PyMOL>load ./selSi.pdb,obj HEADER PROTEIN BINDING 30-JUN-10 2L06 TITLE SOLUTION NMR STRUCTURE OF THE PBS LINKER POLYPEPTIDE DOMAIN (FRAGMENT TITLE 2 254-400) OF PHYCOBILISOME LINKER PROTEIN APCE FROM SYNECHOCYSTIS SP. TITLE 3 PCC 6803. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET SGR209C COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHYCOBILISOME LCM CORE-MEMBRANE LINKER POLYPEPTIDE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES 254-401; 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 1550 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 967 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: 1.41 sec. = 2560.3 frames/hour (1.41 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 465 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 465 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: 5.31 sec. = 678.3 frames/hour (6.71 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, 9.4860963821411133, 7.5729265213012695, 8.5020895004272461, 4.9815177917480469, 7.5596494674682617, 9.2813205718994141, 4.5159182548522949, 8.3050451278686523, 9.0688896179199219, 8.0980005264282227, 7.4088401794433594, 9.3702325820922852, 7.1712565422058105, 9.4910125732421875, 6.4204320907592773, 9.779911994934082, 7.8276834487915039, 7.032984733581543, 6.7477483749389648] -> atom index_map = [None, 2, 18, 35, 46, 67, 87, 101, 111, 121, 131, 153, 177, 194, 216, 237, 247, 264, 286, 300, 307, 326, 337, 347, 366, 381, 403, 417, 427, 443, 462, 484, 494, 504, 525, 549, 566, 585, 605, 620, 644, 656, 675, 689, 711, 721, 742, 753, 770, 781, 800, 811, 832, 851, 866, 877, 894, 910, 934, 948, 955, 967, 986, 997, 1014, 1036, 1051, 1071, 1087, 1111, 1135, 1154, 1164, 1186, 1197, 1211, 1230, 1251, 1275, 1297, 1314, 1334, 1354, 1369, 1383, 1403, 1422, 1436, 1447, 1471, 1481, 1500, 1515, 1534, 1544, 1564, 1588, 1606, 1625, 1644, 1651, 1675, 1682, 1696, 1707, 1718, 1742, 1757, 1772, 1788, 1805, 1827, 1848, 1868, 1879, 1898, 1914, 1925, 1936, 1943, 1950, 1969, 1983, 1993, 2012, 2028, 2040, 2050, 2069, 2085, 2097, 2108, 2125, 2140, 2161, 2171, 2183, 2204, 2224, 2231, 2246, 2261, 2275, 2291, 2305, 2326, 2345, 2369, 2376, 2395, 2410, 2428, 2446, 2464, 2482, 2500] "obj and name CA" index = 1 rmsd = 19.048 "obj and name CA" index = 2 rmsd = 17.690 "obj and name CA" index = 3 rmsd = 16.040 "obj and name CA" index = 4 rmsd = 14.394 "obj and name CA" index = 5 rmsd = 12.694 "obj and name CA" index = 6 rmsd = 10.850 "obj and name CA" index = 7 rmsd = 9.047 "obj and name CA" index = 8 rmsd = 7.618 "obj and name CA" index = 9 rmsd = 6.597 "obj and name CA" index = 10 rmsd = 5.537 "obj and name CA" index = 11 rmsd = 4.650 "obj and name CA" index = 12 rmsd = 3.718 "obj and name CA" index = 13 rmsd = 3.154 "obj and name CA" index = 14 rmsd = 2.709 "obj and name CA" index = 15 rmsd = 2.683 "obj and name CA" index = 16 rmsd = 2.468 "obj and name CA" index = 17 rmsd = 3.209 "obj and name CA" index = 18 rmsd = 3.835 "obj and name CA" index = 19 rmsd = 4.217 "obj and name CA" index = 20 rmsd = 3.517 "obj and name CA" index = 21 rmsd = 3.469 "obj and name CA" index = 22 rmsd = 2.955 "obj and name CA" index = 23 rmsd = 3.066 "obj and name CA" index = 24 rmsd = 3.017 "obj and name CA" index = 25 rmsd = 2.449 "obj and name CA" index = 26 rmsd = 2.254 "obj and name CA" index = 27 rmsd = 2.526 "obj and name CA" index = 28 rmsd = 2.175 "obj and name CA" index = 29 rmsd = 1.620 "obj and name CA" index = 30 rmsd = 1.916 "obj and name CA" index = 31 rmsd = 2.097 "obj and name CA" index = 32 rmsd = 1.512 "obj and name CA" index = 33 rmsd = 1.482 "obj and name CA" index = 34 rmsd = 2.133 "obj and name CA" index = 35 rmsd = 1.962 "obj and name CA" index = 36 rmsd = 1.351 "obj and name CA" index = 37 rmsd = 1.734 "obj and name CA" index = 38 rmsd = 2.427 "obj and name CA" index = 39 rmsd = 2.809 "obj and name CA" index = 40 rmsd = 3.452 "obj and name CA" index = 41 rmsd = 3.050 "obj and name CA" index = 42 rmsd = 4.049 "obj and name CA" index = 43 rmsd = 4.349 "obj and name CA" index = 44 rmsd = 4.014 "obj and name CA" index = 45 rmsd = 2.681 "obj and name CA" index = 46 rmsd = 3.035 "obj and name CA" index = 47 rmsd = 2.476 "obj and name CA" index = 48 rmsd = 2.364 "obj and name CA" index = 49 rmsd = 1.826 "obj and name CA" index = 50 rmsd = 1.906 "obj and name CA" index = 51 rmsd = 2.176 "obj and name CA" index = 52 rmsd = 1.812 "obj and name CA" index = 53 rmsd = 1.674 "obj and name CA" index = 54 rmsd = 2.174 "obj and name CA" index = 55 rmsd = 2.254 "obj and name CA" index = 56 rmsd = 2.000 "obj and name CA" index = 57 rmsd = 2.180 "obj and name CA" index = 58 rmsd = 2.638 "obj and name CA" index = 59 rmsd = 2.694 "obj and name CA" index = 60 rmsd = 2.793 "obj and name CA" index = 61 rmsd = 2.379 "obj and name CA" index = 62 rmsd = 2.319 "obj and name CA" index = 63 rmsd = 1.796 "obj and name CA" index = 64 rmsd = 1.741 "obj and name CA" index = 65 rmsd = 1.757 "obj and name CA" index = 66 rmsd = 1.381 "obj and name CA" index = 67 rmsd = 1.131 "obj and name CA" index = 68 rmsd = 1.436 "obj and name CA" index = 69 rmsd = 1.478 "obj and name CA" index = 70 rmsd = 1.101 "obj and name CA" index = 71 rmsd = 1.126 "obj and name CA" index = 72 rmsd = 1.693 "obj and name CA" index = 73 rmsd = 1.781 "obj and name CA" index = 74 rmsd = 2.466 "obj and name CA" index = 75 rmsd = 2.311 "obj and name CA" index = 76 rmsd = 1.765 "obj and name CA" index = 77 rmsd = 2.156 "obj and name CA" index = 78 rmsd = 2.783 "obj and name CA" index = 79 rmsd = 2.593 "obj and name CA" index = 80 rmsd = 2.458 "obj and name CA" index = 81 rmsd = 2.543 "obj and name CA" index = 82 rmsd = 3.267 "obj and name CA" index = 83 rmsd = 3.357 "obj and name CA" index = 84 rmsd = 3.101 "obj and name CA" index = 85 rmsd = 3.089 "obj and name CA" index = 86 rmsd = 2.641 "obj and name CA" index = 87 rmsd = 2.449 "obj and name CA" index = 88 rmsd = 2.248 "obj and name CA" index = 89 rmsd = 1.930 "obj and name CA" index = 90 rmsd = 1.655 "obj and name CA" index = 91 rmsd = 1.692 "obj and name CA" index = 92 rmsd = 1.629 "obj and name CA" index = 93 rmsd = 1.245 "obj and name CA" index = 94 rmsd = 1.345 "obj and name CA" index = 95 rmsd = 1.720 "obj and name CA" index = 96 rmsd = 1.524 "obj and name CA" index = 97 rmsd = 1.305 "obj and name CA" index = 98 rmsd = 1.781 "obj and name CA" index = 99 rmsd = 2.112 "obj and name CA" index = 100 rmsd = 2.253 "obj and name CA" index = 101 rmsd = 1.937 "obj and name CA" index = 102 rmsd = 1.855 "obj and name CA" index = 103 rmsd = 2.485 "obj and name CA" index = 104 rmsd = 2.215 "obj and name CA" index = 105 rmsd = 2.261 "obj and name CA" index = 106 rmsd = 2.374 "obj and name CA" index = 107 rmsd = 2.103 "obj and name CA" index = 108 rmsd = 1.947 "obj and name CA" index = 109 rmsd = 2.298 "obj and name CA" index = 110 rmsd = 2.413 "obj and name CA" index = 111 rmsd = 2.120 "obj and name CA" index = 112 rmsd = 2.258 "obj and name CA" index = 113 rmsd = 2.755 "obj and name CA" index = 114 rmsd = 2.638 "obj and name CA" index = 115 rmsd = 2.365 "obj and name CA" index = 116 rmsd = 2.905 "obj and name CA" index = 117 rmsd = 3.347 "obj and name CA" index = 118 rmsd = 3.167 "obj and name CA" index = 119 rmsd = 2.741 "obj and name CA" index = 120 rmsd = 2.117 "obj and name CA" index = 121 rmsd = 2.178 "obj and name CA" index = 122 rmsd = 2.444 "obj and name CA" index = 123 rmsd = 1.932 "obj and name CA" index = 124 rmsd = 1.606 "obj and name CA" index = 125 rmsd = 2.114 "obj and name CA" index = 126 rmsd = 2.296 "obj and name CA" index = 127 rmsd = 1.847 "obj and name CA" index = 128 rmsd = 1.863 "obj and name CA" index = 129 rmsd = 2.542 "obj and name CA" index = 130 rmsd = 2.772 "obj and name CA" index = 131 rmsd = 3.278 "obj and name CA" index = 132 rmsd = 3.169 "obj and name CA" index = 133 rmsd = 2.531 "obj and name CA" index = 134 rmsd = 2.719 "obj and name CA" index = 135 rmsd = 3.364 "obj and name CA" index = 136 rmsd = 3.184 "obj and name CA" index = 137 rmsd = 2.876 "obj and name CA" index = 138 rmsd = 2.891 "obj and name CA" index = 139 rmsd = 2.614 "obj and name CA" index = 140 rmsd = 2.616 "obj and name CA" index = 141 rmsd = 2.539 "obj and name CA" index = 142 rmsd = 2.028 "obj and name CA" index = 143 rmsd = 2.114 "obj and name CA" index = 144 rmsd = 2.836 "obj and name CA" index = 145 rmsd = 3.011 "obj and name CA" index = 146 rmsd = 4.939 "obj and name CA" index = 147 rmsd = 7.076 "obj and name CA" index = 148 rmsd = 9.038 "obj and name CA" index = 149 rmsd = 11.586 "obj and name CA" index = 150 rmsd = 13.826 "obj and name CA" index = 151 rmsd = 16.251 "obj and name CA" index = 152 rmsd = 18.473 "obj and name CA" index = 153 rmsd = 19.769 "obj and name CA" index = 154 rmsd = 21.694 "obj and name CA" index = 155 rmsd = 22.492 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 3185 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 2004 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: 1.93 sec. = 1862.7 frames/hour (8.65 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit