PyMOL>load ./selSi.pdb,obj HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 10-SEP-10 2L3A TITLE SOLUTION NMR STRUCTURE OF HOMODIMER PROTEIN SP_0782 (7-79) FROM TITLE 2 STREPTOCOCCUS PNEUMONIAE NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TITLE 3 TARGET SPR104 . COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES 7-79; 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 429 atoms. PyMOL>color cyan,ss s Executive: Colored 1151 atoms. PyMOL>color gray,ss ""+l Executive: Colored 1068 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: 1.62 sec. = 2225.5 frames/hour (1.62 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 492 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 492 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: 6.33 sec. = 568.5 frames/hour (7.95 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, 4.0396013259887695, 4.4524803161621094, 4.4143948554992676, 5.0005111694335938, 4.9035501480102539, 4.085045337677002, 3.0882856845855713, 3.5044159889221191, 3.349562406539917, 3.4028387069702148, 2.5655517578125, 3.2952549457550049, 2.7408039569854736, 4.9809350967407227, 3.2439408302307129, 4.1547465324401855, 4.0943822860717773, 4.2941961288452148, 4.9889006614685059] -> atom index_map = [None, 2, 21, 43, 65, 82, 92, 107, 127, 141, 161, 176, 195, 210, 225, 243, 262, 281, 295, 314, 325, 340, 354, 369, 391, 398, 422, 436, 458, 473, 492, 506, 530, 546, 557, 577, 591, 598, 608, 622, 632, 654, 674, 686, 705, 729, 739, 763, 774, 788, 800, 818, 832, 854, 871, 878, 900, 907, 926, 940, 959, 970, 984, 999, 1014, 1034, 1051, 1065, 1082, 1098, 1110, 1120, 1140, 1162, 1169, 1183, 1202, 1217, 1235, 1253, 1271, 1289, 1307, 1326, 1345, 1367, 1389, 1406, 1416, 1431, 1451, 1465, 1485, 1500, 1519, 1534, 1549, 1567, 1586, 1605, 1619, 1638, 1649, 1664, 1678, 1693, 1715, 1722, 1746, 1760, 1782, 1797, 1816, 1830, 1854, 1870, 1881, 1901, 1915, 1922, 1932, 1946, 1956, 1978, 1998, 2010, 2029, 2053, 2063, 2087, 2098, 2112, 2124, 2142, 2156, 2178, 2195, 2202, 2224, 2231, 2250, 2264, 2283, 2294, 2308, 2323, 2338, 2358, 2375, 2389, 2406, 2422, 2434, 2444, 2464, 2486, 2493, 2507, 2526, 2541, 2559, 2577, 2595, 2613, 2631] "obj and name CA" index = 1 rmsd = 9.979 "obj and name CA" index = 2 rmsd = 8.474 "obj and name CA" index = 3 rmsd = 7.507 "obj and name CA" index = 4 rmsd = 5.991 "obj and name CA" index = 5 rmsd = 4.190 "obj and name CA" index = 6 rmsd = 3.213 "obj and name CA" index = 7 rmsd = 2.115 "obj and name CA" index = 8 rmsd = 1.602 "obj and name CA" index = 9 rmsd = 1.230 "obj and name CA" index = 10 rmsd = 1.250 "obj and name CA" index = 11 rmsd = 1.125 "obj and name CA" index = 12 rmsd = 1.252 "obj and name CA" index = 13 rmsd = 1.207 "obj and name CA" index = 14 rmsd = 1.053 "obj and name CA" index = 15 rmsd = 0.913 "obj and name CA" index = 16 rmsd = 1.004 "obj and name CA" index = 17 rmsd = 0.867 "obj and name CA" index = 18 rmsd = 0.760 "obj and name CA" index = 19 rmsd = 0.906 "obj and name CA" index = 20 rmsd = 1.154 "obj and name CA" index = 21 rmsd = 1.404 "obj and name CA" index = 22 rmsd = 2.034 "obj and name CA" index = 23 rmsd = 2.452 "obj and name CA" index = 24 rmsd = 1.503 "obj and name CA" index = 25 rmsd = 1.169 "obj and name CA" index = 26 rmsd = 0.953 "obj and name CA" index = 27 rmsd = 0.723 "obj and name CA" index = 28 rmsd = 0.650 "obj and name CA" index = 29 rmsd = 0.641 "obj and name CA" index = 30 rmsd = 0.755 "obj and name CA" index = 31 rmsd = 0.850 "obj and name CA" index = 32 rmsd = 0.922 "obj and name CA" index = 33 rmsd = 1.065 "obj and name CA" index = 34 rmsd = 1.272 "obj and name CA" index = 35 rmsd = 1.661 "obj and name CA" index = 36 rmsd = 2.064 "obj and name CA" index = 37 rmsd = 2.543 "obj and name CA" index = 38 rmsd = 1.728 "obj and name CA" index = 39 rmsd = 1.197 "obj and name CA" index = 40 rmsd = 0.971 "obj and name CA" index = 41 rmsd = 0.841 "obj and name CA" index = 42 rmsd = 0.758 "obj and name CA" index = 43 rmsd = 0.657 "obj and name CA" index = 44 rmsd = 0.782 "obj and name CA" index = 45 rmsd = 0.892 "obj and name CA" index = 46 rmsd = 1.168 "obj and name CA" index = 47 rmsd = 1.650 "obj and name CA" index = 48 rmsd = 2.002 "obj and name CA" index = 49 rmsd = 2.478 "obj and name CA" index = 50 rmsd = 3.011 "obj and name CA" index = 51 rmsd = 3.221 "obj and name CA" index = 52 rmsd = 2.227 "obj and name CA" index = 53 rmsd = 1.951 "obj and name CA" index = 54 rmsd = 1.950 "obj and name CA" index = 55 rmsd = 1.504 "obj and name CA" index = 56 rmsd = 0.834 "obj and name CA" index = 57 rmsd = 0.747 "obj and name CA" index = 58 rmsd = 0.767 "obj and name CA" index = 59 rmsd = 0.817 "obj and name CA" index = 60 rmsd = 0.941 "obj and name CA" index = 61 rmsd = 1.012 "obj and name CA" index = 62 rmsd = 0.997 "obj and name CA" index = 63 rmsd = 0.809 "obj and name CA" index = 64 rmsd = 0.657 "obj and name CA" index = 65 rmsd = 0.796 "obj and name CA" index = 66 rmsd = 0.784 "obj and name CA" index = 67 rmsd = 0.687 "obj and name CA" index = 68 rmsd = 0.753 "obj and name CA" index = 69 rmsd = 0.954 "obj and name CA" index = 70 rmsd = 0.849 "obj and name CA" index = 71 rmsd = 0.801 "obj and name CA" index = 72 rmsd = 1.057 "obj and name CA" index = 73 rmsd = 1.164 "obj and name CA" index = 74 rmsd = 1.288 "obj and name CA" index = 75 rmsd = 1.017 "obj and name CA" index = 76 rmsd = 1.613 "obj and name CA" index = 77 rmsd = 2.135 "obj and name CA" index = 78 rmsd = 3.521 "obj and name CA" index = 79 rmsd = 4.684 "obj and name CA" index = 80 rmsd = 5.788 "obj and name CA" index = 81 rmsd = 7.521 "obj and name CA" index = 82 rmsd = 9.438 "obj and name CA" index = 83 rmsd = 11.119 "obj and name CA" index = 84 rmsd = 9.297 "obj and name CA" index = 85 rmsd = 7.671 "obj and name CA" index = 86 rmsd = 6.574 "obj and name CA" index = 87 rmsd = 5.119 "obj and name CA" index = 88 rmsd = 3.540 "obj and name CA" index = 89 rmsd = 1.906 "obj and name CA" index = 90 rmsd = 1.513 "obj and name CA" index = 91 rmsd = 1.249 "obj and name CA" index = 92 rmsd = 1.360 "obj and name CA" index = 93 rmsd = 1.080 "obj and name CA" index = 94 rmsd = 1.173 "obj and name CA" index = 95 rmsd = 1.093 "obj and name CA" index = 96 rmsd = 1.057 "obj and name CA" index = 97 rmsd = 0.912 "obj and name CA" index = 98 rmsd = 1.023 "obj and name CA" index = 99 rmsd = 0.960 "obj and name CA" index = 100 rmsd = 0.904 "obj and name CA" index = 101 rmsd = 1.095 "obj and name CA" index = 102 rmsd = 1.358 "obj and name CA" index = 103 rmsd = 1.672 "obj and name CA" index = 104 rmsd = 2.450 "obj and name CA" index = 105 rmsd = 2.889 "obj and name CA" index = 106 rmsd = 1.816 "obj and name CA" index = 107 rmsd = 1.204 "obj and name CA" index = 108 rmsd = 0.981 "obj and name CA" index = 109 rmsd = 0.805 "obj and name CA" index = 110 rmsd = 0.757 "obj and name CA" index = 111 rmsd = 0.650 "obj and name CA" index = 112 rmsd = 0.706 "obj and name CA" index = 113 rmsd = 0.778 "obj and name CA" index = 114 rmsd = 0.863 "obj and name CA" index = 115 rmsd = 1.087 "obj and name CA" index = 116 rmsd = 1.183 "obj and name CA" index = 117 rmsd = 1.486 "obj and name CA" index = 118 rmsd = 1.688 "obj and name CA" index = 119 rmsd = 2.338 "obj and name CA" index = 120 rmsd = 1.403 "obj and name CA" index = 121 rmsd = 1.103 "obj and name CA" index = 122 rmsd = 0.838 "obj and name CA" index = 123 rmsd = 0.680 "obj and name CA" index = 124 rmsd = 0.623 "obj and name CA" index = 125 rmsd = 0.542 "obj and name CA" index = 126 rmsd = 0.770 "obj and name CA" index = 127 rmsd = 0.786 "obj and name CA" index = 128 rmsd = 0.998 "obj and name CA" index = 129 rmsd = 1.296 "obj and name CA" index = 130 rmsd = 1.866 "obj and name CA" index = 131 rmsd = 2.661 "obj and name CA" index = 132 rmsd = 3.819 "obj and name CA" index = 133 rmsd = 3.775 "obj and name CA" index = 134 rmsd = 2.589 "obj and name CA" index = 135 rmsd = 2.901 "obj and name CA" index = 136 rmsd = 2.235 "obj and name CA" index = 137 rmsd = 1.425 "obj and name CA" index = 138 rmsd = 0.665 "obj and name CA" index = 139 rmsd = 0.519 "obj and name CA" index = 140 rmsd = 0.670 "obj and name CA" index = 141 rmsd = 0.723 "obj and name CA" index = 142 rmsd = 0.640 "obj and name CA" index = 143 rmsd = 0.842 "obj and name CA" index = 144 rmsd = 0.776 "obj and name CA" index = 145 rmsd = 0.680 "obj and name CA" index = 146 rmsd = 0.605 "obj and name CA" index = 147 rmsd = 0.793 "obj and name CA" index = 148 rmsd = 0.791 "obj and name CA" index = 149 rmsd = 0.747 "obj and name CA" index = 150 rmsd = 0.758 "obj and name CA" index = 151 rmsd = 0.894 "obj and name CA" index = 152 rmsd = 0.813 "obj and name CA" index = 153 rmsd = 0.783 "obj and name CA" index = 154 rmsd = 1.114 "obj and name CA" index = 155 rmsd = 1.254 "obj and name CA" index = 156 rmsd = 1.354 "obj and name CA" index = 157 rmsd = 0.953 "obj and name CA" index = 158 rmsd = 1.474 "obj and name CA" index = 159 rmsd = 2.405 "obj and name CA" index = 160 rmsd = 3.302 "obj and name CA" index = 161 rmsd = 3.846 "obj and name CA" index = 162 rmsd = 5.833 "obj and name CA" index = 163 rmsd = 7.343 "obj and name CA" index = 164 rmsd = 9.388 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 882 atoms. PyMOL>color cyan,ss s Executive: Colored 2360 atoms. PyMOL>color gray,ss ""+l Executive: Colored 2218 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: 2.04 sec. = 1763.4 frames/hour (9.99 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit