PyMOL>load ./selSi.pdb,obj HEADER STRUCTURAL PROTEIN 21-OCT-09 2KPW TITLE NMR SOLUTION STRUCTURE OF LAMIN-B1 PROTEIN FROM HOMO TITLE 2 SAPIENS: NORTHEAST STRUCTURAL GENOMICS CONSORTIUM MEGA TITLE 3 TARGET, HR5546A (439-549) COMPND MOL_ID: 1; COMPND 2 MOLECULE: LAMIN-B1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES 439-549; 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 781 atoms. PyMOL>color gray,ss ""+l Executive: Colored 1117 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: 1.11 sec. = 3247.0 frames/hour (1.11 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 366 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 366 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: 3.32 sec. = 1083.7 frames/hour (4.43 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 "", 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, 4.0781197547912598, 5.6981077194213867, 2.3211953639984131, 3.2736296653747559, 6.5604381561279297, 2.6961982250213623, 4.1195759773254395, 5.3273611068725586, 3.0889575481414795, 3.2026913166046143, 3.5863018035888672, 4.7001056671142578, 3.1389522552490234, 2.6804559230804443, 3.311812162399292, 6.1913461685180664, 2.6278035640716553, 5.9900598526000977, 3.8080611228942871] -> atom index_map = [None, 2, 21, 28, 46, 64, 82, 100, 118, 136, 147, 165, 182, 196, 203, 217, 233, 244, 263, 278, 293, 312, 324, 340, 352, 359, 381, 401, 420, 444, 463, 485, 499, 513, 524, 539, 556, 568, 585, 599, 616, 623, 630, 654, 669, 686, 705, 729, 751, 770, 777, 789, 803, 814, 830, 841, 862, 884, 905, 919, 930, 954, 975, 991, 1010, 1032, 1042, 1049, 1066, 1080, 1096, 1110, 1129, 1153, 1163, 1173, 1187, 1197, 1204, 1220, 1234, 1244, 1255, 1269, 1283, 1297, 1309, 1328, 1347, 1371, 1393, 1407, 1424, 1438, 1449, 1473, 1480, 1494, 1501, 1516, 1528, 1544, 1566, 1582, 1601, 1620, 1642, 1656, 1667, 1684, 1691, 1706, 1721, 1737, 1747, 1764, 1788, 1799, 1813, 1829, 1849, 1871, 1885] "obj and name CA" index = 1 rmsd = 14.178 "obj and name CA" index = 2 rmsd = 12.203 "obj and name CA" index = 3 rmsd = 10.986 "obj and name CA" index = 4 rmsd = 9.052 "obj and name CA" index = 5 rmsd = 6.975 "obj and name CA" index = 6 rmsd = 5.710 "obj and name CA" index = 7 rmsd = 4.118 "obj and name CA" index = 8 rmsd = 3.428 "obj and name CA" index = 9 rmsd = 2.800 "obj and name CA" index = 10 rmsd = 3.050 "obj and name CA" index = 11 rmsd = 2.838 "obj and name CA" index = 12 rmsd = 3.177 "obj and name CA" index = 13 rmsd = 2.578 "obj and name CA" index = 14 rmsd = 1.844 "obj and name CA" index = 15 rmsd = 1.427 "obj and name CA" index = 16 rmsd = 1.305 "obj and name CA" index = 17 rmsd = 0.898 "obj and name CA" index = 18 rmsd = 1.061 "obj and name CA" index = 19 rmsd = 1.020 "obj and name CA" index = 20 rmsd = 0.878 "obj and name CA" index = 21 rmsd = 1.162 "obj and name CA" index = 22 rmsd = 1.794 "obj and name CA" index = 23 rmsd = 1.761 "obj and name CA" index = 24 rmsd = 1.583 "obj and name CA" index = 25 rmsd = 1.524 "obj and name CA" index = 26 rmsd = 1.064 "obj and name CA" index = 27 rmsd = 0.742 "obj and name CA" index = 28 rmsd = 0.645 "obj and name CA" index = 29 rmsd = 0.696 "obj and name CA" index = 30 rmsd = 1.035 "obj and name CA" index = 31 rmsd = 1.260 "obj and name CA" index = 32 rmsd = 1.665 "obj and name CA" index = 33 rmsd = 1.958 "obj and name CA" index = 34 rmsd = 2.386 "obj and name CA" index = 35 rmsd = 2.264 "obj and name CA" index = 36 rmsd = 2.029 "obj and name CA" index = 37 rmsd = 1.937 "obj and name CA" index = 38 rmsd = 2.106 "obj and name CA" index = 39 rmsd = 1.904 "obj and name CA" index = 40 rmsd = 2.426 "obj and name CA" index = 41 rmsd = 2.237 "obj and name CA" index = 42 rmsd = 1.712 "obj and name CA" index = 43 rmsd = 1.632 "obj and name CA" index = 44 rmsd = 1.261 "obj and name CA" index = 45 rmsd = 1.332 "obj and name CA" index = 46 rmsd = 1.252 "obj and name CA" index = 47 rmsd = 1.345 "obj and name CA" index = 48 rmsd = 1.521 "obj and name CA" index = 49 rmsd = 2.124 "obj and name CA" index = 50 rmsd = 2.059 "obj and name CA" index = 51 rmsd = 1.862 "obj and name CA" index = 52 rmsd = 1.632 "obj and name CA" index = 53 rmsd = 1.483 "obj and name CA" index = 54 rmsd = 1.590 "obj and name CA" index = 55 rmsd = 1.553 "obj and name CA" index = 56 rmsd = 1.714 "obj and name CA" index = 57 rmsd = 1.547 "obj and name CA" index = 58 rmsd = 2.079 "obj and name CA" index = 59 rmsd = 2.036 "obj and name CA" index = 60 rmsd = 2.159 "obj and name CA" index = 61 rmsd = 1.831 "obj and name CA" index = 62 rmsd = 1.813 "obj and name CA" index = 63 rmsd = 1.554 "obj and name CA" index = 64 rmsd = 1.681 "obj and name CA" index = 65 rmsd = 1.773 "obj and name CA" index = 66 rmsd = 1.617 "obj and name CA" index = 67 rmsd = 1.237 "obj and name CA" index = 68 rmsd = 0.780 "obj and name CA" index = 69 rmsd = 0.748 "obj and name CA" index = 70 rmsd = 0.706 "obj and name CA" index = 71 rmsd = 0.833 "obj and name CA" index = 72 rmsd = 1.025 "obj and name CA" index = 73 rmsd = 1.316 "obj and name CA" index = 74 rmsd = 1.509 "obj and name CA" index = 75 rmsd = 1.721 "obj and name CA" index = 76 rmsd = 1.522 "obj and name CA" index = 77 rmsd = 1.617 "obj and name CA" index = 78 rmsd = 1.537 "obj and name CA" index = 79 rmsd = 1.828 "obj and name CA" index = 80 rmsd = 1.959 "obj and name CA" index = 81 rmsd = 1.887 "obj and name CA" index = 82 rmsd = 2.133 "obj and name CA" index = 83 rmsd = 1.757 "obj and name CA" index = 84 rmsd = 1.476 "obj and name CA" index = 85 rmsd = 1.274 "obj and name CA" index = 86 rmsd = 1.200 "obj and name CA" index = 87 rmsd = 1.250 "obj and name CA" index = 88 rmsd = 1.312 "obj and name CA" index = 89 rmsd = 1.581 "obj and name CA" index = 90 rmsd = 1.785 "obj and name CA" index = 91 rmsd = 1.704 "obj and name CA" index = 92 rmsd = 1.724 "obj and name CA" index = 93 rmsd = 1.693 "obj and name CA" index = 94 rmsd = 1.909 "obj and name CA" index = 95 rmsd = 2.239 "obj and name CA" index = 96 rmsd = 2.799 "obj and name CA" index = 97 rmsd = 2.771 "obj and name CA" index = 98 rmsd = 2.179 "obj and name CA" index = 99 rmsd = 1.662 "obj and name CA" index = 100 rmsd = 1.352 "obj and name CA" index = 101 rmsd = 1.145 "obj and name CA" index = 102 rmsd = 1.049 "obj and name CA" index = 103 rmsd = 1.151 "obj and name CA" index = 104 rmsd = 1.242 "obj and name CA" index = 105 rmsd = 1.627 "obj and name CA" index = 106 rmsd = 2.071 "obj and name CA" index = 107 rmsd = 2.555 "obj and name CA" index = 108 rmsd = 2.689 "obj and name CA" index = 109 rmsd = 2.482 "obj and name CA" index = 110 rmsd = 2.328 "obj and name CA" index = 111 rmsd = 1.933 "obj and name CA" index = 112 rmsd = 1.727 "obj and name CA" index = 113 rmsd = 1.377 "obj and name CA" index = 114 rmsd = 1.194 "obj and name CA" index = 115 rmsd = 1.099 "obj and name CA" index = 116 rmsd = 1.145 "obj and name CA" index = 117 rmsd = 1.243 "obj and name CA" index = 118 rmsd = 1.903 "obj and name CA" index = 119 rmsd = 2.477 "obj and name CA" index = 120 rmsd = 3.400 "obj and name CA" index = 121 rmsd = 4.581 "obj and name CA" index = 122 rmsd = 6.115 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 1598 atoms. PyMOL>color gray,ss ""+l Executive: Colored 2320 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: 1.74 sec. = 2071.8 frames/hour (6.17 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit