PyMOL>load ./selSi.pdb,obj
HEADER    STRUCTURAL GENOMICS, UNKNOWN FUNCTION   20-OCT-09   2KPU
TITLE     NMR STRUCTURE OF YBBR FAMILY PROTEIN DHAF_0833 (RESIDUES 32-118) FROM
TITLE    2 DESULFITOBACTERIUM HAFNIENSE DCB-2: NORTHEAST STRUCTURAL GENOMICS
TITLE    3 CONSORTIUM TARGET DHR29B
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: YBBR FAMILY PROTEIN;
COMPND   3 CHAIN: A;
COMPND   4 FRAGMENT: SEQUENCE DATABASE RESIDUES 32-118;
COMPND   5 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 657 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 865 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: 1.04 sec. = 3445.2 frames/hour (1.04 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 288 atoms.
PyMOL>hide everything,all
PyMOL>show lines,bb
PyMOL>color blue,bb
 Executive: Colored 288 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: 3.66 sec. = 982.4 frames/hour (4.71 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, 2.3536922931671143, 3.4622499942779541, 2.9236404895782471, 4.0767331123352051, 2.7898850440979004, 2.7389316558837891, 4.3905115127563477, 3.4116964340209961, 1.8528409004211426, 3.036280632019043, 2.8222725391387939, 2.9506599903106689, 2.0371339321136475, 3.6696622371673584, 3.8911454677581787, 3.160067081451416, 3.1516244411468506, 2.7683889865875244, 3.1766848564147949]
-> atom index_map =  [None, 2, 15, 26, 43, 57, 76, 88, 112, 124, 138, 152, 171, 185, 204, 215, 234, 253, 263, 285, 299, 313, 327, 337, 351, 362, 379, 398, 415, 429, 451, 470, 484, 495, 511, 535, 551, 573, 587, 602, 609, 630, 644, 658, 669, 688, 702, 718, 732, 747, 766, 786, 796, 817, 833, 845, 864, 875, 882, 893, 908, 922, 929, 944, 962, 974, 995, 1010, 1026, 1048, 1064, 1079, 1093, 1112, 1126, 1140, 1159, 1181, 1200, 1216, 1231, 1250, 1261, 1275, 1299, 1315, 1331, 1345, 1364, 1381, 1400, 1415, 1433, 1451, 1469, 1487, 1505]
"obj and name CA" index = 1
rmsd = 9.294
"obj and name CA" index = 2
rmsd = 7.699
"obj and name CA" index = 3
rmsd = 6.137
"obj and name CA" index = 4
rmsd = 4.814
"obj and name CA" index = 5
rmsd = 2.894
"obj and name CA" index = 6
rmsd = 2.156
"obj and name CA" index = 7
rmsd = 1.547
"obj and name CA" index = 8
rmsd = 1.329
"obj and name CA" index = 9
rmsd = 1.511
"obj and name CA" index = 10
rmsd = 1.311
"obj and name CA" index = 11
rmsd = 1.038
"obj and name CA" index = 12
rmsd = 0.967
"obj and name CA" index = 13
rmsd = 0.817
"obj and name CA" index = 14
rmsd = 0.730
"obj and name CA" index = 15
rmsd = 0.597
"obj and name CA" index = 16
rmsd = 0.632
"obj and name CA" index = 17
rmsd = 0.609
"obj and name CA" index = 18
rmsd = 0.708
"obj and name CA" index = 19
rmsd = 0.989
"obj and name CA" index = 20
rmsd = 0.872
"obj and name CA" index = 21
rmsd = 1.113
"obj and name CA" index = 22
rmsd = 1.415
"obj and name CA" index = 23
rmsd = 1.368
"obj and name CA" index = 24
rmsd = 0.966
"obj and name CA" index = 25
rmsd = 0.874
"obj and name CA" index = 26
rmsd = 0.867
"obj and name CA" index = 27
rmsd = 1.101
"obj and name CA" index = 28
rmsd = 1.045
"obj and name CA" index = 29
rmsd = 0.877
"obj and name CA" index = 30
rmsd = 0.754
"obj and name CA" index = 31
rmsd = 0.774
"obj and name CA" index = 32
rmsd = 0.763
"obj and name CA" index = 33
rmsd = 0.773
"obj and name CA" index = 34
rmsd = 0.932
"obj and name CA" index = 35
rmsd = 0.936
"obj and name CA" index = 36
rmsd = 1.118
"obj and name CA" index = 37
rmsd = 1.016
"obj and name CA" index = 38
rmsd = 1.089
"obj and name CA" index = 39
rmsd = 1.270
"obj and name CA" index = 40
rmsd = 1.370
"obj and name CA" index = 41
rmsd = 1.456
"obj and name CA" index = 42
rmsd = 1.777
"obj and name CA" index = 43
rmsd = 1.742
"obj and name CA" index = 44
rmsd = 1.160
"obj and name CA" index = 45
rmsd = 1.531
"obj and name CA" index = 46
rmsd = 1.629
"obj and name CA" index = 47
rmsd = 1.824
"obj and name CA" index = 48
rmsd = 1.421
"obj and name CA" index = 49
rmsd = 0.948
"obj and name CA" index = 50
rmsd = 0.693
"obj and name CA" index = 51
rmsd = 0.610
"obj and name CA" index = 52
rmsd = 0.631
"obj and name CA" index = 53
rmsd = 0.535
"obj and name CA" index = 54
rmsd = 0.717
"obj and name CA" index = 55
rmsd = 0.815
"obj and name CA" index = 56
rmsd = 1.263
"obj and name CA" index = 57
rmsd = 1.610
"obj and name CA" index = 58
rmsd = 1.894
"obj and name CA" index = 59
rmsd = 1.464
"obj and name CA" index = 60
rmsd = 1.320
"obj and name CA" index = 61
rmsd = 1.222
"obj and name CA" index = 62
rmsd = 1.040
"obj and name CA" index = 63
rmsd = 0.818
"obj and name CA" index = 64
rmsd = 0.810
"obj and name CA" index = 65
rmsd = 0.636
"obj and name CA" index = 66
rmsd = 0.592
"obj and name CA" index = 67
rmsd = 0.595
"obj and name CA" index = 68
rmsd = 0.628
"obj and name CA" index = 69
rmsd = 0.675
"obj and name CA" index = 70
rmsd = 0.695
"obj and name CA" index = 71
rmsd = 0.847
"obj and name CA" index = 72
rmsd = 0.936
"obj and name CA" index = 73
rmsd = 1.327
"obj and name CA" index = 74
rmsd = 1.368
"obj and name CA" index = 75
rmsd = 1.081
"obj and name CA" index = 76
rmsd = 1.071
"obj and name CA" index = 77
rmsd = 0.941
"obj and name CA" index = 78
rmsd = 1.090
"obj and name CA" index = 79
rmsd = 1.121
"obj and name CA" index = 80
rmsd = 0.940
"obj and name CA" index = 81
rmsd = 0.881
"obj and name CA" index = 82
rmsd = 0.906
"obj and name CA" index = 83
rmsd = 0.885
"obj and name CA" index = 84
rmsd = 0.734
"obj and name CA" index = 85
rmsd = 0.706
"obj and name CA" index = 86
rmsd = 0.762
"obj and name CA" index = 87
rmsd = 0.702
"obj and name CA" index = 88
rmsd = 0.817
"obj and name CA" index = 89
rmsd = 0.806
"obj and name CA" index = 90
rmsd = 0.914
"obj and name CA" index = 91
rmsd = 1.204
"obj and name CA" index = 92
rmsd = 1.379
"obj and name CA" index = 93
rmsd = 1.742
"obj and name CA" index = 94
rmsd = 3.571
"obj and name CA" index = 95
rmsd = 5.469
"obj and name CA" index = 96
rmsd = 7.089
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 1340 atoms.
PyMOL>color gray,ss ""+l
 Executive: Colored 1800 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: 1.21 sec. = 2968.4 frames/hour (5.92 sec. accum.).
PyMOL>png sausage.png
 ScenePNG: wrote 600x600 pixel image to file "sausage.png".
PyMOL>quit