PyMOL>load ./selSi.pdb,obj HEADER DNA BINDING PROTEIN 26-JUN-09 2KKO TITLE SOLUTION NMR STRUCTURE OF THE HOMODIMERIC WINGED HELIX-TURN- TITLE 2 HELIX DNA-BINDING DOMAIN (FRAGMENT 1-100) MB0332 FROM TITLE 3 MYCOBACTERIUM BOVIS, A POSSIBLE ARSR-FAMILY TRANSCRIPTIONAL TITLE 4 REGULATOR. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET TITLE 5 MBR242E. COMPND MOL_ID: 1; COMPND 2 MOLECULE: POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN COMPND 3 (POSSIBLY ARSR-FAMILY); COMPND 4 CHAIN: A, B; COMPND 5 FRAGMENT: HTH ARSR-TYPE DNA BINDING DOMAIN RESIDUES 1-100; 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 2145 atoms. PyMOL>color cyan,ss s Executive: Colored 524 atoms. PyMOL>color gray,ss ""+l Executive: Colored 659 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: 2.56 sec. = 1408.6 frames/hour (2.56 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 648 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 648 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: 8.83 sec. = 407.6 frames/hour (11.39 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, 3.4244503974914551, 4.3060145378112793, 3.2881736755371094, 2.1600849628448486, 3.545759916305542, 3.0073559284210205, 2.0433661937713623, 2.7690813541412354, 1.9603515863418579, 4.5261549949645996, 4.5820231437683105, 2.4803051948547363, 2.1104376316070557, 3.2105827331542969, 3.9999339580535889, 2.4249575138092041, 4.3258304595947266, 4.419853687286377, 3.9314138889312744] -> atom index_map = [None, 2, 21, 31, 38, 55, 66, 78, 102, 124, 134, 144, 163, 182, 194, 211, 227, 237, 261, 277, 284, 306, 316, 335, 345, 359, 366, 390, 414, 433, 450, 469, 488, 500, 519, 538, 548, 565, 572, 587, 611, 621, 637, 652, 662, 681, 691, 705, 715, 729, 736, 753, 767, 786, 800, 814, 824, 835, 845, 859, 878, 895, 905, 924, 946, 957, 964, 971, 990, 1006, 1021, 1031, 1055, 1079, 1094, 1101, 1115, 1139, 1156, 1177, 1198, 1222, 1241, 1251, 1258, 1273, 1285, 1301, 1311, 1335, 1354, 1374, 1384, 1403, 1419, 1436, 1452, 1468, 1478, 1490, 1505, 1523, 1542, 1557, 1575, 1593, 1611, 1629, 1647, 1666, 1685, 1695, 1702, 1719, 1730, 1742, 1766, 1788, 1798, 1808, 1827, 1846, 1858, 1875, 1891, 1901, 1925, 1941, 1948, 1970, 1980, 1999, 2009, 2023, 2030, 2054, 2078, 2097, 2114, 2133, 2152, 2164, 2183, 2202, 2212, 2229, 2236, 2251, 2275, 2285, 2301, 2316, 2326, 2345, 2355, 2369, 2379, 2393, 2400, 2417, 2431, 2450, 2464, 2478, 2488, 2499, 2509, 2523, 2542, 2559, 2569, 2588, 2610, 2621, 2628, 2635, 2654, 2670, 2685, 2695, 2719, 2743, 2758, 2765, 2779, 2803, 2820, 2841, 2862, 2886, 2905, 2915, 2922, 2937, 2949, 2965, 2975, 2999, 3018, 3038, 3048, 3067, 3083, 3100, 3116, 3132, 3142, 3154, 3169, 3187, 3206, 3221, 3239, 3257, 3275, 3293, 3311] "obj and name CA" index = 1 rmsd = 9.633 "obj and name CA" index = 2 rmsd = 7.675 "obj and name CA" index = 3 rmsd = 5.474 "obj and name CA" index = 4 rmsd = 4.226 "obj and name CA" index = 5 rmsd = 3.076 "obj and name CA" index = 6 rmsd = 2.145 "obj and name CA" index = 7 rmsd = 1.419 "obj and name CA" index = 8 rmsd = 0.934 "obj and name CA" index = 9 rmsd = 0.979 "obj and name CA" index = 10 rmsd = 0.949 "obj and name CA" index = 11 rmsd = 0.849 "obj and name CA" index = 12 rmsd = 0.760 "obj and name CA" index = 13 rmsd = 0.843 "obj and name CA" index = 14 rmsd = 0.822 "obj and name CA" index = 15 rmsd = 0.694 "obj and name CA" index = 16 rmsd = 0.708 "obj and name CA" index = 17 rmsd = 0.774 "obj and name CA" index = 18 rmsd = 0.772 "obj and name CA" index = 19 rmsd = 0.780 "obj and name CA" index = 20 rmsd = 0.816 "obj and name CA" index = 21 rmsd = 0.838 "obj and name CA" index = 22 rmsd = 0.889 "obj and name CA" index = 23 rmsd = 0.884 "obj and name CA" index = 24 rmsd = 1.720 "obj and name CA" index = 25 rmsd = 1.181 "obj and name CA" index = 26 rmsd = 1.019 "obj and name CA" index = 27 rmsd = 0.893 "obj and name CA" index = 28 rmsd = 0.782 "obj and name CA" index = 29 rmsd = 0.753 "obj and name CA" index = 30 rmsd = 0.675 "obj and name CA" index = 31 rmsd = 0.704 "obj and name CA" index = 32 rmsd = 0.771 "obj and name CA" index = 33 rmsd = 0.721 "obj and name CA" index = 34 rmsd = 0.768 "obj and name CA" index = 35 rmsd = 0.919 "obj and name CA" index = 36 rmsd = 1.093 "obj and name CA" index = 37 rmsd = 1.284 "obj and name CA" index = 38 rmsd = 0.987 "obj and name CA" index = 39 rmsd = 0.923 "obj and name CA" index = 40 rmsd = 0.949 "obj and name CA" index = 41 rmsd = 0.941 "obj and name CA" index = 42 rmsd = 1.055 "obj and name CA" index = 43 rmsd = 1.039 "obj and name CA" index = 44 rmsd = 0.832 "obj and name CA" index = 45 rmsd = 0.946 "obj and name CA" index = 46 rmsd = 1.090 "obj and name CA" index = 47 rmsd = 1.010 "obj and name CA" index = 48 rmsd = 0.980 "obj and name CA" index = 49 rmsd = 1.149 "obj and name CA" index = 50 rmsd = 1.167 "obj and name CA" index = 51 rmsd = 1.272 "obj and name CA" index = 52 rmsd = 1.171 "obj and name CA" index = 53 rmsd = 1.287 "obj and name CA" index = 54 rmsd = 1.274 "obj and name CA" index = 55 rmsd = 0.970 "obj and name CA" index = 56 rmsd = 0.951 "obj and name CA" index = 57 rmsd = 1.070 "obj and name CA" index = 58 rmsd = 1.039 "obj and name CA" index = 59 rmsd = 0.800 "obj and name CA" index = 60 rmsd = 0.808 "obj and name CA" index = 61 rmsd = 0.896 "obj and name CA" index = 62 rmsd = 0.832 "obj and name CA" index = 63 rmsd = 0.752 "obj and name CA" index = 64 rmsd = 0.836 "obj and name CA" index = 65 rmsd = 0.916 "obj and name CA" index = 66 rmsd = 1.582 "obj and name CA" index = 67 rmsd = 1.002 "obj and name CA" index = 68 rmsd = 0.746 "obj and name CA" index = 69 rmsd = 0.806 "obj and name CA" index = 70 rmsd = 0.870 "obj and name CA" index = 71 rmsd = 0.994 "obj and name CA" index = 72 rmsd = 1.312 "obj and name CA" index = 73 rmsd = 1.428 "obj and name CA" index = 74 rmsd = 1.802 "obj and name CA" index = 75 rmsd = 1.684 "obj and name CA" index = 76 rmsd = 1.239 "obj and name CA" index = 77 rmsd = 1.035 "obj and name CA" index = 78 rmsd = 0.816 "obj and name CA" index = 79 rmsd = 0.682 "obj and name CA" index = 80 rmsd = 0.785 "obj and name CA" index = 81 rmsd = 0.786 "obj and name CA" index = 82 rmsd = 0.989 "obj and name CA" index = 83 rmsd = 0.874 "obj and name CA" index = 84 rmsd = 0.893 "obj and name CA" index = 85 rmsd = 0.890 "obj and name CA" index = 86 rmsd = 0.676 "obj and name CA" index = 87 rmsd = 0.752 "obj and name CA" index = 88 rmsd = 0.756 "obj and name CA" index = 89 rmsd = 0.634 "obj and name CA" index = 90 rmsd = 0.656 "obj and name CA" index = 91 rmsd = 0.747 "obj and name CA" index = 92 rmsd = 0.691 "obj and name CA" index = 93 rmsd = 0.734 "obj and name CA" index = 94 rmsd = 0.789 "obj and name CA" index = 95 rmsd = 0.950 "obj and name CA" index = 96 rmsd = 0.980 "obj and name CA" index = 97 rmsd = 0.956 "obj and name CA" index = 98 rmsd = 1.095 "obj and name CA" index = 99 rmsd = 1.439 "obj and name CA" index = 100 rmsd = 1.712 "obj and name CA" index = 101 rmsd = 1.701 "obj and name CA" index = 102 rmsd = 2.223 "obj and name CA" index = 103 rmsd = 2.823 "obj and name CA" index = 104 rmsd = 3.581 "obj and name CA" index = 105 rmsd = 5.272 "obj and name CA" index = 106 rmsd = 6.736 "obj and name CA" index = 107 rmsd = 8.621 "obj and name CA" index = 108 rmsd = 11.221 "obj and name CA" index = 109 rmsd = 9.465 "obj and name CA" index = 110 rmsd = 8.116 "obj and name CA" index = 111 rmsd = 6.328 "obj and name CA" index = 112 rmsd = 4.410 "obj and name CA" index = 113 rmsd = 3.422 "obj and name CA" index = 114 rmsd = 2.009 "obj and name CA" index = 115 rmsd = 1.662 "obj and name CA" index = 116 rmsd = 1.197 "obj and name CA" index = 117 rmsd = 1.097 "obj and name CA" index = 118 rmsd = 1.083 "obj and name CA" index = 119 rmsd = 0.896 "obj and name CA" index = 120 rmsd = 0.757 "obj and name CA" index = 121 rmsd = 0.964 "obj and name CA" index = 122 rmsd = 0.895 "obj and name CA" index = 123 rmsd = 0.778 "obj and name CA" index = 124 rmsd = 0.815 "obj and name CA" index = 125 rmsd = 0.766 "obj and name CA" index = 126 rmsd = 0.735 "obj and name CA" index = 127 rmsd = 0.810 "obj and name CA" index = 128 rmsd = 0.783 "obj and name CA" index = 129 rmsd = 0.732 "obj and name CA" index = 130 rmsd = 0.873 "obj and name CA" index = 131 rmsd = 1.015 "obj and name CA" index = 132 rmsd = 1.290 "obj and name CA" index = 133 rmsd = 1.385 "obj and name CA" index = 134 rmsd = 1.166 "obj and name CA" index = 135 rmsd = 0.940 "obj and name CA" index = 136 rmsd = 0.680 "obj and name CA" index = 137 rmsd = 0.770 "obj and name CA" index = 138 rmsd = 0.708 "obj and name CA" index = 139 rmsd = 0.613 "obj and name CA" index = 140 rmsd = 0.697 "obj and name CA" index = 141 rmsd = 0.773 "obj and name CA" index = 142 rmsd = 0.780 "obj and name CA" index = 143 rmsd = 0.873 "obj and name CA" index = 144 rmsd = 1.179 "obj and name CA" index = 145 rmsd = 1.253 "obj and name CA" index = 146 rmsd = 0.919 "obj and name CA" index = 147 rmsd = 0.846 "obj and name CA" index = 148 rmsd = 0.892 "obj and name CA" index = 149 rmsd = 0.928 "obj and name CA" index = 150 rmsd = 1.065 "obj and name CA" index = 151 rmsd = 0.931 "obj and name CA" index = 152 rmsd = 0.851 "obj and name CA" index = 153 rmsd = 0.969 "obj and name CA" index = 154 rmsd = 1.064 "obj and name CA" index = 155 rmsd = 1.022 "obj and name CA" index = 156 rmsd = 1.029 "obj and name CA" index = 157 rmsd = 1.145 "obj and name CA" index = 158 rmsd = 1.144 "obj and name CA" index = 159 rmsd = 1.302 "obj and name CA" index = 160 rmsd = 1.213 "obj and name CA" index = 161 rmsd = 1.302 "obj and name CA" index = 162 rmsd = 1.208 "obj and name CA" index = 163 rmsd = 0.964 "obj and name CA" index = 164 rmsd = 0.915 "obj and name CA" index = 165 rmsd = 0.944 "obj and name CA" index = 166 rmsd = 0.844 "obj and name CA" index = 167 rmsd = 0.640 "obj and name CA" index = 168 rmsd = 0.714 "obj and name CA" index = 169 rmsd = 0.781 "obj and name CA" index = 170 rmsd = 0.692 "obj and name CA" index = 171 rmsd = 0.624 "obj and name CA" index = 172 rmsd = 0.812 "obj and name CA" index = 173 rmsd = 0.777 "obj and name CA" index = 174 rmsd = 1.225 "obj and name CA" index = 175 rmsd = 0.745 "obj and name CA" index = 176 rmsd = 0.631 "obj and name CA" index = 177 rmsd = 0.726 "obj and name CA" index = 178 rmsd = 0.702 "obj and name CA" index = 179 rmsd = 0.941 "obj and name CA" index = 180 rmsd = 1.087 "obj and name CA" index = 181 rmsd = 1.323 "obj and name CA" index = 182 rmsd = 1.676 "obj and name CA" index = 183 rmsd = 1.629 "obj and name CA" index = 184 rmsd = 1.162 "obj and name CA" index = 185 rmsd = 0.949 "obj and name CA" index = 186 rmsd = 0.787 "obj and name CA" index = 187 rmsd = 0.684 "obj and name CA" index = 188 rmsd = 0.683 "obj and name CA" index = 189 rmsd = 0.623 "obj and name CA" index = 190 rmsd = 0.751 "obj and name CA" index = 191 rmsd = 0.859 "obj and name CA" index = 192 rmsd = 0.866 "obj and name CA" index = 193 rmsd = 0.966 "obj and name CA" index = 194 rmsd = 0.744 "obj and name CA" index = 195 rmsd = 0.687 "obj and name CA" index = 196 rmsd = 0.768 "obj and name CA" index = 197 rmsd = 0.714 "obj and name CA" index = 198 rmsd = 0.615 "obj and name CA" index = 199 rmsd = 0.686 "obj and name CA" index = 200 rmsd = 0.696 "obj and name CA" index = 201 rmsd = 0.699 "obj and name CA" index = 202 rmsd = 0.773 "obj and name CA" index = 203 rmsd = 0.906 "obj and name CA" index = 204 rmsd = 0.884 "obj and name CA" index = 205 rmsd = 0.889 "obj and name CA" index = 206 rmsd = 1.119 "obj and name CA" index = 207 rmsd = 1.240 "obj and name CA" index = 208 rmsd = 1.352 "obj and name CA" index = 209 rmsd = 1.538 "obj and name CA" index = 210 rmsd = 2.068 "obj and name CA" index = 211 rmsd = 2.763 "obj and name CA" index = 212 rmsd = 3.635 "obj and name CA" index = 213 rmsd = 5.388 "obj and name CA" index = 214 rmsd = 6.937 "obj and name CA" index = 215 rmsd = 9.006 "obj and name CA" index = 216 rmsd = 11.222 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 4421 atoms. PyMOL>color cyan,ss s Executive: Colored 1072 atoms. PyMOL>color gray,ss ""+l Executive: Colored 1379 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: 2.57 sec. = 1399.8 frames/hour (13.96 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit