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 24 atoms. PyMOL>color cyan,ss s Executive: Colored 66 atoms. PyMOL>color gray,ss ""+l Executive: Colored 2554 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: 1.49 sec. = 2412.5 frames/hour (1.49 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 492 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 492 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: 6.73 sec. = 535.0 frames/hour (8.22 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, 5.5160651206970215, 5.4155669212341309, 6.8523397445678711, 4.0837984085083008, 4.5334300994873047, 4.299654483795166, 5.8979048728942871, 6.4707989692687988, 4.587742805480957, 5.0002632141113281, 4.4714174270629883, 3.8021547794342041, 6.6231999397277832, 4.83050537109375, 3.0818769931793213, 4.8069772720336914, 4.7968316078186035, 6.8424797058105469, 6.2119660377502441] -> atom index_map = [None, 2, 21, 43, 65, 82, 92, 107, 127, 141, 161, 176, 195, 210, 225, 242, 261, 280, 294, 313, 324, 339, 353, 368, 390, 397, 421, 435, 457, 472, 491, 505, 529, 545, 556, 576, 590, 597, 607, 621, 631, 653, 673, 685, 704, 728, 738, 762, 773, 787, 799, 816, 830, 852, 869, 876, 898, 905, 924, 938, 957, 968, 982, 997, 1012, 1032, 1049, 1063, 1080, 1096, 1108, 1118, 1138, 1160, 1167, 1181, 1200, 1215, 1232, 1249, 1266, 1283, 1300, 1318, 1337, 1359, 1381, 1398, 1408, 1423, 1443, 1457, 1477, 1492, 1511, 1526, 1541, 1558, 1577, 1596, 1610, 1629, 1640, 1655, 1669, 1684, 1706, 1713, 1737, 1751, 1773, 1788, 1807, 1821, 1845, 1861, 1872, 1892, 1906, 1913, 1923, 1937, 1947, 1969, 1989, 2001, 2020, 2044, 2054, 2078, 2089, 2103, 2115, 2132, 2146, 2168, 2185, 2192, 2214, 2221, 2240, 2254, 2273, 2284, 2298, 2313, 2328, 2348, 2365, 2379, 2396, 2412, 2424, 2434, 2454, 2476, 2483, 2497, 2516, 2531, 2548, 2565, 2582, 2599, 2616] "obj and name CA" index = 1 rmsd = 11.892 "obj and name CA" index = 2 rmsd = 10.560 "obj and name CA" index = 3 rmsd = 9.420 "obj and name CA" index = 4 rmsd = 7.781 "obj and name CA" index = 5 rmsd = 5.713 "obj and name CA" index = 6 rmsd = 3.823 "obj and name CA" index = 7 rmsd = 2.268 "obj and name CA" index = 8 rmsd = 1.739 "obj and name CA" index = 9 rmsd = 1.327 "obj and name CA" index = 10 rmsd = 1.391 "obj and name CA" index = 11 rmsd = 1.215 "obj and name CA" index = 12 rmsd = 1.340 "obj and name CA" index = 13 rmsd = 1.244 "obj and name CA" index = 14 rmsd = 1.085 "obj and name CA" index = 15 rmsd = 0.996 "obj and name CA" index = 16 rmsd = 1.045 "obj and name CA" index = 17 rmsd = 1.009 "obj and name CA" index = 18 rmsd = 1.031 "obj and name CA" index = 19 rmsd = 1.322 "obj and name CA" index = 20 rmsd = 1.560 "obj and name CA" index = 21 rmsd = 1.918 "obj and name CA" index = 22 rmsd = 2.298 "obj and name CA" index = 23 rmsd = 2.894 "obj and name CA" index = 24 rmsd = 2.318 "obj and name CA" index = 25 rmsd = 1.763 "obj and name CA" index = 26 rmsd = 1.355 "obj and name CA" index = 27 rmsd = 0.981 "obj and name CA" index = 28 rmsd = 0.843 "obj and name CA" index = 29 rmsd = 0.686 "obj and name CA" index = 30 rmsd = 0.822 "obj and name CA" index = 31 rmsd = 0.894 "obj and name CA" index = 32 rmsd = 0.964 "obj and name CA" index = 33 rmsd = 1.248 "obj and name CA" index = 34 rmsd = 1.347 "obj and name CA" index = 35 rmsd = 1.807 "obj and name CA" index = 36 rmsd = 2.034 "obj and name CA" index = 37 rmsd = 2.650 "obj and name CA" index = 38 rmsd = 1.861 "obj and name CA" index = 39 rmsd = 1.234 "obj and name CA" index = 40 rmsd = 0.932 "obj and name CA" index = 41 rmsd = 0.730 "obj and name CA" index = 42 rmsd = 0.632 "obj and name CA" index = 43 rmsd = 0.557 "obj and name CA" index = 44 rmsd = 0.625 "obj and name CA" index = 45 rmsd = 0.950 "obj and name CA" index = 46 rmsd = 1.440 "obj and name CA" index = 47 rmsd = 2.034 "obj and name CA" index = 48 rmsd = 2.822 "obj and name CA" index = 49 rmsd = 3.622 "obj and name CA" index = 50 rmsd = 4.134 "obj and name CA" index = 51 rmsd = 4.422 "obj and name CA" index = 52 rmsd = 3.556 "obj and name CA" index = 53 rmsd = 3.320 "obj and name CA" index = 54 rmsd = 2.581 "obj and name CA" index = 55 rmsd = 1.477 "obj and name CA" index = 56 rmsd = 0.562 "obj and name CA" index = 57 rmsd = 0.510 "obj and name CA" index = 58 rmsd = 0.638 "obj and name CA" index = 59 rmsd = 0.707 "obj and name CA" index = 60 rmsd = 0.923 "obj and name CA" index = 61 rmsd = 1.123 "obj and name CA" index = 62 rmsd = 1.154 "obj and name CA" index = 63 rmsd = 0.919 "obj and name CA" index = 64 rmsd = 0.704 "obj and name CA" index = 65 rmsd = 0.826 "obj and name CA" index = 66 rmsd = 0.866 "obj and name CA" index = 67 rmsd = 0.746 "obj and name CA" index = 68 rmsd = 0.659 "obj and name CA" index = 69 rmsd = 0.795 "obj and name CA" index = 70 rmsd = 0.717 "obj and name CA" index = 71 rmsd = 0.667 "obj and name CA" index = 72 rmsd = 0.747 "obj and name CA" index = 73 rmsd = 0.893 "obj and name CA" index = 74 rmsd = 1.114 "obj and name CA" index = 75 rmsd = 1.063 "obj and name CA" index = 76 rmsd = 1.629 "obj and name CA" index = 77 rmsd = 2.577 "obj and name CA" index = 78 rmsd = 4.200 "obj and name CA" index = 79 rmsd = 6.022 "obj and name CA" index = 80 rmsd = 7.752 "obj and name CA" index = 81 rmsd = 10.046 "obj and name CA" index = 82 rmsd = 11.795 "obj and name CA" index = 83 rmsd = 11.892 "obj and name CA" index = 84 rmsd = 10.559 "obj and name CA" index = 85 rmsd = 9.420 "obj and name CA" index = 86 rmsd = 7.780 "obj and name CA" index = 87 rmsd = 5.712 "obj and name CA" index = 88 rmsd = 3.822 "obj and name CA" index = 89 rmsd = 2.268 "obj and name CA" index = 90 rmsd = 1.739 "obj and name CA" index = 91 rmsd = 1.327 "obj and name CA" index = 92 rmsd = 1.391 "obj and name CA" index = 93 rmsd = 1.215 "obj and name CA" index = 94 rmsd = 1.339 "obj and name CA" index = 95 rmsd = 1.244 "obj and name CA" index = 96 rmsd = 1.085 "obj and name CA" index = 97 rmsd = 0.996 "obj and name CA" index = 98 rmsd = 1.045 "obj and name CA" index = 99 rmsd = 1.008 "obj and name CA" index = 100 rmsd = 1.031 "obj and name CA" index = 101 rmsd = 1.322 "obj and name CA" index = 102 rmsd = 1.560 "obj and name CA" index = 103 rmsd = 1.918 "obj and name CA" index = 104 rmsd = 2.298 "obj and name CA" index = 105 rmsd = 2.894 "obj and name CA" index = 106 rmsd = 2.318 "obj and name CA" index = 107 rmsd = 1.764 "obj and name CA" index = 108 rmsd = 1.354 "obj and name CA" index = 109 rmsd = 0.981 "obj and name CA" index = 110 rmsd = 0.843 "obj and name CA" index = 111 rmsd = 0.686 "obj and name CA" index = 112 rmsd = 0.822 "obj and name CA" index = 113 rmsd = 0.895 "obj and name CA" index = 114 rmsd = 0.964 "obj and name CA" index = 115 rmsd = 1.248 "obj and name CA" index = 116 rmsd = 1.347 "obj and name CA" index = 117 rmsd = 1.807 "obj and name CA" index = 118 rmsd = 2.033 "obj and name CA" index = 119 rmsd = 2.650 "obj and name CA" index = 120 rmsd = 1.861 "obj and name CA" index = 121 rmsd = 1.234 "obj and name CA" index = 122 rmsd = 0.932 "obj and name CA" index = 123 rmsd = 0.731 "obj and name CA" index = 124 rmsd = 0.632 "obj and name CA" index = 125 rmsd = 0.557 "obj and name CA" index = 126 rmsd = 0.625 "obj and name CA" index = 127 rmsd = 0.950 "obj and name CA" index = 128 rmsd = 1.439 "obj and name CA" index = 129 rmsd = 2.034 "obj and name CA" index = 130 rmsd = 2.822 "obj and name CA" index = 131 rmsd = 3.622 "obj and name CA" index = 132 rmsd = 4.134 "obj and name CA" index = 133 rmsd = 4.422 "obj and name CA" index = 134 rmsd = 3.556 "obj and name CA" index = 135 rmsd = 3.319 "obj and name CA" index = 136 rmsd = 2.581 "obj and name CA" index = 137 rmsd = 1.477 "obj and name CA" index = 138 rmsd = 0.563 "obj and name CA" index = 139 rmsd = 0.510 "obj and name CA" index = 140 rmsd = 0.638 "obj and name CA" index = 141 rmsd = 0.707 "obj and name CA" index = 142 rmsd = 0.923 "obj and name CA" index = 143 rmsd = 1.123 "obj and name CA" index = 144 rmsd = 1.154 "obj and name CA" index = 145 rmsd = 0.919 "obj and name CA" index = 146 rmsd = 0.704 "obj and name CA" index = 147 rmsd = 0.826 "obj and name CA" index = 148 rmsd = 0.866 "obj and name CA" index = 149 rmsd = 0.746 "obj and name CA" index = 150 rmsd = 0.659 "obj and name CA" index = 151 rmsd = 0.795 "obj and name CA" index = 152 rmsd = 0.717 "obj and name CA" index = 153 rmsd = 0.667 "obj and name CA" index = 154 rmsd = 0.747 "obj and name CA" index = 155 rmsd = 0.893 "obj and name CA" index = 156 rmsd = 1.114 "obj and name CA" index = 157 rmsd = 1.063 "obj and name CA" index = 158 rmsd = 1.629 "obj and name CA" index = 159 rmsd = 2.577 "obj and name CA" index = 160 rmsd = 4.201 "obj and name CA" index = 161 rmsd = 6.022 "obj and name CA" index = 162 rmsd = 7.752 "obj and name CA" index = 163 rmsd = 10.046 "obj and name CA" index = 164 rmsd = 11.795 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 72 atoms. PyMOL>color cyan,ss s Executive: Colored 198 atoms. PyMOL>color gray,ss ""+l Executive: Colored 5170 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: 2.47 sec. = 1460.2 frames/hour (10.69 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit