PyMOL>load ./selSi.pdb,obj HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 18-SEP-07 2JVD TITLE SOLUTION NMR STRUCTURE OF THE FOLDED N-TERMINAL FRAGMENT OF TITLE 2 UPF0291 PROTEIN YNZC FROM BACILLUS SUBTILIS. NORTHEAST TITLE 3 STRUCTURAL GENOMICS TARGET SR384-1-46 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UPF0291 PROTEIN YNZC; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-46; 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 563 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 223 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: 0.78 sec. = 4588.3 frames/hour (0.78 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 144 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 144 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: 1.86 sec. = 1936.6 frames/hour (2.64 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, 3.9400906562805176, 3.8898110389709473, 2.1557879447937012, 2.6596465110778809, 4.2530694007873535, 3.2902369499206543, 3.408360481262207, 3.6589727401733398, 3.7445955276489258, 3.8544120788574219, 3.7516200542449951, 4.5430679321289062, 4.0495400428771973, 3.1489772796630859, 4.0337820053100586, 4.3944439888000488, 3.7607095241546631, 3.4840719699859619, 3.880746603012085] -> atom index_map = [None, 2, 21, 40, 51, 65, 75, 97, 116, 126, 150, 169, 183, 198, 217, 227, 237, 259, 269, 291, 301, 308, 324, 343, 357, 372, 387, 402, 424, 434, 449, 466, 483, 505, 524, 548, 565, 580, 601, 620, 642, 649, 669, 693, 704, 715, 732, 754, 773] "obj and name CA" index = 1 rmsd = 3.117 "obj and name CA" index = 2 rmsd = 2.207 "obj and name CA" index = 3 rmsd = 2.290 "obj and name CA" index = 4 rmsd = 2.287 "obj and name CA" index = 5 rmsd = 1.916 "obj and name CA" index = 6 rmsd = 1.237 "obj and name CA" index = 7 rmsd = 1.470 "obj and name CA" index = 8 rmsd = 1.387 "obj and name CA" index = 9 rmsd = 0.875 "obj and name CA" index = 10 rmsd = 0.890 "obj and name CA" index = 11 rmsd = 1.333 "obj and name CA" index = 12 rmsd = 1.142 "obj and name CA" index = 13 rmsd = 0.900 "obj and name CA" index = 14 rmsd = 1.481 "obj and name CA" index = 15 rmsd = 1.723 "obj and name CA" index = 16 rmsd = 1.587 "obj and name CA" index = 17 rmsd = 1.871 "obj and name CA" index = 18 rmsd = 2.360 "obj and name CA" index = 19 rmsd = 2.309 "obj and name CA" index = 20 rmsd = 2.406 "obj and name CA" index = 21 rmsd = 2.211 "obj and name CA" index = 22 rmsd = 1.859 "obj and name CA" index = 23 rmsd = 2.210 "obj and name CA" index = 24 rmsd = 2.310 "obj and name CA" index = 25 rmsd = 2.019 "obj and name CA" index = 26 rmsd = 1.384 "obj and name CA" index = 27 rmsd = 1.560 "obj and name CA" index = 28 rmsd = 1.627 "obj and name CA" index = 29 rmsd = 1.094 "obj and name CA" index = 30 rmsd = 0.975 "obj and name CA" index = 31 rmsd = 1.569 "obj and name CA" index = 32 rmsd = 1.385 "obj and name CA" index = 33 rmsd = 1.110 "obj and name CA" index = 34 rmsd = 1.701 "obj and name CA" index = 35 rmsd = 2.089 "obj and name CA" index = 36 rmsd = 1.852 "obj and name CA" index = 37 rmsd = 2.122 "obj and name CA" index = 38 rmsd = 2.771 "obj and name CA" index = 39 rmsd = 2.667 "obj and name CA" index = 40 rmsd = 3.298 "obj and name CA" index = 41 rmsd = 3.218 "obj and name CA" index = 42 rmsd = 3.779 "obj and name CA" index = 43 rmsd = 3.372 "obj and name CA" index = 44 rmsd = 3.444 "obj and name CA" index = 45 rmsd = 5.171 "obj and name CA" index = 46 rmsd = 6.555 "obj and name CA" index = 47 rmsd = 8.833 "obj and name CA" index = 48 rmsd = 10.640 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 1157 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 463 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: 1.00 sec. = 3592.7 frames/hour (3.65 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit