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 18 atoms. PyMOL>color cyan,ss s Executive: Colored 64 atoms. PyMOL>color gray,ss ""+l Executive: Colored 2566 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: 1.61 sec. = 2237.5 frames/hour (1.61 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: 7.40 sec. = 486.3 frames/hour (9.01 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, 4.3821229934692383, 5.5846638679504395, 5.2613625526428223, 4.8271474838256836, 4.1941051483154297, 5.3214340209960938, 5.7311630249023438, 4.0093441009521484, 7.7800555229187012, 3.3378562927246094, 6.4969267845153809, 5.9115023612976074, 6.5444731712341309, 4.0706400871276855, 3.8991324901580811, 7.5967731475830078, 7.3275527954101562, 5.7777400016784668, 6.7961106300354004] -> 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 = 12.863 "obj and name CA" index = 2 rmsd = 11.773 "obj and name CA" index = 3 rmsd = 11.008 "obj and name CA" index = 4 rmsd = 9.652 "obj and name CA" index = 5 rmsd = 7.678 "obj and name CA" index = 6 rmsd = 5.835 "obj and name CA" index = 7 rmsd = 3.755 "obj and name CA" index = 8 rmsd = 2.764 "obj and name CA" index = 9 rmsd = 1.829 "obj and name CA" index = 10 rmsd = 1.466 "obj and name CA" index = 11 rmsd = 1.229 "obj and name CA" index = 12 rmsd = 1.300 "obj and name CA" index = 13 rmsd = 1.364 "obj and name CA" index = 14 rmsd = 1.240 "obj and name CA" index = 15 rmsd = 1.212 "obj and name CA" index = 16 rmsd = 1.214 "obj and name CA" index = 17 rmsd = 1.209 "obj and name CA" index = 18 rmsd = 1.140 "obj and name CA" index = 19 rmsd = 1.321 "obj and name CA" index = 20 rmsd = 1.571 "obj and name CA" index = 21 rmsd = 2.053 "obj and name CA" index = 22 rmsd = 2.971 "obj and name CA" index = 23 rmsd = 3.088 "obj and name CA" index = 24 rmsd = 2.289 "obj and name CA" index = 25 rmsd = 1.964 "obj and name CA" index = 26 rmsd = 1.312 "obj and name CA" index = 27 rmsd = 0.863 "obj and name CA" index = 28 rmsd = 0.905 "obj and name CA" index = 29 rmsd = 0.854 "obj and name CA" index = 30 rmsd = 0.942 "obj and name CA" index = 31 rmsd = 0.983 "obj and name CA" index = 32 rmsd = 0.999 "obj and name CA" index = 33 rmsd = 1.332 "obj and name CA" index = 34 rmsd = 1.693 "obj and name CA" index = 35 rmsd = 2.563 "obj and name CA" index = 36 rmsd = 2.752 "obj and name CA" index = 37 rmsd = 3.329 "obj and name CA" index = 38 rmsd = 2.002 "obj and name CA" index = 39 rmsd = 1.460 "obj and name CA" index = 40 rmsd = 1.057 "obj and name CA" index = 41 rmsd = 0.894 "obj and name CA" index = 42 rmsd = 0.795 "obj and name CA" index = 43 rmsd = 0.704 "obj and name CA" index = 44 rmsd = 0.795 "obj and name CA" index = 45 rmsd = 0.951 "obj and name CA" index = 46 rmsd = 1.860 "obj and name CA" index = 47 rmsd = 2.538 "obj and name CA" index = 48 rmsd = 3.714 "obj and name CA" index = 49 rmsd = 4.438 "obj and name CA" index = 50 rmsd = 5.119 "obj and name CA" index = 51 rmsd = 5.657 "obj and name CA" index = 52 rmsd = 4.590 "obj and name CA" index = 53 rmsd = 3.696 "obj and name CA" index = 54 rmsd = 2.566 "obj and name CA" index = 55 rmsd = 1.437 "obj and name CA" index = 56 rmsd = 0.840 "obj and name CA" index = 57 rmsd = 0.656 "obj and name CA" index = 58 rmsd = 0.798 "obj and name CA" index = 59 rmsd = 0.781 "obj and name CA" index = 60 rmsd = 0.928 "obj and name CA" index = 61 rmsd = 1.076 "obj and name CA" index = 62 rmsd = 1.040 "obj and name CA" index = 63 rmsd = 1.004 "obj and name CA" index = 64 rmsd = 0.923 "obj and name CA" index = 65 rmsd = 1.015 "obj and name CA" index = 66 rmsd = 1.029 "obj and name CA" index = 67 rmsd = 1.037 "obj and name CA" index = 68 rmsd = 1.155 "obj and name CA" index = 69 rmsd = 1.398 "obj and name CA" index = 70 rmsd = 1.349 "obj and name CA" index = 71 rmsd = 1.140 "obj and name CA" index = 72 rmsd = 1.384 "obj and name CA" index = 73 rmsd = 1.919 "obj and name CA" index = 74 rmsd = 2.098 "obj and name CA" index = 75 rmsd = 1.798 "obj and name CA" index = 76 rmsd = 3.004 "obj and name CA" index = 77 rmsd = 4.221 "obj and name CA" index = 78 rmsd = 5.841 "obj and name CA" index = 79 rmsd = 8.157 "obj and name CA" index = 80 rmsd = 9.969 "obj and name CA" index = 81 rmsd = 12.063 "obj and name CA" index = 82 rmsd = 13.941 "obj and name CA" index = 83 rmsd = 12.863 "obj and name CA" index = 84 rmsd = 11.773 "obj and name CA" index = 85 rmsd = 11.008 "obj and name CA" index = 86 rmsd = 9.652 "obj and name CA" index = 87 rmsd = 7.678 "obj and name CA" index = 88 rmsd = 5.835 "obj and name CA" index = 89 rmsd = 3.755 "obj and name CA" index = 90 rmsd = 2.764 "obj and name CA" index = 91 rmsd = 1.829 "obj and name CA" index = 92 rmsd = 1.466 "obj and name CA" index = 93 rmsd = 1.229 "obj and name CA" index = 94 rmsd = 1.300 "obj and name CA" index = 95 rmsd = 1.364 "obj and name CA" index = 96 rmsd = 1.240 "obj and name CA" index = 97 rmsd = 1.212 "obj and name CA" index = 98 rmsd = 1.214 "obj and name CA" index = 99 rmsd = 1.209 "obj and name CA" index = 100 rmsd = 1.140 "obj and name CA" index = 101 rmsd = 1.320 "obj and name CA" index = 102 rmsd = 1.571 "obj and name CA" index = 103 rmsd = 2.053 "obj and name CA" index = 104 rmsd = 2.971 "obj and name CA" index = 105 rmsd = 3.088 "obj and name CA" index = 106 rmsd = 2.289 "obj and name CA" index = 107 rmsd = 1.965 "obj and name CA" index = 108 rmsd = 1.312 "obj and name CA" index = 109 rmsd = 0.863 "obj and name CA" index = 110 rmsd = 0.906 "obj and name CA" index = 111 rmsd = 0.854 "obj and name CA" index = 112 rmsd = 0.942 "obj and name CA" index = 113 rmsd = 0.983 "obj and name CA" index = 114 rmsd = 0.999 "obj and name CA" index = 115 rmsd = 1.332 "obj and name CA" index = 116 rmsd = 1.693 "obj and name CA" index = 117 rmsd = 2.563 "obj and name CA" index = 118 rmsd = 2.752 "obj and name CA" index = 119 rmsd = 3.330 "obj and name CA" index = 120 rmsd = 2.002 "obj and name CA" index = 121 rmsd = 1.459 "obj and name CA" index = 122 rmsd = 1.057 "obj and name CA" index = 123 rmsd = 0.894 "obj and name CA" index = 124 rmsd = 0.795 "obj and name CA" index = 125 rmsd = 0.704 "obj and name CA" index = 126 rmsd = 0.796 "obj and name CA" index = 127 rmsd = 0.951 "obj and name CA" index = 128 rmsd = 1.860 "obj and name CA" index = 129 rmsd = 2.538 "obj and name CA" index = 130 rmsd = 3.715 "obj and name CA" index = 131 rmsd = 4.438 "obj and name CA" index = 132 rmsd = 5.119 "obj and name CA" index = 133 rmsd = 5.657 "obj and name CA" index = 134 rmsd = 4.590 "obj and name CA" index = 135 rmsd = 3.697 "obj and name CA" index = 136 rmsd = 2.566 "obj and name CA" index = 137 rmsd = 1.437 "obj and name CA" index = 138 rmsd = 0.840 "obj and name CA" index = 139 rmsd = 0.656 "obj and name CA" index = 140 rmsd = 0.798 "obj and name CA" index = 141 rmsd = 0.781 "obj and name CA" index = 142 rmsd = 0.928 "obj and name CA" index = 143 rmsd = 1.076 "obj and name CA" index = 144 rmsd = 1.040 "obj and name CA" index = 145 rmsd = 1.004 "obj and name CA" index = 146 rmsd = 0.924 "obj and name CA" index = 147 rmsd = 1.015 "obj and name CA" index = 148 rmsd = 1.029 "obj and name CA" index = 149 rmsd = 1.037 "obj and name CA" index = 150 rmsd = 1.155 "obj and name CA" index = 151 rmsd = 1.398 "obj and name CA" index = 152 rmsd = 1.349 "obj and name CA" index = 153 rmsd = 1.140 "obj and name CA" index = 154 rmsd = 1.384 "obj and name CA" index = 155 rmsd = 1.919 "obj and name CA" index = 156 rmsd = 2.098 "obj and name CA" index = 157 rmsd = 1.798 "obj and name CA" index = 158 rmsd = 3.004 "obj and name CA" index = 159 rmsd = 4.221 "obj and name CA" index = 160 rmsd = 5.841 "obj and name CA" index = 161 rmsd = 8.157 "obj and name CA" index = 162 rmsd = 9.969 "obj and name CA" index = 163 rmsd = 12.063 "obj and name CA" index = 164 rmsd = 13.941 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 54 atoms. PyMOL>color cyan,ss s Executive: Colored 192 atoms. PyMOL>color gray,ss ""+l Executive: Colored 5198 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: 2.20 sec. = 1637.6 frames/hour (11.21 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit