PyMOL>load ./selSi.pdb,obj HEADER TRANSCRIPTION REGULATOR 03-SEP-10 2L33 TITLE SOLUTION NMR STRUCTURE OF DRBM 2 DOMAIN OF INTERLEUKIN ENHANCER- TITLE 2 BINDING FACTOR 3 FROM HOMO SAPIENS, NORTHEAST STRUCTURAL GENOMICS TITLE 3 CONSORTIUM TARGET HR4527E COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTERLEUKIN ENHANCER-BINDING FACTOR 3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DRBM 2 DOMAIN RESIDUES 521-600; COMPND 5 SYNONYM: NUCLEAR FACTOR OF ACTIVATED T-CELLS 90 KDA, NF-AT-90, COMPND 6 DOUBLE-STRANDED RNA-BINDING PROTEIN 76, DRBP76, TRANSLATIONAL CONTROL COMPND 7 PROTEIN 80, TCP80, NUCLEAR FACTOR ASSOCIATED WITH DSRNA, NFAR, M- COMPND 8 PHASE PHOSPHOPROTEIN 4, MPP4; COMPND 9 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 457 atoms. PyMOL>color cyan,ss s Executive: Colored 399 atoms. PyMOL>color gray,ss ""+l Executive: Colored 580 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: 0.94 sec. = 3829.4 frames/hour (0.94 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 273 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 273 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: 2.79 sec. = 1290.4 frames/hour (3.73 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, 5.4059615135192871, 4.1857061386108398, 4.0656943321228027, 4.5360894203186035, 3.5724368095397949, 4.3164172172546387, 4.4532122611999512, 4.0292925834655762, 3.248302698135376, 3.5537576675415039, 4.7605729103088379, 8.5117807388305664, 3.3783133029937744, 4.8453106880187988, 7.1280794143676758, 5.0761380195617676, 6.718390941619873, 5.6526312828063965, 3.8505790233612061] -> atom index_map = [None, 2, 21, 28, 46, 64, 82, 100, 118, 136, 147, 165, 182, 201, 215, 237, 255, 262, 284, 298, 312, 328, 345, 360, 379, 393, 408, 430, 454, 478, 485, 504, 526, 547, 562, 581, 600, 611, 626, 640, 647, 654, 665, 683, 695, 717, 741, 761, 777, 794, 809, 825, 840, 856, 868, 875, 892, 914, 934, 951, 958, 968, 975, 986, 1000, 1022, 1044, 1060, 1070, 1092, 1102, 1123, 1133, 1143, 1162, 1172, 1182, 1201, 1216, 1238, 1257, 1277, 1291, 1303, 1317, 1331, 1350, 1360, 1379, 1391, 1401, 1415] "obj and name CA" index = 1 rmsd = 13.939 "obj and name CA" index = 2 rmsd = 12.034 "obj and name CA" index = 3 rmsd = 10.358 "obj and name CA" index = 4 rmsd = 8.524 "obj and name CA" index = 5 rmsd = 6.675 "obj and name CA" index = 6 rmsd = 5.783 "obj and name CA" index = 7 rmsd = 4.789 "obj and name CA" index = 8 rmsd = 4.192 "obj and name CA" index = 9 rmsd = 3.169 "obj and name CA" index = 10 rmsd = 2.734 "obj and name CA" index = 11 rmsd = 2.256 "obj and name CA" index = 12 rmsd = 2.203 "obj and name CA" index = 13 rmsd = 1.898 "obj and name CA" index = 14 rmsd = 2.608 "obj and name CA" index = 15 rmsd = 3.047 "obj and name CA" index = 16 rmsd = 2.791 "obj and name CA" index = 17 rmsd = 2.341 "obj and name CA" index = 18 rmsd = 2.076 "obj and name CA" index = 19 rmsd = 1.521 "obj and name CA" index = 20 rmsd = 1.534 "obj and name CA" index = 21 rmsd = 1.994 "obj and name CA" index = 22 rmsd = 1.793 "obj and name CA" index = 23 rmsd = 1.480 "obj and name CA" index = 24 rmsd = 1.906 "obj and name CA" index = 25 rmsd = 2.224 "obj and name CA" index = 26 rmsd = 2.082 "obj and name CA" index = 27 rmsd = 2.133 "obj and name CA" index = 28 rmsd = 2.506 "obj and name CA" index = 29 rmsd = 2.649 "obj and name CA" index = 30 rmsd = 1.977 "obj and name CA" index = 31 rmsd = 1.917 "obj and name CA" index = 32 rmsd = 1.572 "obj and name CA" index = 33 rmsd = 1.771 "obj and name CA" index = 34 rmsd = 1.828 "obj and name CA" index = 35 rmsd = 1.898 "obj and name CA" index = 36 rmsd = 2.225 "obj and name CA" index = 37 rmsd = 2.639 "obj and name CA" index = 38 rmsd = 3.124 "obj and name CA" index = 39 rmsd = 3.751 "obj and name CA" index = 40 rmsd = 4.586 "obj and name CA" index = 41 rmsd = 4.496 "obj and name CA" index = 42 rmsd = 4.403 "obj and name CA" index = 43 rmsd = 3.952 "obj and name CA" index = 44 rmsd = 3.166 "obj and name CA" index = 45 rmsd = 2.713 "obj and name CA" index = 46 rmsd = 2.170 "obj and name CA" index = 47 rmsd = 1.764 "obj and name CA" index = 48 rmsd = 1.406 "obj and name CA" index = 49 rmsd = 1.315 "obj and name CA" index = 50 rmsd = 1.314 "obj and name CA" index = 51 rmsd = 1.768 "obj and name CA" index = 52 rmsd = 1.873 "obj and name CA" index = 53 rmsd = 2.563 "obj and name CA" index = 54 rmsd = 2.564 "obj and name CA" index = 55 rmsd = 2.224 "obj and name CA" index = 56 rmsd = 1.815 "obj and name CA" index = 57 rmsd = 1.445 "obj and name CA" index = 58 rmsd = 1.393 "obj and name CA" index = 59 rmsd = 1.452 "obj and name CA" index = 60 rmsd = 1.946 "obj and name CA" index = 61 rmsd = 2.245 "obj and name CA" index = 62 rmsd = 2.851 "obj and name CA" index = 63 rmsd = 2.592 "obj and name CA" index = 64 rmsd = 2.133 "obj and name CA" index = 65 rmsd = 2.107 "obj and name CA" index = 66 rmsd = 2.069 "obj and name CA" index = 67 rmsd = 1.650 "obj and name CA" index = 68 rmsd = 1.298 "obj and name CA" index = 69 rmsd = 1.440 "obj and name CA" index = 70 rmsd = 1.428 "obj and name CA" index = 71 rmsd = 1.090 "obj and name CA" index = 72 rmsd = 1.028 "obj and name CA" index = 73 rmsd = 1.259 "obj and name CA" index = 74 rmsd = 1.372 "obj and name CA" index = 75 rmsd = 1.347 "obj and name CA" index = 76 rmsd = 1.424 "obj and name CA" index = 77 rmsd = 1.789 "obj and name CA" index = 78 rmsd = 2.013 "obj and name CA" index = 79 rmsd = 2.006 "obj and name CA" index = 80 rmsd = 1.936 "obj and name CA" index = 81 rmsd = 2.148 "obj and name CA" index = 82 rmsd = 2.616 "obj and name CA" index = 83 rmsd = 2.916 "obj and name CA" index = 84 rmsd = 2.867 "obj and name CA" index = 85 rmsd = 3.188 "obj and name CA" index = 86 rmsd = 4.158 "obj and name CA" index = 87 rmsd = 5.662 "obj and name CA" index = 88 rmsd = 7.139 "obj and name CA" index = 89 rmsd = 8.559 "obj and name CA" index = 90 rmsd = 10.821 "obj and name CA" index = 91 rmsd = 12.862 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 938 atoms. PyMOL>color cyan,ss s Executive: Colored 818 atoms. PyMOL>color gray,ss ""+l Executive: Colored 1207 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: 1.19 sec. = 3020.5 frames/hour (4.92 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit