PyMOL>load ./selSi.pdb,obj 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 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 132 atoms. PyMOL>color cyan,ss s Executive: Colored 24 atoms. PyMOL>color gray,ss ""+l Executive: Colored 3170 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: 2.76 sec. = 1306.4 frames/hour (2.76 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: 7.85 sec. = 458.9 frames/hour (10.60 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 18 states [1, 18] of object "obj and name CA" (18 total states) to get new single-state object "yesfit_ALL"... -------------------------------------------------------------------------------- -> proceeding WITH FITTING to reference state... intrafit_rmsds = [-1.0, 4.7300758361816406, 3.7923910617828369, 3.8826127052307129, 3.532473087310791, 4.4091720581054688, 4.1689777374267578, 4.5709347724914551, 4.1622762680053711, 4.1565966606140137, 4.3947644233703613, 3.681328296661377, 3.7385826110839844, 4.0324978828430176, 3.1432392597198486, 4.2721376419067383, 3.9048857688903809, 5.0009355545043945] -> 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, 1522, 1541, 1556, 1573, 1590, 1607, 1624, 1641, 1659, 1678, 1688, 1695, 1712, 1723, 1735, 1759, 1781, 1791, 1801, 1820, 1839, 1851, 1868, 1884, 1894, 1918, 1934, 1941, 1963, 1973, 1992, 2002, 2016, 2023, 2047, 2071, 2090, 2107, 2126, 2145, 2157, 2176, 2195, 2205, 2222, 2229, 2244, 2268, 2278, 2294, 2309, 2319, 2338, 2348, 2362, 2372, 2386, 2393, 2410, 2424, 2443, 2457, 2471, 2481, 2492, 2502, 2516, 2535, 2552, 2562, 2581, 2603, 2614, 2621, 2628, 2647, 2663, 2678, 2688, 2712, 2736, 2751, 2758, 2772, 2796, 2813, 2834, 2855, 2879, 2898, 2908, 2915, 2930, 2942, 2958, 2968, 2992, 3011, 3031, 3041, 3060, 3076, 3093, 3109, 3125, 3135, 3147, 3162, 3179, 3198, 3213, 3230, 3247, 3264, 3281, 3298] "obj and name CA" index = 1 rmsd = 12.300 "obj and name CA" index = 2 rmsd = 10.451 "obj and name CA" index = 3 rmsd = 8.215 "obj and name CA" index = 4 rmsd = 6.389 "obj and name CA" index = 5 rmsd = 4.305 "obj and name CA" index = 6 rmsd = 2.247 "obj and name CA" index = 7 rmsd = 1.769 "obj and name CA" index = 8 rmsd = 1.036 "obj and name CA" index = 9 rmsd = 1.109 "obj and name CA" index = 10 rmsd = 0.989 "obj and name CA" index = 11 rmsd = 0.766 "obj and name CA" index = 12 rmsd = 0.746 "obj and name CA" index = 13 rmsd = 0.814 "obj and name CA" index = 14 rmsd = 0.765 "obj and name CA" index = 15 rmsd = 0.680 "obj and name CA" index = 16 rmsd = 0.691 "obj and name CA" index = 17 rmsd = 0.664 "obj and name CA" index = 18 rmsd = 0.637 "obj and name CA" index = 19 rmsd = 0.697 "obj and name CA" index = 20 rmsd = 0.679 "obj and name CA" index = 21 rmsd = 0.698 "obj and name CA" index = 22 rmsd = 0.723 "obj and name CA" index = 23 rmsd = 0.730 "obj and name CA" index = 24 rmsd = 1.226 "obj and name CA" index = 25 rmsd = 1.312 "obj and name CA" index = 26 rmsd = 1.031 "obj and name CA" index = 27 rmsd = 1.009 "obj and name CA" index = 28 rmsd = 0.796 "obj and name CA" index = 29 rmsd = 0.747 "obj and name CA" index = 30 rmsd = 0.713 "obj and name CA" index = 31 rmsd = 0.646 "obj and name CA" index = 32 rmsd = 0.711 "obj and name CA" index = 33 rmsd = 0.779 "obj and name CA" index = 34 rmsd = 0.711 "obj and name CA" index = 35 rmsd = 0.808 "obj and name CA" index = 36 rmsd = 0.888 "obj and name CA" index = 37 rmsd = 0.892 "obj and name CA" index = 38 rmsd = 0.803 "obj and name CA" index = 39 rmsd = 0.839 "obj and name CA" index = 40 rmsd = 0.912 "obj and name CA" index = 41 rmsd = 0.935 "obj and name CA" index = 42 rmsd = 1.075 "obj and name CA" index = 43 rmsd = 1.033 "obj and name CA" index = 44 rmsd = 0.901 "obj and name CA" index = 45 rmsd = 1.020 "obj and name CA" index = 46 rmsd = 1.154 "obj and name CA" index = 47 rmsd = 1.136 "obj and name CA" index = 48 rmsd = 1.111 "obj and name CA" index = 49 rmsd = 1.295 "obj and name CA" index = 50 rmsd = 1.172 "obj and name CA" index = 51 rmsd = 1.259 "obj and name CA" index = 52 rmsd = 1.222 "obj and name CA" index = 53 rmsd = 1.311 "obj and name CA" index = 54 rmsd = 1.235 "obj and name CA" index = 55 rmsd = 1.015 "obj and name CA" index = 56 rmsd = 1.043 "obj and name CA" index = 57 rmsd = 1.117 "obj and name CA" index = 58 rmsd = 0.987 "obj and name CA" index = 59 rmsd = 0.818 "obj and name CA" index = 60 rmsd = 0.924 "obj and name CA" index = 61 rmsd = 0.921 "obj and name CA" index = 62 rmsd = 0.776 "obj and name CA" index = 63 rmsd = 0.810 "obj and name CA" index = 64 rmsd = 0.899 "obj and name CA" index = 65 rmsd = 0.872 "obj and name CA" index = 66 rmsd = 1.596 "obj and name CA" index = 67 rmsd = 0.895 "obj and name CA" index = 68 rmsd = 0.671 "obj and name CA" index = 69 rmsd = 0.663 "obj and name CA" index = 70 rmsd = 0.744 "obj and name CA" index = 71 rmsd = 0.887 "obj and name CA" index = 72 rmsd = 1.118 "obj and name CA" index = 73 rmsd = 1.252 "obj and name CA" index = 74 rmsd = 1.559 "obj and name CA" index = 75 rmsd = 1.549 "obj and name CA" index = 76 rmsd = 1.230 "obj and name CA" index = 77 rmsd = 0.957 "obj and name CA" index = 78 rmsd = 0.827 "obj and name CA" index = 79 rmsd = 0.692 "obj and name CA" index = 80 rmsd = 0.645 "obj and name CA" index = 81 rmsd = 0.633 "obj and name CA" index = 82 rmsd = 0.712 "obj and name CA" index = 83 rmsd = 0.752 "obj and name CA" index = 84 rmsd = 0.672 "obj and name CA" index = 85 rmsd = 0.585 "obj and name CA" index = 86 rmsd = 0.504 "obj and name CA" index = 87 rmsd = 0.542 "obj and name CA" index = 88 rmsd = 0.493 "obj and name CA" index = 89 rmsd = 0.447 "obj and name CA" index = 90 rmsd = 0.535 "obj and name CA" index = 91 rmsd = 0.526 "obj and name CA" index = 92 rmsd = 0.435 "obj and name CA" index = 93 rmsd = 0.473 "obj and name CA" index = 94 rmsd = 0.524 "obj and name CA" index = 95 rmsd = 0.509 "obj and name CA" index = 96 rmsd = 0.600 "obj and name CA" index = 97 rmsd = 0.761 "obj and name CA" index = 98 rmsd = 0.717 "obj and name CA" index = 99 rmsd = 1.019 "obj and name CA" index = 100 rmsd = 1.399 "obj and name CA" index = 101 rmsd = 1.375 "obj and name CA" index = 102 rmsd = 1.357 "obj and name CA" index = 103 rmsd = 3.176 "obj and name CA" index = 104 rmsd = 4.744 "obj and name CA" index = 105 rmsd = 6.726 "obj and name CA" index = 106 rmsd = 8.320 "obj and name CA" index = 107 rmsd = 10.138 "obj and name CA" index = 108 rmsd = 11.961 "obj and name CA" index = 109 rmsd = 12.301 "obj and name CA" index = 110 rmsd = 10.451 "obj and name CA" index = 111 rmsd = 8.215 "obj and name CA" index = 112 rmsd = 6.390 "obj and name CA" index = 113 rmsd = 4.305 "obj and name CA" index = 114 rmsd = 2.248 "obj and name CA" index = 115 rmsd = 1.770 "obj and name CA" index = 116 rmsd = 1.037 "obj and name CA" index = 117 rmsd = 1.109 "obj and name CA" index = 118 rmsd = 0.989 "obj and name CA" index = 119 rmsd = 0.767 "obj and name CA" index = 120 rmsd = 0.746 "obj and name CA" index = 121 rmsd = 0.815 "obj and name CA" index = 122 rmsd = 0.765 "obj and name CA" index = 123 rmsd = 0.680 "obj and name CA" index = 124 rmsd = 0.690 "obj and name CA" index = 125 rmsd = 0.665 "obj and name CA" index = 126 rmsd = 0.637 "obj and name CA" index = 127 rmsd = 0.697 "obj and name CA" index = 128 rmsd = 0.679 "obj and name CA" index = 129 rmsd = 0.698 "obj and name CA" index = 130 rmsd = 0.723 "obj and name CA" index = 131 rmsd = 0.730 "obj and name CA" index = 132 rmsd = 1.225 "obj and name CA" index = 133 rmsd = 1.313 "obj and name CA" index = 134 rmsd = 1.032 "obj and name CA" index = 135 rmsd = 1.009 "obj and name CA" index = 136 rmsd = 0.796 "obj and name CA" index = 137 rmsd = 0.747 "obj and name CA" index = 138 rmsd = 0.713 "obj and name CA" index = 139 rmsd = 0.647 "obj and name CA" index = 140 rmsd = 0.711 "obj and name CA" index = 141 rmsd = 0.779 "obj and name CA" index = 142 rmsd = 0.711 "obj and name CA" index = 143 rmsd = 0.808 "obj and name CA" index = 144 rmsd = 0.888 "obj and name CA" index = 145 rmsd = 0.892 "obj and name CA" index = 146 rmsd = 0.803 "obj and name CA" index = 147 rmsd = 0.839 "obj and name CA" index = 148 rmsd = 0.912 "obj and name CA" index = 149 rmsd = 0.935 "obj and name CA" index = 150 rmsd = 1.075 "obj and name CA" index = 151 rmsd = 1.033 "obj and name CA" index = 152 rmsd = 0.900 "obj and name CA" index = 153 rmsd = 1.020 "obj and name CA" index = 154 rmsd = 1.154 "obj and name CA" index = 155 rmsd = 1.136 "obj and name CA" index = 156 rmsd = 1.111 "obj and name CA" index = 157 rmsd = 1.295 "obj and name CA" index = 158 rmsd = 1.171 "obj and name CA" index = 159 rmsd = 1.259 "obj and name CA" index = 160 rmsd = 1.221 "obj and name CA" index = 161 rmsd = 1.311 "obj and name CA" index = 162 rmsd = 1.234 "obj and name CA" index = 163 rmsd = 1.015 "obj and name CA" index = 164 rmsd = 1.043 "obj and name CA" index = 165 rmsd = 1.117 "obj and name CA" index = 166 rmsd = 0.987 "obj and name CA" index = 167 rmsd = 0.818 "obj and name CA" index = 168 rmsd = 0.924 "obj and name CA" index = 169 rmsd = 0.921 "obj and name CA" index = 170 rmsd = 0.776 "obj and name CA" index = 171 rmsd = 0.810 "obj and name CA" index = 172 rmsd = 0.899 "obj and name CA" index = 173 rmsd = 0.872 "obj and name CA" index = 174 rmsd = 1.596 "obj and name CA" index = 175 rmsd = 0.895 "obj and name CA" index = 176 rmsd = 0.671 "obj and name CA" index = 177 rmsd = 0.663 "obj and name CA" index = 178 rmsd = 0.744 "obj and name CA" index = 179 rmsd = 0.887 "obj and name CA" index = 180 rmsd = 1.118 "obj and name CA" index = 181 rmsd = 1.252 "obj and name CA" index = 182 rmsd = 1.559 "obj and name CA" index = 183 rmsd = 1.548 "obj and name CA" index = 184 rmsd = 1.230 "obj and name CA" index = 185 rmsd = 0.957 "obj and name CA" index = 186 rmsd = 0.827 "obj and name CA" index = 187 rmsd = 0.692 "obj and name CA" index = 188 rmsd = 0.644 "obj and name CA" index = 189 rmsd = 0.633 "obj and name CA" index = 190 rmsd = 0.712 "obj and name CA" index = 191 rmsd = 0.752 "obj and name CA" index = 192 rmsd = 0.672 "obj and name CA" index = 193 rmsd = 0.584 "obj and name CA" index = 194 rmsd = 0.504 "obj and name CA" index = 195 rmsd = 0.542 "obj and name CA" index = 196 rmsd = 0.493 "obj and name CA" index = 197 rmsd = 0.448 "obj and name CA" index = 198 rmsd = 0.535 "obj and name CA" index = 199 rmsd = 0.526 "obj and name CA" index = 200 rmsd = 0.435 "obj and name CA" index = 201 rmsd = 0.473 "obj and name CA" index = 202 rmsd = 0.524 "obj and name CA" index = 203 rmsd = 0.509 "obj and name CA" index = 204 rmsd = 0.600 "obj and name CA" index = 205 rmsd = 0.761 "obj and name CA" index = 206 rmsd = 0.717 "obj and name CA" index = 207 rmsd = 1.019 "obj and name CA" index = 208 rmsd = 1.399 "obj and name CA" index = 209 rmsd = 1.375 "obj and name CA" index = 210 rmsd = 1.357 "obj and name CA" index = 211 rmsd = 3.176 "obj and name CA" index = 212 rmsd = 4.744 "obj and name CA" index = 213 rmsd = 6.726 "obj and name CA" index = 214 rmsd = 8.321 "obj and name CA" index = 215 rmsd = 10.138 "obj and name CA" index = 216 rmsd = 11.961 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 396 atoms. PyMOL>color cyan,ss s Executive: Colored 72 atoms. PyMOL>color gray,ss ""+l Executive: Colored 6388 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: 2.55 sec. = 1409.3 frames/hour (13.16 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit