CA" index = 36
rmsd = 0.952
"obj and name CA" index = 37
rmsd = 0.960
"obj and name CA" index = 38
rmsd = 0.905
"obj and name CA" index = 39
rmsd = 0.870
"obj and name CA" index = 40
rmsd = 1.009
"obj and name CA" index = 41
rmsd = 1.208
"obj and name CA" index = 42
rmsd = 1.264
"obj and name CA" index = 43
rmsd = 1.299
"obj and name CA" index = 44
rmsd = 1.011
"obj and name CA" index = 45
rmsd = 0.945
"obj and name CA" index = 46
rmsd = 0.915
"obj and name CA" index = 47
rmsd = 1.164
"obj and name CA" index = 48
rmsd = 0.947
"obj and name CA" index = 49
rmsd = 0.641
"obj and name CA" index = 50
rmsd = 0.504
"obj and name CA" index = 51
rmsd = 0.392
"obj and name CA" index = 52
rmsd = 0.490
"obj and name CA" index = 53
rmsd = 0.617
"obj and name CA" index = 54
rmsd = 0.835
"obj and name CA" index = 55
rmsd = 1.161
"obj and name CA" index = 56
rmsd = 1.468
"obj and name CA" index = 57
rmsd = 1.304
"obj and name CA" index = 58
rmsd = 1.113
"obj and name CA" index = 59
rmsd = 0.850
"obj and name CA" index = 60
rmsd = 0.827
"obj and name CA" index = 61
rmsd = 0.633
"obj and name CA" index = 62
rmsd = 0.525
"obj and name CA" index = 63
rmsd = 0.631
"obj and name CA" index = 64
rmsd = 0.578
"obj and name CA" index = 65
rmsd = 0.658
"obj and name CA" index = 66
rmsd = 0.546
"obj and name CA" index = 67
rmsd = 0.572
"obj and name CA" index = 68
rmsd = 0.518
"obj and name CA" index = 69
rmsd = 0.703
"obj and name CA" index = 70
rmsd = 0.639
"obj and name CA" index = 71
rmsd = 0.594
"obj and name CA" index = 72
rmsd = 0.739
"obj and name CA" index = 73
rmsd = 0.876
"obj and name CA" index = 74
rmsd = 0.821
"obj and name CA" index = 75
rmsd = 0.631
"obj and name CA" index = 76
rmsd = 0.542
"obj and name CA" index = 77
rmsd = 0.478
"obj and name CA" index = 78
rmsd = 0.515
"obj and name CA" index = 79
rmsd = 0.856
"obj and name CA" index = 80
rmsd = 0.929
"obj and name CA" index = 81
rmsd = 0.863
"obj and name CA" index = 82
rmsd = 1.198
"obj and name CA" index = 83
rmsd = 1.663
"obj and name CA" index = 84
rmsd = 2.506
"obj and name CA" index = 85
rmsd = 4.318
"obj and name CA" index = 86
rmsd = 5.673
PyMOL>cartoon putty, yesfit_ALL and name CA
PyMOL>show cartoon, yesfit_ALL and name CA
PyMOL>color red, ss h
 Executive: Colored 45 atoms.
PyMOL>color cyan,ss s
 Executive: Colored 87 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 2750 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: 1.27 sec. = 2824.1 frames/hour (5.27 sec. accum.).
PyMOL>png sausage.png
 ScenePNG: wrote 600x600 pixel image to file "sausage.png".
PyMOL>quit