PyMOL>load ./selSi.pdb,obj HEADER STRUCTURAL GENOMICS 05-JUN-07 2JQN TITLE SOLUTION NMR STRUCTURE OF CC0527 FROM CAULOBACTER TITLE 2 CRESCENTUS. NORTHEAST STRUCTURAL GENOMICS TARGET CCR55 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN; COMPND 3 CHAIN: A; COMPND 4 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 584 atoms. PyMOL>color cyan,ss s Executive: Colored 616 atoms. PyMOL>color gray,ss ""+l Executive: Colored 574 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: 1.86 sec. = 1931.0 frames/hour (1.86 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 348 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 348 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: 8.00 sec. = 450.2 frames/hour (9.86 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, 1.7296245098114014, 2.1391570568084717, 2.6957149505615234, 2.2317123413085938, 2.2849104404449463, 2.4313042163848877, 2.0207197666168213, 2.2083308696746826, 1.8648018836975098, 1.9904410839080811, 2.4387094974517822, 2.1703934669494629, 1.874411940574646, 2.4189305305480957, 2.1881263256072998, 2.2473978996276855, 2.2436237335205078, 2.4567747116088867, 2.1815657615661621] -> atom index_map = [None, 2, 21, 35, 54, 73, 94, 116, 135, 154, 165, 189, 199, 214, 238, 250, 260, 270, 292, 302, 319, 326, 350, 370, 385, 392, 403, 413, 429, 441, 460, 470, 482, 489, 509, 528, 546, 565, 576, 586, 593, 608, 625, 635, 652, 667, 681, 691, 701, 723, 747, 767, 791, 798, 815, 825, 839, 858, 874, 893, 912, 922, 938, 953, 963, 978, 992, 1011, 1018, 1033, 1045, 1064, 1086, 1110, 1125, 1135, 1146, 1170, 1177, 1184, 1194, 1218, 1238, 1252, 1270, 1289, 1310, 1334, 1348, 1367, 1386, 1402, 1413, 1428, 1444, 1458, 1482, 1497, 1507, 1519, 1538, 1550, 1569, 1581, 1591, 1603, 1610, 1626, 1640, 1657, 1676, 1683, 1695, 1713, 1732, 1742, 1761] "obj and name CA" index = 1 rmsd = 2.777 "obj and name CA" index = 2 rmsd = 1.139 "obj and name CA" index = 3 rmsd = 0.903 "obj and name CA" index = 4 rmsd = 0.745 "obj and name CA" index = 5 rmsd = 0.706 "obj and name CA" index = 6 rmsd = 0.692 "obj and name CA" index = 7 rmsd = 0.654 "obj and name CA" index = 8 rmsd = 0.672 "obj and name CA" index = 9 rmsd = 0.762 "obj and name CA" index = 10 rmsd = 0.695 "obj and name CA" index = 11 rmsd = 0.878 "obj and name CA" index = 12 rmsd = 0.788 "obj and name CA" index = 13 rmsd = 0.570 "obj and name CA" index = 14 rmsd = 0.746 "obj and name CA" index = 15 rmsd = 0.845 "obj and name CA" index = 16 rmsd = 0.677 "obj and name CA" index = 17 rmsd = 0.636 "obj and name CA" index = 18 rmsd = 0.920 "obj and name CA" index = 19 rmsd = 0.838 "obj and name CA" index = 20 rmsd = 0.744 "obj and name CA" index = 21 rmsd = 0.684 "obj and name CA" index = 22 rmsd = 0.737 "obj and name CA" index = 23 rmsd = 1.181 "obj and name CA" index = 24 rmsd = 1.407 "obj and name CA" index = 25 rmsd = 1.634 "obj and name CA" index = 26 rmsd = 1.998 "obj and name CA" index = 27 rmsd = 1.650 "obj and name CA" index = 28 rmsd = 1.213 "obj and name CA" index = 29 rmsd = 1.754 "obj and name CA" index = 30 rmsd = 1.999 "obj and name CA" index = 31 rmsd = 1.753 "obj and name CA" index = 32 rmsd = 1.927 "obj and name CA" index = 33 rmsd = 0.864 "obj and name CA" index = 34 rmsd = 0.706 "obj and name CA" index = 35 rmsd = 0.892 "obj and name CA" index = 36 rmsd = 0.833 "obj and name CA" index = 37 rmsd = 0.883 "obj and name CA" index = 38 rmsd = 0.921 "obj and name CA" index = 39 rmsd = 0.910 "obj and name CA" index = 40 rmsd = 0.892 "obj and name CA" index = 41 rmsd = 0.795 "obj and name CA" index = 42 rmsd = 0.672 "obj and name CA" index = 43 rmsd = 0.717 "obj and name CA" index = 44 rmsd = 0.812 "obj and name CA" index = 45 rmsd = 0.803 "obj and name CA" index = 46 rmsd = 0.760 "obj and name CA" index = 47 rmsd = 0.931 "obj and name CA" index = 48 rmsd = 1.192 "obj and name CA" index = 49 rmsd = 1.178 "obj and name CA" index = 50 rmsd = 0.948 "obj and name CA" index = 51 rmsd = 1.195 "obj and name CA" index = 52 rmsd = 1.292 "obj and name CA" index = 53 rmsd = 1.247 "obj and name CA" index = 54 rmsd = 1.344 "obj and name CA" index = 55 rmsd = 1.242 "obj and name CA" index = 56 rmsd = 0.932 "obj and name CA" index = 57 rmsd = 0.680 "obj and name CA" index = 58 rmsd = 0.635 "obj and name CA" index = 59 rmsd = 0.550 "obj and name CA" index = 60 rmsd = 0.654 "obj and name CA" index = 61 rmsd = 0.694 "obj and name CA" index = 62 rmsd = 0.800 "obj and name CA" index = 63 rmsd = 1.060 "obj and name CA" index = 64 rmsd = 1.265 "obj and name CA" index = 65 rmsd = 2.772 "obj and name CA" index = 66 rmsd = 2.349 "obj and name CA" index = 67 rmsd = 2.655 "obj and name CA" index = 68 rmsd = 1.754 "obj and name CA" index = 69 rmsd = 1.096 "obj and name CA" index = 70 rmsd = 0.627 "obj and name CA" index = 71 rmsd = 0.651 "obj and name CA" index = 72 rmsd = 0.665 "obj and name CA" index = 73 rmsd = 0.824 "obj and name CA" index = 74 rmsd = 1.256 "obj and name CA" index = 75 rmsd = 1.902 "obj and name CA" index = 76 rmsd = 2.411 "obj and name CA" index = 77 rmsd = 3.059 "obj and name CA" index = 78 rmsd = 2.187 "obj and name CA" index = 79 rmsd = 1.225 "obj and name CA" index = 80 rmsd = 0.959 "obj and name CA" index = 81 rmsd = 0.658 "obj and name CA" index = 82 rmsd = 0.588 "obj and name CA" index = 83 rmsd = 0.595 "obj and name CA" index = 84 rmsd = 0.603 "obj and name CA" index = 85 rmsd = 0.737 "obj and name CA" index = 86 rmsd = 0.850 "obj and name CA" index = 87 rmsd = 0.766 "obj and name CA" index = 88 rmsd = 0.691 "obj and name CA" index = 89 rmsd = 0.635 "obj and name CA" index = 90 rmsd = 0.631 "obj and name CA" index = 91 rmsd = 1.777 "obj and name CA" index = 92 rmsd = 1.007 "obj and name CA" index = 93 rmsd = 0.670 "obj and name CA" index = 94 rmsd = 0.764 "obj and name CA" index = 95 rmsd = 0.763 "obj and name CA" index = 96 rmsd = 0.734 "obj and name CA" index = 97 rmsd = 0.900 "obj and name CA" index = 98 rmsd = 0.890 "obj and name CA" index = 99 rmsd = 1.119 "obj and name CA" index = 100 rmsd = 1.892 "obj and name CA" index = 101 rmsd = 1.289 "obj and name CA" index = 102 rmsd = 1.887 "obj and name CA" index = 103 rmsd = 2.523 "obj and name CA" index = 104 rmsd = 1.508 "obj and name CA" index = 105 rmsd = 1.670 "obj and name CA" index = 106 rmsd = 0.979 "obj and name CA" index = 107 rmsd = 1.730 "obj and name CA" index = 108 rmsd = 1.135 "obj and name CA" index = 109 rmsd = 0.890 "obj and name CA" index = 110 rmsd = 1.209 "obj and name CA" index = 111 rmsd = 1.616 "obj and name CA" index = 112 rmsd = 1.689 "obj and name CA" index = 113 rmsd = 1.596 "obj and name CA" index = 114 rmsd = 2.377 "obj and name CA" index = 115 rmsd = 3.211 "obj and name CA" index = 116 rmsd = 4.635 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 1194 atoms. PyMOL>color cyan,ss s Executive: Colored 1255 atoms. PyMOL>color gray,ss ""+l Executive: Colored 1215 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: 2.24 sec. = 1607.8 frames/hour (12.10 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit