PyMOL>load ./selSi.pdb,obj HEADER MEMBRANE PROTEIN 15-DEC-06 2JN0 TITLE SOLUTION NMR STRUCTURE OF THE YGDR PROTEIN FROM ESCHERICHIA TITLE 2 COLI. NORTHEAST STRUCTURAL GENOMICS TARGET ER382A. COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL LIPOPROTEIN YGDR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HYPOTHETICAL LIPOPROTEIN YGDR, RESIDUES 2-53; 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 333 atoms. PyMOL>color gray,ss ""+l Executive: Colored 435 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. = 3820.9 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 150 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 150 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: 3.72 sec. = 967.3 frames/hour (4.66 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, 1.8046447038650513, 1.6707296371459961, 2.351510763168335, 1.5611250400543213, 2.2392909526824951, 1.9014605283737183, 1.7354958057403564, 1.8111639022827148, 1.4728488922119141, 2.0710229873657227, 1.9849474430084229, 2.5884692668914795, 2.0670545101165771, 1.7144372463226318, 2.1669435501098633, 2.443925142288208, 1.3993740081787109, 2.2593207359313965, 1.714423656463623] -> atom index_map = [None, 2, 14, 35, 51, 68, 78, 92, 114, 126, 133, 157, 174, 193, 212, 226, 238, 245, 267, 281, 296, 315, 327, 339, 351, 365, 372, 391, 407, 418, 439, 457, 469, 486, 503, 510, 524, 534, 551, 568, 587, 601, 625, 637, 649, 665, 676, 693, 712, 731, 746] "obj and name CA" index = 1 rmsd = 3.462 "obj and name CA" index = 2 rmsd = 1.279 "obj and name CA" index = 3 rmsd = 0.604 "obj and name CA" index = 4 rmsd = 0.436 "obj and name CA" index = 5 rmsd = 0.629 "obj and name CA" index = 6 rmsd = 0.583 "obj and name CA" index = 7 rmsd = 0.970 "obj and name CA" index = 8 rmsd = 1.071 "obj and name CA" index = 9 rmsd = 1.004 "obj and name CA" index = 10 rmsd = 0.827 "obj and name CA" index = 11 rmsd = 0.693 "obj and name CA" index = 12 rmsd = 0.479 "obj and name CA" index = 13 rmsd = 0.555 "obj and name CA" index = 14 rmsd = 0.510 "obj and name CA" index = 15 rmsd = 0.995 "obj and name CA" index = 16 rmsd = 1.131 "obj and name CA" index = 17 rmsd = 1.049 "obj and name CA" index = 18 rmsd = 0.640 "obj and name CA" index = 19 rmsd = 0.613 "obj and name CA" index = 20 rmsd = 0.609 "obj and name CA" index = 21 rmsd = 0.597 "obj and name CA" index = 22 rmsd = 1.213 "obj and name CA" index = 23 rmsd = 1.354 "obj and name CA" index = 24 rmsd = 1.063 "obj and name CA" index = 25 rmsd = 0.743 "obj and name CA" index = 26 rmsd = 0.389 "obj and name CA" index = 27 rmsd = 0.335 "obj and name CA" index = 28 rmsd = 0.358 "obj and name CA" index = 29 rmsd = 0.427 "obj and name CA" index = 30 rmsd = 0.478 "obj and name CA" index = 31 rmsd = 0.507 "obj and name CA" index = 32 rmsd = 0.782 "obj and name CA" index = 33 rmsd = 0.843 "obj and name CA" index = 34 rmsd = 0.846 "obj and name CA" index = 35 rmsd = 0.670 "obj and name CA" index = 36 rmsd = 0.525 "obj and name CA" index = 37 rmsd = 0.484 "obj and name CA" index = 38 rmsd = 0.438 "obj and name CA" index = 39 rmsd = 0.377 "obj and name CA" index = 40 rmsd = 0.462 "obj and name CA" index = 41 rmsd = 0.610 "obj and name CA" index = 42 rmsd = 0.769 "obj and name CA" index = 43 rmsd = 0.688 "obj and name CA" index = 44 rmsd = 0.689 "obj and name CA" index = 45 rmsd = 0.852 "obj and name CA" index = 46 rmsd = 1.057 "obj and name CA" index = 47 rmsd = 0.827 "obj and name CA" index = 48 rmsd = 1.905 "obj and name CA" index = 49 rmsd = 3.580 "obj and name CA" index = 50 rmsd = 4.954 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 690 atoms. PyMOL>color gray,ss ""+l Executive: Colored 896 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: 1.44 sec. = 2499.4 frames/hour (6.10 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit