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 45 atoms. PyMOL>color cyan,ss s Executive: Colored 33 atoms. PyMOL>color gray,ss ""+l Executive: Colored 3063 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: 1.66 sec. = 2165.7 frames/hour (1.66 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 606 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 606 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: 6.08 sec. = 592.1 frames/hour (7.74 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, 3.2889742851257324, 8.845402717590332, 11.650009155273438, 4.0007519721984863, 3.8601417541503906, 6.9473471641540527, 8.7593269348144531, 4.7435665130615234, 3.9190359115600586, 3.6892731189727783, 4.7993035316467285, 6.0901756286621094, 5.2877645492553711, 5.4882683753967285, 4.1749248504638672, 4.3149809837341309, 7.8532137870788574, 3.6293771266937256, 8.0202884674072266] -> atom index_map = [None, 2, 21, 45, 57, 72, 96, 116, 127, 144, 155, 170, 191, 207, 228, 235, 249, 264, 278, 292, 304, 324, 343, 359, 370, 386, 396, 410, 427, 446, 460, 477, 484, 506, 525, 544, 555, 574, 584, 599, 606, 621, 628, 652, 666, 676, 687, 707, 726, 736, 747, 766, 773, 794, 809, 825, 839, 849, 865, 877, 894, 905, 916, 932, 939, 958, 968, 990, 1000, 1022, 1039, 1058, 1068, 1085, 1100, 1122, 1129, 1145, 1167, 1186, 1200, 1214, 1230, 1247, 1258, 1272, 1291, 1301, 1313, 1333, 1345, 1364, 1380, 1390, 1402, 1412, 1436, 1451, 1458, 1477, 1493, 1504, 1523, 1543, 1554, 1571, 1590, 1604, 1615, 1626, 1645, 1669, 1686, 1703, 1722, 1743, 1757, 1779, 1795, 1816, 1833, 1840, 1859, 1881, 1895, 1902, 1909, 1925, 1945, 1964, 1983, 1998, 2005, 2025, 2035, 2049, 2064, 2081, 2100, 2117, 2138, 2152, 2166, 2173, 2180, 2194, 2216, 2228, 2247, 2259, 2278, 2297, 2311, 2333, 2352, 2367, 2381, 2400, 2417, 2428, 2443, 2462, 2476, 2487, 2506, 2520, 2544, 2563, 2582, 2592, 2606, 2620, 2639, 2654, 2678, 2692, 2711, 2723, 2738, 2745, 2755, 2776, 2793, 2810, 2817, 2839, 2849, 2859, 2878, 2897, 2914, 2933, 2952, 2959, 2976, 2998, 3017, 3032, 3049, 3066, 3083, 3100, 3117] "obj and name CA" index = 1 rmsd = 24.651 "obj and name CA" index = 2 rmsd = 22.618 "obj and name CA" index = 3 rmsd = 20.858 "obj and name CA" index = 4 rmsd = 19.194 "obj and name CA" index = 5 rmsd = 16.952 "obj and name CA" index = 6 rmsd = 15.431 "obj and name CA" index = 7 rmsd = 13.522 "obj and name CA" index = 8 rmsd = 11.558 "obj and name CA" index = 9 rmsd = 10.295 "obj and name CA" index = 10 rmsd = 8.871 "obj and name CA" index = 11 rmsd = 7.823 "obj and name CA" index = 12 rmsd = 7.072 "obj and name CA" index = 13 rmsd = 5.818 "obj and name CA" index = 14 rmsd = 5.939 "obj and name CA" index = 15 rmsd = 4.858 "obj and name CA" index = 16 rmsd = 4.509 "obj and name CA" index = 17 rmsd = 3.696 "obj and name CA" index = 18 rmsd = 3.971 "obj and name CA" index = 19 rmsd = 3.486 "obj and name CA" index = 20 rmsd = 2.943 "obj and name CA" index = 21 rmsd = 2.633 "obj and name CA" index = 22 rmsd = 3.017 "obj and name CA" index = 23 rmsd = 2.881 "obj and name CA" index = 24 rmsd = 2.637 "obj and name CA" index = 25 rmsd = 2.867 "obj and name CA" index = 26 rmsd = 2.928 "obj and name CA" index = 27 rmsd = 2.562 "obj and name CA" index = 28 rmsd = 2.615 "obj and name CA" index = 29 rmsd = 3.111 "obj and name CA" index = 30 rmsd = 3.399 "obj and name CA" index = 31 rmsd = 3.209 "obj and name CA" index = 32 rmsd = 2.769 "obj and name CA" index = 33 rmsd = 2.303 "obj and name CA" index = 34 rmsd = 1.991 "obj and name CA" index = 35 rmsd = 1.802 "obj and name CA" index = 36 rmsd = 1.715 "obj and name CA" index = 37 rmsd = 2.304 "obj and name CA" index = 38 rmsd = 2.477 "obj and name CA" index = 39 rmsd = 2.777 "obj and name CA" index = 40 rmsd = 2.997 "obj and name CA" index = 41 rmsd = 2.441 "obj and name CA" index = 42 rmsd = 2.412 "obj and name CA" index = 43 rmsd = 2.113 "obj and name CA" index = 44 rmsd = 2.279 "obj and name CA" index = 45 rmsd = 2.799 "obj and name CA" index = 46 rmsd = 2.619 "obj and name CA" index = 47 rmsd = 2.541 "obj and name CA" index = 48 rmsd = 3.049 "obj and name CA" index = 49 rmsd = 3.347 "obj and name CA" index = 50 rmsd = 3.263 "obj and name CA" index = 51 rmsd = 3.523 "obj and name CA" index = 52 rmsd = 3.055 "obj and name CA" index = 53 rmsd = 2.986 "obj and name CA" index = 54 rmsd = 2.550 "obj and name CA" index = 55 rmsd = 2.439 "obj and name CA" index = 56 rmsd = 2.110 "obj and name CA" index = 57 rmsd = 1.896 "obj and name CA" index = 58 rmsd = 1.893 "obj and name CA" index = 59 rmsd = 2.260 "obj and name CA" index = 60 rmsd = 2.553 "obj and name CA" index = 61 rmsd = 2.916 "obj and name CA" index = 62 rmsd = 3.074 "obj and name CA" index = 63 rmsd = 2.673 "obj and name CA" index = 64 rmsd = 2.739 "obj and name CA" index = 65 rmsd = 3.272 "obj and name CA" index = 66 rmsd = 3.272 "obj and name CA" index = 67 rmsd = 3.042 "obj and name CA" index = 68 rmsd = 3.522 "obj and name CA" index = 69 rmsd = 3.835 "obj and name CA" index = 70 rmsd = 3.726 "obj and name CA" index = 71 rmsd = 3.761 "obj and name CA" index = 72 rmsd = 4.344 "obj and name CA" index = 73 rmsd = 4.493 "obj and name CA" index = 74 rmsd = 4.354 "obj and name CA" index = 75 rmsd = 4.644 "obj and name CA" index = 76 rmsd = 4.135 "obj and name CA" index = 77 rmsd = 3.985 "obj and name CA" index = 78 rmsd = 3.114 "obj and name CA" index = 79 rmsd = 3.020 "obj and name CA" index = 80 rmsd = 2.810 "obj and name CA" index = 81 rmsd = 2.574 "obj and name CA" index = 82 rmsd = 2.554 "obj and name CA" index = 83 rmsd = 2.450 "obj and name CA" index = 84 rmsd = 2.535 "obj and name CA" index = 85 rmsd = 2.517 "obj and name CA" index = 86 rmsd = 3.079 "obj and name CA" index = 87 rmsd = 3.107 "obj and name CA" index = 88 rmsd = 2.631 "obj and name CA" index = 89 rmsd = 2.262 "obj and name CA" index = 90 rmsd = 2.117 "obj and name CA" index = 91 rmsd = 2.341 "obj and name CA" index = 92 rmsd = 2.481 "obj and name CA" index = 93 rmsd = 2.834 "obj and name CA" index = 94 rmsd = 2.792 "obj and name CA" index = 95 rmsd = 2.487 "obj and name CA" index = 96 rmsd = 2.663 "obj and name CA" index = 97 rmsd = 2.349 "obj and name CA" index = 98 rmsd = 1.840 "obj and name CA" index = 99 rmsd = 1.618 "obj and name CA" index = 100 rmsd = 1.306 "obj and name CA" index = 101 rmsd = 1.278 "obj and name CA" index = 102 rmsd = 1.339 "obj and name CA" index = 103 rmsd = 1.741 "obj and name CA" index = 104 rmsd = 1.968 "obj and name CA" index = 105 rmsd = 1.945 "obj and name CA" index = 106 rmsd = 2.311 "obj and name CA" index = 107 rmsd = 2.593 "obj and name CA" index = 108 rmsd = 2.847 "obj and name CA" index = 109 rmsd = 2.374 "obj and name CA" index = 110 rmsd = 2.057 "obj and name CA" index = 111 rmsd = 2.478 "obj and name CA" index = 112 rmsd = 2.250 "obj and name CA" index = 113 rmsd = 1.726 "obj and name CA" index = 114 rmsd = 1.737 "obj and name CA" index = 115 rmsd = 2.093 "obj and name CA" index = 116 rmsd = 1.929 "obj and name CA" index = 117 rmsd = 1.769 "obj and name CA" index = 118 rmsd = 1.896 "obj and name CA" index = 119 rmsd = 2.129 "obj and name CA" index = 120 rmsd = 2.099 "obj and name CA" index = 121 rmsd = 1.885 "obj and name CA" index = 122 rmsd = 2.469 "obj and name CA" index = 123 rmsd = 2.587 "obj and name CA" index = 124 rmsd = 2.581 "obj and name CA" index = 125 rmsd = 2.304 "obj and name CA" index = 126 rmsd = 1.878 "obj and name CA" index = 127 rmsd = 1.639 "obj and name CA" index = 128 rmsd = 1.694 "obj and name CA" index = 129 rmsd = 1.506 "obj and name CA" index = 130 rmsd = 1.813 "obj and name CA" index = 131 rmsd = 2.033 "obj and name CA" index = 132 rmsd = 2.109 "obj and name CA" index = 133 rmsd = 2.559 "obj and name CA" index = 134 rmsd = 3.305 "obj and name CA" index = 135 rmsd = 3.358 "obj and name CA" index = 136 rmsd = 3.039 "obj and name CA" index = 137 rmsd = 3.768 "obj and name CA" index = 138 rmsd = 4.439 "obj and name CA" index = 139 rmsd = 4.729 "obj and name CA" index = 140 rmsd = 5.355 "obj and name CA" index = 141 rmsd = 6.201 "obj and name CA" index = 142 rmsd = 5.881 "obj and name CA" index = 143 rmsd = 5.030 "obj and name CA" index = 144 rmsd = 4.641 "obj and name CA" index = 145 rmsd = 4.327 "obj and name CA" index = 146 rmsd = 4.494 "obj and name CA" index = 147 rmsd = 3.678 "obj and name CA" index = 148 rmsd = 4.011 "obj and name CA" index = 149 rmsd = 3.206 "obj and name CA" index = 150 rmsd = 2.455 "obj and name CA" index = 151 rmsd = 2.444 "obj and name CA" index = 152 rmsd = 2.318 "obj and name CA" index = 153 rmsd = 2.178 "obj and name CA" index = 154 rmsd = 2.410 "obj and name CA" index = 155 rmsd = 2.346 "obj and name CA" index = 156 rmsd = 1.910 "obj and name CA" index = 157 rmsd = 2.144 "obj and name CA" index = 158 rmsd = 2.466 "obj and name CA" index = 159 rmsd = 2.181 "obj and name CA" index = 160 rmsd = 1.946 "obj and name CA" index = 161 rmsd = 2.270 "obj and name CA" index = 162 rmsd = 2.284 "obj and name CA" index = 163 rmsd = 1.983 "obj and name CA" index = 164 rmsd = 2.181 "obj and name CA" index = 165 rmsd = 1.902 "obj and name CA" index = 166 rmsd = 2.184 "obj and name CA" index = 167 rmsd = 2.199 "obj and name CA" index = 168 rmsd = 2.306 "obj and name CA" index = 169 rmsd = 2.755 "obj and name CA" index = 170 rmsd = 2.657 "obj and name CA" index = 171 rmsd = 2.889 "obj and name CA" index = 172 rmsd = 3.097 "obj and name CA" index = 173 rmsd = 3.481 "obj and name CA" index = 174 rmsd = 4.045 "obj and name CA" index = 175 rmsd = 4.422 "obj and name CA" index = 176 rmsd = 5.233 "obj and name CA" index = 177 rmsd = 5.589 "obj and name CA" index = 178 rmsd = 6.305 "obj and name CA" index = 179 rmsd = 6.839 "obj and name CA" index = 180 rmsd = 6.609 "obj and name CA" index = 181 rmsd = 5.479 "obj and name CA" index = 182 rmsd = 4.975 "obj and name CA" index = 183 rmsd = 4.351 "obj and name CA" index = 184 rmsd = 3.733 "obj and name CA" index = 185 rmsd = 3.488 "obj and name CA" index = 186 rmsd = 2.818 "obj and name CA" index = 187 rmsd = 2.216 "obj and name CA" index = 188 rmsd = 1.925 "obj and name CA" index = 189 rmsd = 1.881 "obj and name CA" index = 190 rmsd = 1.627 "obj and name CA" index = 191 rmsd = 1.672 "obj and name CA" index = 192 rmsd = 1.652 "obj and name CA" index = 193 rmsd = 2.103 "obj and name CA" index = 194 rmsd = 2.684 "obj and name CA" index = 195 rmsd = 3.034 "obj and name CA" index = 196 rmsd = 3.873 "obj and name CA" index = 197 rmsd = 5.915 "obj and name CA" index = 198 rmsd = 6.841 "obj and name CA" index = 199 rmsd = 8.595 "obj and name CA" index = 200 rmsd = 10.499 "obj and name CA" index = 201 rmsd = 12.647 "obj and name CA" index = 202 rmsd = 14.368 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 135 atoms. PyMOL>color cyan,ss s Executive: Colored 99 atoms. PyMOL>color gray,ss ""+l Executive: Colored 6242 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: 1.74 sec. = 2066.9 frames/hour (9.48 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit