PyMOL>load ./selSi.pdb,obj HEADER BIOSYNTHETIC PROTEIN 30-JUN-08 2K5P TITLE NMR SOLUTION STRUCTURE OF A THIAMINE BIOSYNTHESIS PROTEIN TITLE 2 FROM GEOBACTER METALLIREDUCENS: NORTHEAST STRUCTURAL TITLE 3 GENOMICS CONSORTIUM TARGET GMR137 COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIAMINE-BIOSYNTHESIS PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: THIS PROTEIN; 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 Executive: Colored 219 atoms. PyMOL>color cyan,ss s Executive: Colored 309 atoms. PyMOL>color gray,ss ""+l Executive: Colored 652 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: 0.89 sec. = 4053.4 frames/hour (0.89 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 234 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 234 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: 2.80 sec. = 1284.5 frames/hour (3.69 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, 8.4679098129272461, 5.0950946807861328, 10.249485015869141, 6.6399440765380859, 6.3463807106018066, 9.3870944976806641, 9.351710319519043, 7.2694382667541504, 5.527918815612793, 3.1963703632354736, 8.3752326965332031, 6.5026993751525879, 4.3373470306396484, 7.4630250930786133, 8.3800601959228516, 6.099393367767334, 9.2736759185791016, 7.7846274375915527, 6.527158260345459] -> atom index_map = [None, 2, 21, 35, 54, 68, 84, 98, 105, 127, 141, 152, 166, 182, 194, 201, 211, 226, 237, 256, 270, 286, 300, 315, 334, 353, 364, 374, 393, 415, 431, 441, 458, 468, 483, 504, 520, 534, 550, 565, 584, 598, 605, 620, 636, 655, 670, 694, 709, 719, 739, 751, 761, 775, 789, 805, 827, 839, 846, 858, 868, 884, 899, 919, 938, 959, 979, 996, 1003, 1010, 1017, 1039, 1058, 1073, 1091, 1109, 1127, 1145, 1163] "obj and name CA" index = 1 rmsd = 3.275 "obj and name CA" index = 2 rmsd = 3.092 "obj and name CA" index = 3 rmsd = 2.354 "obj and name CA" index = 4 rmsd = 2.558 "obj and name CA" index = 5 rmsd = 2.617 "obj and name CA" index = 6 rmsd = 3.277 "obj and name CA" index = 7 rmsd = 3.369 "obj and name CA" index = 8 rmsd = 3.480 "obj and name CA" index = 9 rmsd = 3.375 "obj and name CA" index = 10 rmsd = 3.439 "obj and name CA" index = 11 rmsd = 3.632 "obj and name CA" index = 12 rmsd = 3.601 "obj and name CA" index = 13 rmsd = 4.284 "obj and name CA" index = 14 rmsd = 4.680 "obj and name CA" index = 15 rmsd = 3.848 "obj and name CA" index = 16 rmsd = 3.967 "obj and name CA" index = 17 rmsd = 3.117 "obj and name CA" index = 18 rmsd = 2.587 "obj and name CA" index = 19 rmsd = 1.852 "obj and name CA" index = 20 rmsd = 1.103 "obj and name CA" index = 21 rmsd = 1.901 "obj and name CA" index = 22 rmsd = 2.549 "obj and name CA" index = 23 rmsd = 2.146 "obj and name CA" index = 24 rmsd = 2.694 "obj and name CA" index = 25 rmsd = 3.567 "obj and name CA" index = 26 rmsd = 3.744 "obj and name CA" index = 27 rmsd = 3.987 "obj and name CA" index = 28 rmsd = 4.461 "obj and name CA" index = 29 rmsd = 4.153 "obj and name CA" index = 30 rmsd = 4.867 "obj and name CA" index = 31 rmsd = 4.173 "obj and name CA" index = 32 rmsd = 3.411 "obj and name CA" index = 33 rmsd = 3.357 "obj and name CA" index = 34 rmsd = 3.646 "obj and name CA" index = 35 rmsd = 3.016 "obj and name CA" index = 36 rmsd = 2.727 "obj and name CA" index = 37 rmsd = 1.906 "obj and name CA" index = 38 rmsd = 2.058 "obj and name CA" index = 39 rmsd = 2.016 "obj and name CA" index = 40 rmsd = 2.860 "obj and name CA" index = 41 rmsd = 3.322 "obj and name CA" index = 42 rmsd = 3.053 "obj and name CA" index = 43 rmsd = 2.550 "obj and name CA" index = 44 rmsd = 2.086 "obj and name CA" index = 45 rmsd = 2.470 "obj and name CA" index = 46 rmsd = 2.414 "obj and name CA" index = 47 rmsd = 2.674 "obj and name CA" index = 48 rmsd = 2.262 "obj and name CA" index = 49 rmsd = 1.447 "obj and name CA" index = 50 rmsd = 2.190 "obj and name CA" index = 51 rmsd = 2.730 "obj and name CA" index = 52 rmsd = 2.158 "obj and name CA" index = 53 rmsd = 2.408 "obj and name CA" index = 54 rmsd = 1.966 "obj and name CA" index = 55 rmsd = 2.771 "obj and name CA" index = 56 rmsd = 3.221 "obj and name CA" index = 57 rmsd = 3.103 "obj and name CA" index = 58 rmsd = 2.339 "obj and name CA" index = 59 rmsd = 2.156 "obj and name CA" index = 60 rmsd = 1.621 "obj and name CA" index = 61 rmsd = 2.323 "obj and name CA" index = 62 rmsd = 2.694 "obj and name CA" index = 63 rmsd = 3.496 "obj and name CA" index = 64 rmsd = 4.692 "obj and name CA" index = 65 rmsd = 3.754 "obj and name CA" index = 66 rmsd = 3.894 "obj and name CA" index = 67 rmsd = 3.953 "obj and name CA" index = 68 rmsd = 4.571 "obj and name CA" index = 69 rmsd = 5.904 "obj and name CA" index = 70 rmsd = 5.787 "obj and name CA" index = 71 rmsd = 5.725 "obj and name CA" index = 72 rmsd = 5.329 "obj and name CA" index = 73 rmsd = 5.748 "obj and name CA" index = 74 rmsd = 5.961 "obj and name CA" index = 75 rmsd = 7.846 "obj and name CA" index = 76 rmsd = 9.840 "obj and name CA" index = 77 rmsd = 11.734 "obj and name CA" index = 78 rmsd = 14.436 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 446 atoms. PyMOL>color cyan,ss s Executive: Colored 628 atoms. PyMOL>color gray,ss ""+l Executive: Colored 1364 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: 0.95 sec. = 3782.6 frames/hour (4.64 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit