PyMOL>load ./selSi.pdb,obj HEADER DNA BINDING PROTEIN 02-AUG-10 2L1P TITLE NMR SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF DNA-BINDING PROTEIN TITLE 2 SATB1 FROM HOMO SAPIENS: NORTHEAST STRUCTURAL GENOMICS TARGET TITLE 3 HR4435B(179-250) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-BINDING PROTEIN SATB1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES 179-250; COMPND 5 SYNONYM: SPECIAL AT-RICH SEQUENCE-BINDING PROTEIN 1; COMPND 6 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 786 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 555 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: 1.24 sec. = 2904.0 frames/hour (1.24 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 249 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 249 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: 4.93 sec. = 730.0 frames/hour (6.17 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, 2.7421047687530518, 2.4826750755310059, 2.7711374759674072, 4.8294515609741211, 2.6373357772827148, 4.3520317077636719, 2.5706629753112793, 4.9510607719421387, 4.1945939064025879, 4.0848588943481445, 4.4561014175415039, 5.0475525856018066, 5.4273366928100586, 4.3024935722351074, 4.0694165229797363, 4.7640419006347656, 2.7517423629760742, 3.6576545238494873, 4.4152045249938965] -> atom index_map = [None, 2, 21, 28, 46, 64, 82, 100, 118, 136, 147, 165, 182, 201, 215, 229, 244, 261, 285, 296, 314, 328, 342, 358, 382, 396, 406, 425, 447, 459, 478, 497, 519, 531, 548, 562, 579, 590, 601, 620, 630, 652, 667, 678, 692, 711, 722, 739, 750, 767, 786, 797, 808, 827, 843, 857, 868, 882, 903, 924, 934, 948, 964, 975, 985, 995, 1017, 1028, 1045, 1060, 1080, 1087, 1111, 1135, 1156, 1178, 1196, 1216, 1238, 1260, 1274, 1296, 1308, 1325] "obj and name CA" index = 1 rmsd = 8.453 "obj and name CA" index = 2 rmsd = 7.110 "obj and name CA" index = 3 rmsd = 5.924 "obj and name CA" index = 4 rmsd = 4.820 "obj and name CA" index = 5 rmsd = 4.359 "obj and name CA" index = 6 rmsd = 3.987 "obj and name CA" index = 7 rmsd = 3.590 "obj and name CA" index = 8 rmsd = 2.993 "obj and name CA" index = 9 rmsd = 2.982 "obj and name CA" index = 10 rmsd = 2.131 "obj and name CA" index = 11 rmsd = 2.025 "obj and name CA" index = 12 rmsd = 1.974 "obj and name CA" index = 13 rmsd = 2.102 "obj and name CA" index = 14 rmsd = 2.251 "obj and name CA" index = 15 rmsd = 2.531 "obj and name CA" index = 16 rmsd = 2.515 "obj and name CA" index = 17 rmsd = 1.888 "obj and name CA" index = 18 rmsd = 2.081 "obj and name CA" index = 19 rmsd = 1.988 "obj and name CA" index = 20 rmsd = 2.230 "obj and name CA" index = 21 rmsd = 1.966 "obj and name CA" index = 22 rmsd = 1.446 "obj and name CA" index = 23 rmsd = 1.512 "obj and name CA" index = 24 rmsd = 1.718 "obj and name CA" index = 25 rmsd = 1.696 "obj and name CA" index = 26 rmsd = 1.638 "obj and name CA" index = 27 rmsd = 1.779 "obj and name CA" index = 28 rmsd = 2.094 "obj and name CA" index = 29 rmsd = 1.952 "obj and name CA" index = 30 rmsd = 1.839 "obj and name CA" index = 31 rmsd = 2.296 "obj and name CA" index = 32 rmsd = 2.526 "obj and name CA" index = 33 rmsd = 2.237 "obj and name CA" index = 34 rmsd = 2.110 "obj and name CA" index = 35 rmsd = 1.774 "obj and name CA" index = 36 rmsd = 1.952 "obj and name CA" index = 37 rmsd = 1.966 "obj and name CA" index = 38 rmsd = 1.581 "obj and name CA" index = 39 rmsd = 1.412 "obj and name CA" index = 40 rmsd = 1.626 "obj and name CA" index = 41 rmsd = 1.553 "obj and name CA" index = 42 rmsd = 1.132 "obj and name CA" index = 43 rmsd = 1.232 "obj and name CA" index = 44 rmsd = 1.044 "obj and name CA" index = 45 rmsd = 1.228 "obj and name CA" index = 46 rmsd = 1.184 "obj and name CA" index = 47 rmsd = 1.209 "obj and name CA" index = 48 rmsd = 1.187 "obj and name CA" index = 49 rmsd = 1.053 "obj and name CA" index = 50 rmsd = 1.214 "obj and name CA" index = 51 rmsd = 1.161 "obj and name CA" index = 52 rmsd = 1.222 "obj and name CA" index = 53 rmsd = 1.353 "obj and name CA" index = 54 rmsd = 1.450 "obj and name CA" index = 55 rmsd = 1.697 "obj and name CA" index = 56 rmsd = 3.450 "obj and name CA" index = 57 rmsd = 3.939 "obj and name CA" index = 58 rmsd = 2.528 "obj and name CA" index = 59 rmsd = 2.913 "obj and name CA" index = 60 rmsd = 2.263 "obj and name CA" index = 61 rmsd = 1.665 "obj and name CA" index = 62 rmsd = 1.776 "obj and name CA" index = 63 rmsd = 1.937 "obj and name CA" index = 64 rmsd = 1.856 "obj and name CA" index = 65 rmsd = 1.478 "obj and name CA" index = 66 rmsd = 1.498 "obj and name CA" index = 67 rmsd = 1.449 "obj and name CA" index = 68 rmsd = 1.229 "obj and name CA" index = 69 rmsd = 0.863 "obj and name CA" index = 70 rmsd = 1.077 "obj and name CA" index = 71 rmsd = 1.052 "obj and name CA" index = 72 rmsd = 0.846 "obj and name CA" index = 73 rmsd = 0.948 "obj and name CA" index = 74 rmsd = 1.423 "obj and name CA" index = 75 rmsd = 1.558 "obj and name CA" index = 76 rmsd = 1.537 "obj and name CA" index = 77 rmsd = 2.037 "obj and name CA" index = 78 rmsd = 1.865 "obj and name CA" index = 79 rmsd = 2.903 "obj and name CA" index = 80 rmsd = 3.958 "obj and name CA" index = 81 rmsd = 5.340 "obj and name CA" index = 82 rmsd = 7.071 "obj and name CA" index = 83 rmsd = 9.052 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 1612 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 1153 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: 1.43 sec. = 2525.9 frames/hour (7.60 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit