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 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 130 atoms. PyMOL>color cyan,ss s Executive: Colored 24 atoms. PyMOL>color gray,ss ""+l Executive: Colored 3174 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: 2.62 sec. = 1374.0 frames/hour (2.62 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 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: 9.68 sec. = 371.9 frames/hour (12.30 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, 7.5109972953796387, 5.022669792175293, 6.6045689582824707, 4.405698299407959, 5.7846760749816895, 5.7732415199279785, 3.8455667495727539, 6.0972151756286621, 6.6235346794128418, 4.8417205810546875, 4.1738080978393555, 6.506047248840332, 6.0857009887695312, 6.758063793182373, 3.8488049507141113, 3.3771426677703857, 3.8494727611541748, 7.2815079689025879, 7.0825376510620117] -> 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 = 12.869 "obj and name CA" index = 2 rmsd = 11.033 "obj and name CA" index = 3 rmsd = 9.078 "obj and name CA" index = 4 rmsd = 7.274 "obj and name CA" index = 5 rmsd = 5.182 "obj and name CA" index = 6 rmsd = 3.117 "obj and name CA" index = 7 rmsd = 2.563 "obj and name CA" index = 8 rmsd = 1.743 "obj and name CA" index = 9 rmsd = 1.642 "obj and name CA" index = 10 rmsd = 1.609 "obj and name CA" index = 11 rmsd = 1.399 "obj and name CA" index = 12 rmsd = 1.267 "obj and name CA" index = 13 rmsd = 1.196 "obj and name CA" index = 14 rmsd = 1.155 "obj and name CA" index = 15 rmsd = 1.146 "obj and name CA" index = 16 rmsd = 0.987 "obj and name CA" index = 17 rmsd = 1.025 "obj and name CA" index = 18 rmsd = 1.048 "obj and name CA" index = 19 rmsd = 0.985 "obj and name CA" index = 20 rmsd = 0.972 "obj and name CA" index = 21 rmsd = 1.044 "obj and name CA" index = 22 rmsd = 1.096 "obj and name CA" index = 23 rmsd = 1.090 "obj and name CA" index = 24 rmsd = 1.827 "obj and name CA" index = 25 rmsd = 1.387 "obj and name CA" index = 26 rmsd = 1.311 "obj and name CA" index = 27 rmsd = 1.262 "obj and name CA" index = 28 rmsd = 1.038 "obj and name CA" index = 29 rmsd = 0.936 "obj and name CA" index = 30 rmsd = 0.829 "obj and name CA" index = 31 rmsd = 0.829 "obj and name CA" index = 32 rmsd = 0.980 "obj and name CA" index = 33 rmsd = 0.989 "obj and name CA" index = 34 rmsd = 0.949 "obj and name CA" index = 35 rmsd = 1.115 "obj and name CA" index = 36 rmsd = 1.248 "obj and name CA" index = 37 rmsd = 1.292 "obj and name CA" index = 38 rmsd = 1.115 "obj and name CA" index = 39 rmsd = 1.256 "obj and name CA" index = 40 rmsd = 1.454 "obj and name CA" index = 41 rmsd = 1.440 "obj and name CA" index = 42 rmsd = 1.751 "obj and name CA" index = 43 rmsd = 1.511 "obj and name CA" index = 44 rmsd = 1.163 "obj and name CA" index = 45 rmsd = 1.402 "obj and name CA" index = 46 rmsd = 1.597 "obj and name CA" index = 47 rmsd = 1.312 "obj and name CA" index = 48 rmsd = 1.255 "obj and name CA" index = 49 rmsd = 1.645 "obj and name CA" index = 50 rmsd = 1.666 "obj and name CA" index = 51 rmsd = 1.946 "obj and name CA" index = 52 rmsd = 1.946 "obj and name CA" index = 53 rmsd = 2.159 "obj and name CA" index = 54 rmsd = 1.950 "obj and name CA" index = 55 rmsd = 1.447 "obj and name CA" index = 56 rmsd = 1.625 "obj and name CA" index = 57 rmsd = 1.827 "obj and name CA" index = 58 rmsd = 1.543 "obj and name CA" index = 59 rmsd = 1.229 "obj and name CA" index = 60 rmsd = 1.529 "obj and name CA" index = 61 rmsd = 1.644 "obj and name CA" index = 62 rmsd = 1.259 "obj and name CA" index = 63 rmsd = 1.309 "obj and name CA" index = 64 rmsd = 1.716 "obj and name CA" index = 65 rmsd = 1.631 "obj and name CA" index = 66 rmsd = 1.941 "obj and name CA" index = 67 rmsd = 1.181 "obj and name CA" index = 68 rmsd = 0.887 "obj and name CA" index = 69 rmsd = 0.938 "obj and name CA" index = 70 rmsd = 1.163 "obj and name CA" index = 71 rmsd = 1.334 "obj and name CA" index = 72 rmsd = 1.970 "obj and name CA" index = 73 rmsd = 2.290 "obj and name CA" index = 74 rmsd = 3.166 "obj and name CA" index = 75 rmsd = 2.978 "obj and name CA" index = 76 rmsd = 2.148 "obj and name CA" index = 77 rmsd = 1.626 "obj and name CA" index = 78 rmsd = 1.266 "obj and name CA" index = 79 rmsd = 0.947 "obj and name CA" index = 80 rmsd = 0.770 "obj and name CA" index = 81 rmsd = 0.787 "obj and name CA" index = 82 rmsd = 0.938 "obj and name CA" index = 83 rmsd = 1.183 "obj and name CA" index = 84 rmsd = 1.143 "obj and name CA" index = 85 rmsd = 1.152 "obj and name CA" index = 86 rmsd = 0.992 "obj and name CA" index = 87 rmsd = 0.905 "obj and name CA" index = 88 rmsd = 0.979 "obj and name CA" index = 89 rmsd = 0.983 "obj and name CA" index = 90 rmsd = 0.848 "obj and name CA" index = 91 rmsd = 0.903 "obj and name CA" index = 92 rmsd = 0.869 "obj and name CA" index = 93 rmsd = 0.852 "obj and name CA" index = 94 rmsd = 0.949 "obj and name CA" index = 95 rmsd = 1.181 "obj and name CA" index = 96 rmsd = 1.218 "obj and name CA" index = 97 rmsd = 1.217 "obj and name CA" index = 98 rmsd = 1.472 "obj and name CA" index = 99 rmsd = 2.081 "obj and name CA" index = 100 rmsd = 2.724 "obj and name CA" index = 101 rmsd = 2.709 "obj and name CA" index = 102 rmsd = 3.169 "obj and name CA" index = 103 rmsd = 5.185 "obj and name CA" index = 104 rmsd = 6.324 "obj and name CA" index = 105 rmsd = 7.704 "obj and name CA" index = 106 rmsd = 9.666 "obj and name CA" index = 107 rmsd = 11.394 "obj and name CA" index = 108 rmsd = 13.074 "obj and name CA" index = 109 rmsd = 12.869 "obj and name CA" index = 110 rmsd = 11.034 "obj and name CA" index = 111 rmsd = 9.078 "obj and name CA" index = 112 rmsd = 7.274 "obj and name CA" index = 113 rmsd = 5.183 "obj and name CA" index = 114 rmsd = 3.117 "obj and name CA" index = 115 rmsd = 2.563 "obj and name CA" index = 116 rmsd = 1.743 "obj and name CA" index = 117 rmsd = 1.642 "obj and name CA" index = 118 rmsd = 1.609 "obj and name CA" index = 119 rmsd = 1.399 "obj and name CA" index = 120 rmsd = 1.267 "obj and name CA" index = 121 rmsd = 1.196 "obj and name CA" index = 122 rmsd = 1.155 "obj and name CA" index = 123 rmsd = 1.145 "obj and name CA" index = 124 rmsd = 0.987 "obj and name CA" index = 125 rmsd = 1.025 "obj and name CA" index = 126 rmsd = 1.048 "obj and name CA" index = 127 rmsd = 0.985 "obj and name CA" index = 128 rmsd = 0.972 "obj and name CA" index = 129 rmsd = 1.044 "obj and name CA" index = 130 rmsd = 1.096 "obj and name CA" index = 131 rmsd = 1.090 "obj and name CA" index = 132 rmsd = 1.828 "obj and name CA" index = 133 rmsd = 1.387 "obj and name CA" index = 134 rmsd = 1.311 "obj and name CA" index = 135 rmsd = 1.262 "obj and name CA" index = 136 rmsd = 1.038 "obj and name CA" index = 137 rmsd = 0.936 "obj and name CA" index = 138 rmsd = 0.829 "obj and name CA" index = 139 rmsd = 0.829 "obj and name CA" index = 140 rmsd = 0.980 "obj and name CA" index = 141 rmsd = 0.989 "obj and name CA" index = 142 rmsd = 0.949 "obj and name CA" index = 143 rmsd = 1.115 "obj and name CA" index = 144 rmsd = 1.248 "obj and name CA" index = 145 rmsd = 1.292 "obj and name CA" index = 146 rmsd = 1.116 "obj and name CA" index = 147 rmsd = 1.256 "obj and name CA" index = 148 rmsd = 1.455 "obj and name CA" index = 149 rmsd = 1.440 "obj and name CA" index = 150 rmsd = 1.752 "obj and name CA" index = 151 rmsd = 1.511 "obj and name CA" index = 152 rmsd = 1.164 "obj and name CA" index = 153 rmsd = 1.402 "obj and name CA" index = 154 rmsd = 1.597 "obj and name CA" index = 155 rmsd = 1.312 "obj and name CA" index = 156 rmsd = 1.255 "obj and name CA" index = 157 rmsd = 1.646 "obj and name CA" index = 158 rmsd = 1.666 "obj and name CA" index = 159 rmsd = 1.946 "obj and name CA" index = 160 rmsd = 1.946 "obj and name CA" index = 161 rmsd = 2.159 "obj and name CA" index = 162 rmsd = 1.951 "obj and name CA" index = 163 rmsd = 1.447 "obj and name CA" index = 164 rmsd = 1.625 "obj and name CA" index = 165 rmsd = 1.827 "obj and name CA" index = 166 rmsd = 1.543 "obj and name CA" index = 167 rmsd = 1.229 "obj and name CA" index = 168 rmsd = 1.529 "obj and name CA" index = 169 rmsd = 1.644 "obj and name CA" index = 170 rmsd = 1.260 "obj and name CA" index = 171 rmsd = 1.309 "obj and name CA" index = 172 rmsd = 1.716 "obj and name CA" index = 173 rmsd = 1.631 "obj and name CA" index = 174 rmsd = 1.941 "obj and name CA" index = 175 rmsd = 1.181 "obj and name CA" index = 176 rmsd = 0.887 "obj and name CA" index = 177 rmsd = 0.938 "obj and name CA" index = 178 rmsd = 1.164 "obj and name CA" index = 179 rmsd = 1.334 "obj and name CA" index = 180 rmsd = 1.970 "obj and name CA" index = 181 rmsd = 2.289 "obj and name CA" index = 182 rmsd = 3.166 "obj and name CA" index = 183 rmsd = 2.978 "obj and name CA" index = 184 rmsd = 2.148 "obj and name CA" index = 185 rmsd = 1.626 "obj and name CA" index = 186 rmsd = 1.266 "obj and name CA" index = 187 rmsd = 0.948 "obj and name CA" index = 188 rmsd = 0.770 "obj and name CA" index = 189 rmsd = 0.787 "obj and name CA" index = 190 rmsd = 0.938 "obj and name CA" index = 191 rmsd = 1.184 "obj and name CA" index = 192 rmsd = 1.143 "obj and name CA" index = 193 rmsd = 1.152 "obj and name CA" index = 194 rmsd = 0.992 "obj and name CA" index = 195 rmsd = 0.904 "obj and name CA" index = 196 rmsd = 0.979 "obj and name CA" index = 197 rmsd = 0.983 "obj and name CA" index = 198 rmsd = 0.848 "obj and name CA" index = 199 rmsd = 0.903 "obj and name CA" index = 200 rmsd = 0.869 "obj and name CA" index = 201 rmsd = 0.852 "obj and name CA" index = 202 rmsd = 0.950 "obj and name CA" index = 203 rmsd = 1.181 "obj and name CA" index = 204 rmsd = 1.218 "obj and name CA" index = 205 rmsd = 1.218 "obj and name CA" index = 206 rmsd = 1.472 "obj and name CA" index = 207 rmsd = 2.081 "obj and name CA" index = 208 rmsd = 2.723 "obj and name CA" index = 209 rmsd = 2.709 "obj and name CA" index = 210 rmsd = 3.169 "obj and name CA" index = 211 rmsd = 5.185 "obj and name CA" index = 212 rmsd = 6.325 "obj and name CA" index = 213 rmsd = 7.704 "obj and name CA" index = 214 rmsd = 9.666 "obj and name CA" index = 215 rmsd = 11.394 "obj and name CA" index = 216 rmsd = 13.075 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 390 atoms. PyMOL>color cyan,ss s Executive: Colored 72 atoms. PyMOL>color gray,ss ""+l Executive: Colored 6396 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: 2.77 sec. = 1300.6 frames/hour (15.07 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit