id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18814 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.6.1-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. 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All rights reserved. How to cite UCSF ChimeraX > open > /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3985_00049_volume_series/J3985_class_01_00049_volume.mrc Opened J3985_class_01_00049_volume.mrc as #1, grid size 128,128,128, pixel 2.74, shown at level 0.0714, step 1, values float32 > open > /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3985_00049_volume_series/J3985_class_00_00049_volume.mrc Opened J3985_class_00_00049_volume.mrc as #2, grid size 128,128,128, pixel 2.74, shown at level 0.0704, step 1, values float32 > volume #2 level 0.1464 > volume #2 level 0.1878 > volume #1 level 0.1749 > volume #1 level 0.2362 > volume #2 level 0.2672 > volume #1 level 0.2324 > volume #1 level 0.2937 > volume #1 level 0.1634 > volume #1 level 0.1979 > volume #2 level 0.2879 > volume #1 level 0.2247 > volume #1 level 0.2055 > volume #2 level 0.3432 > volume #1 level 0.3014 > volume #1 level 0.1557 > ui tool show ""Segment Map"" Select a density map in the Segment map field Segmenting J3985_class_01_00049_volume.mrc, density threshold 0.155709 Showing 1 region surfaces 187 watershed regions, grouped to 1 regions Showing J3985_class_01_00049_volume.seg - 1 regions, 1 surfaces Ungrouped to 3 regions > select #3.3 1 model selected Ungrouped to 8 regions > select #3.6 1 model selected Ungrouped to 5 regions > select #3.3 1 model selected > select add #3.14 2 models selected > select add #3.9 3 models selected Grouped 3 regions Ungrouped to 3 regions > select #3.6 1 model selected Ungrouped to 3 regions > select #3.3 1 model selected Ungrouped to 15 regions > select #3.31 1 model selected > select add #3.9 2 models selected > select add #3.14 3 models selected Grouped 3 regions Saving 1 regions to mrc file... Opened J3985_class_01_00049_volume_region_234.mrc as #4, grid size 21,17,18, pixel 2.74, shown at step 1, values float32 Wrote J3985_class_01_00049_volume_region_234.mrc > volume resample #4 onGrid 1 Invalid ""onGrid"" argument: invalid density maps specifier > volume resample #4 onGrid #1 Opened J3985_class_01_00049_volume_region_234.mrc resampled as #5, grid size 128,128,128, pixel 2.74, shown at step 1, values float32 > hide #!3 models > volume #5 level 0.2124 > volume #5 level 0.1251 > save > /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3985_00049_volume_series/J3985_class_01_00049_volume_region_p.mrc > models #5 > open /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3986_006_volume_map.mrc Opened cryosparc_P9_J3986_006_volume_map.mrc as #6, grid size 480,480,480, pixel 0.732, shown at level 0.0101, step 2, values float32 > volume #6 level 0.0249 > volume #6 level 0.01868 > volume #6 level 0.03345 > volume #!5-6 hide > volume #1 level 0.2702 > volume #2 level 0.1264 > volume #1 level 0.1478 > volume #1 level 0.1123 > volume #2 level 0.1797 > volume #1 level 0.2623 > volume #2 level 0.3574 > volume #1 level 0.3294 > open /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3984_007_volume_map.mrc Opened cryosparc_P9_J3984_007_volume_map.mrc as #7, grid size 480,480,480, pixel 0.732, shown at level 0.0104, step 2, values float32 > volume #!1,7 hide > volume #7 level 0.02771 > volume #7 level 0.04405 > volume #7 level 0.03924 > volume #7 level 0.04789 > volume #7 level 0.0575 > open /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3983_007_volume_map.mrc Opened cryosparc_P9_J3983_007_volume_map.mrc as #8, grid size 480,480,480, pixel 0.732, shown at level 0.0105, step 2, values float32 > volume #8 level 0.0575 > volume #8 level 0.04195 > volume #7 level 0.03636 > select add #7 3 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #3.3,0.99455,-0.074938,-0.072552,27.272,0.072407,0.99669,-0.036905,-6.1312,0.075078,0.03145,0.99668,-18.795,#7,0.99455,-0.074938,-0.072552,27.272,0.072407,0.99669,-0.036905,-6.1312,0.075078,0.03145,0.99668,-18.795 > view matrix models > #3.3,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93,#7,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93 > fitmap #7 inMap #8 Fit map cryosparc_P9_J3984_007_volume_map.mrc in map cryosparc_P9_J3983_007_volume_map.mrc using 49963 points correlation = 0.9959, correlation about mean = 0.984, overlap = 500.7 steps = 380, shift = 16.1, angle = 34.3 degrees Position of cryosparc_P9_J3984_007_volume_map.mrc (#7) relative to cryosparc_P9_J3983_007_volume_map.mrc (#8) coordinates: Matrix rotation and translation -0.72583440 0.68279829 -0.08337219 201.41842056 -0.29586248 -0.41930957 -0.85828018 446.74544623 -0.62099100 -0.59830258 0.50636370 306.03816839 Axis 0.22676305 0.46893301 -0.85362776 Axis point 224.32984314 270.00684921 0.00000000 Rotation angle (degrees) 145.02379031 Shift along axis -6.07473264 > fitmap #7 inMap #8 Fit map cryosparc_P9_J3984_007_volume_map.mrc in map cryosparc_P9_J3983_007_volume_map.mrc using 49963 points correlation = 0.9959, correlation about mean = 0.984, overlap = 500.7 steps = 64, shift = 0.012, angle = 0.00824 degrees Position of cryosparc_P9_J3984_007_volume_map.mrc (#7) relative to cryosparc_P9_J3983_007_volume_map.mrc (#8) coordinates: Matrix rotation and translation -0.72583244 0.68280184 -0.08336017 201.41856784 -0.29596038 -0.41938679 -0.85820870 446.76271306 -0.62094664 -0.59824441 0.50648682 306.00978970 Axis 0.22673791 0.46887682 -0.85366530 Axis point 224.32617617 269.99245085 0.00000000 Rotation angle (degrees) 145.02139829 Shift along axis -6.08403693 > fitmap #7 inMap #8 Fit map cryosparc_P9_J3984_007_volume_map.mrc in map cryosparc_P9_J3983_007_volume_map.mrc using 49963 points correlation = 0.9959, correlation about mean = 0.984, overlap = 500.7 steps = 44, shift = 0.0118, angle = 0.00629 degrees Position of cryosparc_P9_J3984_007_volume_map.mrc (#7) relative to cryosparc_P9_J3983_007_volume_map.mrc (#8) coordinates: Matrix rotation and translation -0.72584163 0.68278694 -0.08340211 201.42434440 -0.29586571 -0.41935773 -0.85825554 446.75301724 -0.62098100 -0.59828178 0.50640054 306.02837341 Axis 0.22676494 0.46890903 -0.85364043 Axis point 224.32912008 270.00287478 0.00000000 Rotation angle (degrees) 145.02471726 Shift along axis -6.07568669 > fitmap #7 inMap #8 Fit map cryosparc_P9_J3984_007_volume_map.mrc in map cryosparc_P9_J3983_007_volume_map.mrc using 49963 points correlation = 0.9959, correlation about mean = 0.984, overlap = 500.7 steps = 100, shift = 0.0117, angle = 0.00919 degrees Position of cryosparc_P9_J3984_007_volume_map.mrc (#7) relative to cryosparc_P9_J3983_007_volume_map.mrc (#8) coordinates: Matrix rotation and translation -0.72585579 0.68276216 -0.08348176 201.44447216 -0.29589017 -0.41949591 -0.85817958 446.76049346 -0.62095280 -0.59821318 0.50651615 305.99878042 Axis 0.22676890 0.46883644 -0.85367925 Axis point 224.32788267 269.98130269 0.00000000 Rotation angle (degrees) 145.02655337 Shift along axis -6.08586737 > volume #8 level 0.0364 > select subtract #7 1 model selected > view matrix models > #3.3,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93 > volume #7 level 0.06423 > view matrix models > #3.3,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93 > volume #7 level 0.02003 > volume #8 level 0.02571 > volume #8 level 0.04417 > open /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3969_006_volume_map.mrc Opened cryosparc_P9_J3969_006_volume_map.mrc as #9, grid size 480,480,480, pixel 0.732, shown at level 0.0103, step 2, values float32 > volume #9 level 0.03176 > volume #9 level 0.01519 > open /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3951_008_volume_map.mrc Opened cryosparc_P9_J3951_008_volume_map.mrc as #10, grid size 480,480,480, pixel 0.732, shown at level 0.0114, step 2, values float32 > volume #!8,10 hide > volume #10 level 0.03828 > volume #10 level 0.02869 > volume #10 level 0.04979 > fitmap #1 inMap #10 Fit map J3985_class_01_00049_volume.mrc in map cryosparc_P9_J3951_008_volume_map.mrc using 6629 points correlation = 0.8689, correlation about mean = 0.602, overlap = 377 steps = 96, shift = 1.6, angle = 4.19 degrees Position of J3985_class_01_00049_volume.mrc (#1) relative to cryosparc_P9_J3951_008_volume_map.mrc (#10) coordinates: Matrix rotation and translation 0.99743315 -0.00176327 -0.07158214 11.61334330 0.00282388 0.99988770 0.01471808 -3.39292521 0.07154815 -0.01488244 0.99732611 -10.23271671 Axis -0.20242295 -0.97879565 0.03136921 Axis point 149.23497483 0.00000000 158.72238428 Rotation angle (degrees) 4.19295196 Shift along axis 0.64918094 > fitmap #1 inMap #10 Fit map J3985_class_01_00049_volume.mrc in map cryosparc_P9_J3951_008_volume_map.mrc using 6629 points correlation = 0.8688, correlation about mean = 0.6019, overlap = 377 steps = 40, shift = 0.0111, angle = 0.00583 degrees Position of J3985_class_01_00049_volume.mrc (#1) relative to cryosparc_P9_J3951_008_volume_map.mrc (#10) coordinates: Matrix rotation and translation 0.99743292 -0.00175838 -0.07158540 11.60987325 0.00281177 0.99988921 0.01461711 -3.38346500 0.07155176 -0.01478087 0.99732736 -10.24684374 Axis -0.20108561 -0.97907475 0.03126035 Axis point 149.42296601 0.00000000 158.67147531 Rotation angle (degrees) 4.19195597 Shift along axis 0.65776684 > fitmap #1 inMap #10 Fit map J3985_class_01_00049_volume.mrc in map cryosparc_P9_J3951_008_volume_map.mrc using 6629 points correlation = 0.8688, correlation about mean = 0.6019, overlap = 377 steps = 60, shift = 0.00202, angle = 0.00304 degrees Position of J3985_class_01_00049_volume.mrc (#1) relative to cryosparc_P9_J3951_008_volume_map.mrc (#10) coordinates: Matrix rotation and translation 0.99743293 -0.00175093 -0.07158545 11.60870841 0.00280811 0.99988844 0.01467011 -3.38985788 0.07155178 -0.01483347 0.99732658 -10.23757914 Axis -0.20177899 -0.97893465 0.03117985 Axis point 149.29375605 0.00000000 158.66352892 Rotation angle (degrees) 4.19255884 Shift along axis 0.65684980 > fitmap #1 inMap #10 Fit map J3985_class_01_00049_volume.mrc in map cryosparc_P9_J3951_008_volume_map.mrc using 6629 points correlation = 0.8688, correlation about mean = 0.6019, overlap = 377 steps = 96, shift = 0.002, angle = 0.00324 degrees Position of J3985_class_01_00049_volume.mrc (#1) relative to cryosparc_P9_J3951_008_volume_map.mrc (#10) coordinates: Matrix rotation and translation 0.99743159 -0.00171901 -0.07160488 11.60617014 0.00277352 0.99988913 0.01463001 -3.37850973 0.07157180 -0.01479103 0.99732578 -10.24880751 Axis -0.20118700 -0.97907100 0.03072081 Axis point 149.40364660 0.00000000 158.57590880 Rotation angle (degrees) 4.19313151 Shift along axis 0.65793867 > open > /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3989_00048_volume_series/J3989_class_01_00048_volume.mrc Opened J3989_class_01_00048_volume.mrc as #11, grid size 128,128,128, pixel 2.74, shown at level 0.0696, step 1, values float32 > open > /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3989_00048_volume_series/J3989_class_00_00048_volume.mrc Opened J3989_class_00_00048_volume.mrc as #12, grid size 128,128,128, pixel 2.74, shown at level 0.0695, step 1, values float32 > volume #!1,10-12 hide > volume #12 level 0.1515 > volume #11 level 0.1326 > volume #11 level 0.1548 > volume #1 level 0.211 > volume #2 level 0.1832 > volume #!2 hide > open > /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3968_00116_volume_series/J3968_class_01_00116_volume.mrc Opened J3968_class_01_00116_volume.mrc as #13, grid size 144,144,144, pixel 2.75, shown at level 0.0545, step 1, values float32 > open > /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3968_00116_volume_series/J3968_class_00_00116_volume.mrc Opened J3968_class_00_00116_volume.mrc as #14, grid size 144,144,144, pixel 2.75, shown at level 0.0495, step 1, values float32 > volume #14 level 0.115 > volume #13 level 0.1179 > select add #13 3 models selected > hide #!14 models > fitmap #13 inMap #11 Fit map J3968_class_01_00116_volume.mrc in map J3989_class_01_00048_volume.mrc using 15819 points correlation = 0.8706, correlation about mean = 0.722, overlap = 2919 steps = 140, shift = 37.7, angle = 1.37 degrees Position of J3968_class_01_00116_volume.mrc (#13) relative to J3989_class_01_00048_volume.mrc (#11) coordinates: Matrix rotation and translation 0.99971437 0.01959626 0.01368115 -28.66197852 -0.01958627 0.99980780 -0.00086396 -16.84931847 -0.01369545 0.00059576 0.99990604 -19.58306288 Axis 0.03052447 0.57247681 -0.81935252 Axis point -1036.02962297 1456.12966984 0.00000000 Rotation angle (degrees) 1.37011058 Shift along axis 5.52469615 > fitmap #13 inMap #11 Fit map J3968_class_01_00116_volume.mrc in map J3989_class_01_00048_volume.mrc using 15819 points correlation = 0.8705, correlation about mean = 0.7217, overlap = 2919 steps = 56, shift = 0.023, angle = 0.0138 degrees Position of J3968_class_01_00116_volume.mrc (#13) relative to J3989_class_01_00048_volume.mrc (#11) coordinates: Matrix rotation and translation 0.99971346 0.01976263 0.01350659 -28.68065746 -0.01975270 0.99980452 -0.00086839 -16.82188386 -0.01352112 0.00060135 0.99990840 -19.61515682 Axis 0.03068551 0.56428859 -0.82500714 Axis point -1031.91078715 1445.31671200 0.00000000 Rotation angle (degrees) 1.37227811 Shift along axis 5.81016679 > fitmap #11 inMap #14 Fit map J3989_class_01_00048_volume.mrc in map J3968_class_00_00116_volume.mrc using 11649 points correlation = 0.8966, correlation about mean = 0.7157, overlap = 2894 steps = 124, shift = 38, angle = 1.45 degrees Position of J3989_class_01_00048_volume.mrc (#11) relative to J3968_class_00_00116_volume.mrc (#14) coordinates: Matrix rotation and translation 0.99969266 -0.02253533 -0.01033133 28.08037343 0.02259070 0.99973088 0.00527456 16.14208619 0.01020969 -0.00550634 0.99993272 21.38876177 Axis -0.21247458 -0.40483111 0.88936287 Axis point -815.69812369 1318.66977759 0.00000000 Rotation angle (degrees) 1.45374188 Shift along axis 6.52118636 > fitmap #11 inMap #14 Fit map J3989_class_01_00048_volume.mrc in map J3968_class_00_00116_volume.mrc using 11649 points correlation = 0.8967, correlation about mean = 0.7151, overlap = 2889 steps = 80, shift = 0.042, angle = 0.00904 degrees Position of J3989_class_01_00048_volume.mrc (#11) relative to J3968_class_00_00116_volume.mrc (#14) coordinates: Matrix rotation and translation 0.99969400 -0.02251644 -0.01024267 28.07371662 0.02257002 0.99973202 0.00514573 16.13692320 0.01012406 -0.00537533 0.99993430 21.40764237 Axis -0.20801043 -0.40266782 0.89139794 Axis point -819.63745883 1320.26275326 0.00000000 Rotation angle (degrees) 1.44915013 Shift along axis 6.74528284 > fitmap #11 inMap #14 Fit map J3989_class_01_00048_volume.mrc in map J3968_class_00_00116_volume.mrc using 11649 points correlation = 0.8965, correlation about mean = 0.7152, overlap = 2893 steps = 80, shift = 0.0478, angle = 0.0308 degrees Position of J3989_class_01_00048_volume.mrc (#11) relative to J3968_class_00_00116_volume.mrc (#14) coordinates: Matrix rotation and translation 0.99968804 -0.02285456 -0.01007459 28.12280975 0.02291102 0.99972224 0.00552539 16.05278061 0.00994551 -0.00575449 0.99993398 21.48943495 Axis -0.22026445 -0.39093637 0.89367350 Axis point -799.73209073 1306.33286302 0.00000000 Rotation angle (degrees) 1.46723678 Shift along axis 6.73446774 > fitmap #11 inMap #14 Fit map J3989_class_01_00048_volume.mrc in map J3968_class_00_00116_volume.mrc using 11649 points correlation = 0.8965, correlation about mean = 0.7151, overlap = 2893 steps = 64, shift = 0.00592, angle = 0.0116 degrees Position of J3989_class_01_00048_volume.mrc (#11) relative to J3968_class_00_00116_volume.mrc (#14) coordinates: Matrix rotation and translation 0.99969172 -0.02267013 -0.01012540 28.09508155 0.02272756 0.99972605 0.00559283 16.07389740 0.00999584 -0.00582123 0.99993310 21.49281283 Axis -0.22401656 -0.39490657 0.89099123 Axis point -804.48634434 1314.55289352 0.00000000 Rotation angle (degrees) 1.45982216 Shift along axis 6.50845650 > hide #!11 models > select subtract #13 1 model selected > volume #14 level 0.2241 > volume #14 level 0.06262 > volume #14 level 0.2241 > volume #14 level 0.4248 > volume #14 level 0.115 > volume #14 level 0.1717 > volume #14 level 0.211 > volume #14 level 0.1237 > volume #14 level 0.06698 > volume #14 level 0.2764 > volume #14 level 0.2241 > volume #14 level 0.2197 > volume #14 level 0.2808 > view matrix models > #3.3,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93 > volume #14 level 0.1673 > volume #14 level 0.211 > view matrix models > #3.3,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93 > volume #14 level 0.09752 > volume #14 level 0.1804 > volume #14 level 0.307 > volume #14 level 0.08007 > volume #14 level 0.1062 > view matrix models > #3.3,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93 > volume #14 level 0.1542 > volume #14 level 0.1979 > view matrix models > #3.3,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93 > volume #14 level 0.1499 > volume #14 level 0.2066 > volume #14 level 0.1019 > volume #14 level 0.1542 > volume #14 level 0.2022 > view matrix models > #3.3,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93 > volume #14 level 0.115 > volume #14 level 0.403 > volume #14 level 0.1019 > open /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3967_007_volume_map.mrc Opened cryosparc_P9_J3967_007_volume_map.mrc as #15, grid size 324,324,324, pixel 1.22, shown at level 0.0302, step 2, values float32 > volume #15 level 0.08332 > volume #15 level 0.101 > volume #15 level 0.08996 > volume #15 level 0.07669 > volume #15 level 0.09438 > volume #15 level 0.163 > volume #15 level 0.1696 Segmenting cryosparc_P9_J3967_007_volume_map.mrc, density threshold 0.169599 Showing 17 region surfaces 1009 watershed regions, grouped to 17 regions Showing cryosparc_P9_J3967_007_volume_map.seg - 17 regions, 17 surfaces Segmenting cryosparc_P9_J3967_007_volume_map.mrc, density threshold 0.169599 Showing 17 region surfaces 1009 watershed regions, grouped to 17 regions Showing cryosparc_P9_J3967_007_volume_map.seg - 17 regions, 17 surfaces > select #3.17 1 model selected Deleted 1 regions > select #3.3 1 model selected > select clear > select #3.1 1 model selected > select add #3.7 2 models selected > select add #3.8 3 models selected > select add #3.12 4 models selected > select add #3.10 5 models selected > select add #3.16 6 models selected > select add #3.2 7 models selected > select add #3.3 8 models selected > select add #3.11 9 models selected > select add #3.6 10 models selected > select add #3.4 11 models selected > select add #3.5 12 models selected > select subtract #3.2 11 models selected > select add #3.9 12 models selected > select clear Drag select of 1359, 48002 of 48056 triangles, 1356, 1362, 1341, 1360, 1345, 1335, 1339, 1350, 1357, 1358, 1344, 1347, 1281, 1361, 1338, 15 cryosparc_P9_J3967_007_volume_map.mrc > view matrix models > #15,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.1,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.2,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.3,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.4,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.5,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.6,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.7,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.8,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.9,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.10,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.11,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.12,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.13,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.14,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.15,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.16,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796 Saving 16 regions to mrc file... Opened cryosparc_P9_J3967_007_volume_map_16_regions.mrc as #16, grid size 73,125,114, pixel 1.22, shown at step 1, values float32 Wrote cryosparc_P9_J3967_007_volume_map_16_regions.mrc > volume resample #16 onGrid #15 Opened cryosparc_P9_J3967_007_volume_map_16_regions.mrc resampled as #17, grid size 324,324,324, pixel 1.22, shown at step 1, values float32 > hide #!3 models > volume #17 level 0.09743 > save > /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3967_007_volume_map_16_regions.mrc > models #17 > volume #16 level 0.296 > volume #16 level 0.2176 > volume #16 level 0.2393 > close #16 > close #17 > volume #15 level 0.06784 > volume #15 level 0.03687 > volume #15 level 0.0966 > volume #15 level 0.08111 > volume #15 level 0.1254 > view matrix models > #15,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.1,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.2,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.3,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.4,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.5,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.6,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.7,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.8,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.9,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.10,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.11,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.12,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.13,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.14,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.15,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.16,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69 > close session > open > /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3977_00142_volumes/J3977_class_03_00142_volume.mrc Opened J3977_class_03_00142_volume.mrc as #1, grid size 128,128,128, pixel 3.09, shown at level 0.0569, step 1, values float32 > open > /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3977_00142_volumes/J3977_class_02_00142_volume.mrc Opened J3977_class_02_00142_volume.mrc as #2, grid size 128,128,128, pixel 3.09, shown at level 0.0652, step 1, values float32 > open > /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3977_00142_volumes/J3977_class_01_00142_volume.mrc Opened J3977_class_01_00142_volume.mrc as #3, grid size 128,128,128, pixel 3.09, shown at level 0.0644, step 1, values float32 > open > /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3977_00142_volumes/J3977_class_00_00142_volume.mrc Opened J3977_class_00_00142_volume.mrc as #4, grid size 128,128,128, pixel 3.09, shown at level 0.0511, step 1, values float32 > surface dust #1 size 30.9 > surface dust #2 size 30.9 > surface dust #3 size 30.9 > surface dust #4 size 30.9 > volume #!1-2,4 hide > select add #4 2 models selected > view matrix models > #4,0.94781,0.16804,0.27096,-68.241,-0.31283,0.32602,0.8921,34.283,0.061569,-0.93031,0.36157,273.55 > view matrix models > #4,0.95967,0.13122,0.24861,-59.846,-0.27903,0.33713,0.89916,24.083,0.034174,-0.93227,0.36015,279.75 > view matrix models > #4,0.81403,-0.58022,0.026318,142.13,0.23948,0.37658,0.89489,-88.181,-0.52915,-0.72217,0.4455,340.15 > volume #3 level 0.08997 > volume #3 level 0.1412 > volume #4 level 0.1357 > view matrix models > #4,-0.98182,-0.15393,0.11102,400.77,-0.16014,0.98586,-0.049341,48.503,-0.10186,-0.066224,-0.99259,395.11 > view matrix models > #4,-0.88503,0.34552,0.312,251.01,0.33497,0.93805,-0.088657,-33.002,-0.3233,0.026046,-0.94594,412.92 > volume #4 level 0.3894 > volume #4 z flip Expected a keyword > volume #4 zflip Expected a keyword > volume #4 flipNormals Missing ""flipNormals"" keyword's argument > volume flip #4 Opened J3977_class_00_00142_volume.mrc z flip as #5, grid size 128,128,128, pixel 3.09, shown at step 1, values float32 > select #5 2 models selected > view matrix models > #5,-0.85933,0.30635,0.40953,234.55,-0.2375,0.47014,-0.85004,313.88,-0.45294,-0.82772,-0.33125,480.43 > fitmap #5 inMap #3 Fit map J3977_class_00_00142_volume.mrc z flip in map J3977_class_01_00142_volume.mrc using 4563 points correlation = 0.9699, correlation about mean = 0.7826, overlap = 2457 steps = 132, shift = 31.6, angle = 38.4 degrees Position of J3977_class_00_00142_volume.mrc z flip (#5) relative to J3977_class_01_00142_volume.mrc (#3) coordinates: Matrix rotation and translation -0.99116610 0.00155516 -0.13261718 420.28508914 0.12896783 0.24454249 -0.96102354 304.65893499 0.03093599 -0.96963731 -0.24258280 429.65932782 Axis -0.04151142 -0.78819365 0.61402571 Axis point 188.06887356 0.00000000 347.37550767 Rotation angle (degrees) 174.04473730 Shift along axis 6.24500964 > fitmap #5 inMap #3 Fit map J3977_class_00_00142_volume.mrc z flip in map J3977_class_01_00142_volume.mrc using 4563 points correlation = 0.9699, correlation about mean = 0.7826, overlap = 2457 steps = 48, shift = 0.0213, angle = 0.0281 degrees Position of J3977_class_00_00142_volume.mrc z flip (#5) relative to J3977_class_01_00142_volume.mrc (#3) coordinates: Matrix rotation and translation -0.99117083 0.00165958 -0.13258052 420.24478315 0.12894289 0.24500496 -0.96090909 304.53529817 0.03088818 -0.96952039 -0.24305576 429.72894017 Axis -0.04152874 -0.78834163 0.61383453 Axis point 188.06053369 0.00000000 347.28922017 Rotation angle (degrees) 174.04894559 Shift along axis 6.25237502 > volume #3 level 0.6852 > volume #5 level 0.188 > volume #3 level 0.1028 > volume #3 level 0.138 > volume #5 level 0.1598 > volume #5 level 0.1679 > volume #3 level 0.07077 > volume #3 level 0.1988 > volume #5 level 0.2806 > volume #1 level 0.2265 > fitmap #5 inMap #1 Fit map J3977_class_00_00142_volume.mrc z flip in map J3977_class_03_00142_volume.mrc using 6115 points correlation = 0.9725, correlation about mean = 0.8601, overlap = 2909 steps = 84, shift = 2.02, angle = 4.3 degrees Position of J3977_class_00_00142_volume.mrc z flip (#5) relative to J3977_class_03_00142_volume.mrc (#1) coordinates: Matrix rotation and translation -0.99754203 0.02498920 -0.06546303 405.36740821 0.06977180 0.26807185 -0.96086906 311.85792420 -0.00646256 -0.96307476 -0.26915648 438.89272991 Axis -0.02976493 -0.79618479 0.60432096 Axis point 191.78070263 0.00000000 342.51916349 Rotation angle (degrees) 177.87659093 Shift along axis 4.86980674 > fitmap #5 inMap #1 Fit map J3977_class_00_00142_volume.mrc z flip in map J3977_class_03_00142_volume.mrc using 6115 points correlation = 0.9725, correlation about mean = 0.8601, overlap = 2909 steps = 44, shift = 0.0143, angle = 0.0162 degrees Position of J3977_class_00_00142_volume.mrc z flip (#5) relative to J3977_class_03_00142_volume.mrc (#1) coordinates: Matrix rotation and translation -0.99754942 0.02519611 -0.06527087 405.29719322 0.06964248 0.26808225 -0.96087554 311.87541512 -0.00671237 -0.96306647 -0.26918001 438.93275976 Axis -0.02978898 -0.79618924 0.60431392 Axis point 191.77820368 0.00000000 342.50753611 Rotation angle (degrees) 177.89251633 Shift along axis 4.86793646 > volume #1 level 0.3043 > volume #1 level 0.2513 > volume sel hide > volume #1 level 0.1453 > volume #4 level 0.1961 > close #4 > volume #5 level 0.2122 > volume #1 level 0.2053 > fitmap #5 inMap #1 Fit map J3977_class_00_00142_volume.mrc z flip in map J3977_class_03_00142_volume.mrc using 7583 points correlation = 0.9685, correlation about mean = 0.8754, overlap = 2994 steps = 48, shift = 0.038, angle = 0.0347 degrees Position of J3977_class_00_00142_volume.mrc z flip (#5) relative to J3977_class_03_00142_volume.mrc (#1) coordinates: Matrix rotation and translation -0.99750974 0.02523858 -0.06585823 405.37295159 0.07022047 0.26819842 -0.96080105 311.75529366 -0.00658618 -0.96303302 -0.26930280 438.93804803 Axis -0.02998281 -0.79622383 0.60425876 Axis point 191.71948602 0.00000000 342.50624022 Rotation angle (degrees) 177.86691692 Shift along axis 4.85094606 > fitmap #5 inMap #1 Fit map J3977_class_00_00142_volume.mrc z flip in map J3977_class_03_00142_volume.mrc using 7583 points correlation = 0.9684, correlation about mean = 0.8752, overlap = 2994 steps = 44, shift = 0.0584, angle = 0.026 degrees Position of J3977_class_00_00142_volume.mrc z flip (#5) relative to J3977_class_03_00142_volume.mrc (#1) coordinates: Matrix rotation and translation -0.99752439 0.02490787 -0.06576214 405.45522347 0.07003701 0.26791788 -0.96089271 311.91208460 -0.00631494 -0.96311971 -0.26899910 438.84730228 Axis -0.02982470 -0.79613522 0.60438332 Axis point 191.77259653 0.00000000 342.57395662 Rotation angle (degrees) 177.86037271 Shift along axis 4.81521528 > select subtract #5 Nothing selected > show #!5 models > volume #5 level 0.2525 > hide #!5 models > show #!1 models > volume #1 level 0.2795 > volume #1 level 0.276 > volume #1 level 0.08519 > volume #1 level 0.1665 > volume #2 level 0.1703 > volume #2 level 0.1327 > volume #2 level 0.1928 > volume #1 level 0.223 > fitmap #1 inMap #2 Fit map J3977_class_03_00142_volume.mrc in map J3977_class_02_00142_volume.mrc using 7452 points correlation = 0.9571, correlation about mean = 0.8286, overlap = 2948 steps = 84, shift = 1.2, angle = 2.65 degrees Position of J3977_class_03_00142_volume.mrc (#1) relative to J3977_class_02_00142_volume.mrc (#2) coordinates: Matrix rotation and translation 0.99892948 -0.04344038 -0.01590040 11.73510950 0.04345212 0.99905543 0.00039400 -9.71668965 0.01586826 -0.00108448 0.99987350 -3.49169470 Axis -0.01597843 -0.34333482 0.93907715 Axis point 230.39658326 264.41720009 0.00000000 Rotation angle (degrees) 2.65172634 Shift along axis -0.13040143 > hide #!1 models > volume #2 level 0.08769 > volume #2 level 0.0539 > volume #2 level 0.03889 > volume #3 level 0.03877 > volume #3 level 0.08037 > volume #2 level 0.0539 > volume #2 level 0.06517 > volume #2 level 0.07267 > volume #2 level 0.07643 > volume #2 level 0.08018 > volume #!2 hide > volume #5 level 0.06724 > volume #5 level 0.1156 > volume #5 level 0.5102 > volume #5 level 0.3088 > volume #5 level 0.2364 > volume #5 level 0.2202 > volume #5 level 0.2162 > volume #5 level 0.2122 > volume #5 level 0.2082 > volume #5 level 0.2041 > volume #5 level 0.2001 > volume #5 level 0.1961 > volume #5 level 0.1921 > volume #5 level 0.188 > volume #5 level 0.184 > volume #5 level 0.18 > volume #5 level 0.176 > volume #5 level 0.1719 > volume #5 level 0.1679 > volume #5 level 0.1639 > volume #5 level 0.1598 > volume #5 level 0.1558 > volume #5 level 0.1518 > volume #5 level 0.1478 > volume #5 level 0.1437 > volume #5 level 0.1397 > open /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3954_006_volume_map.mrc Opened cryosparc_P9_J3954_006_volume_map.mrc as #4, grid size 324,324,324, pixel 1.22, shown at level 0.0183, step 2, values float32 > volume #!4-5 hide > volume #4 level 0.06737 > volume #4 level 0.08168 > volume #4 level 0.03262 > volume #4 level 0.0551 > volume #4 level 0.0735 > ui tool show Segmentations > ui view fourup Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/segmentations/ui/orthoplanes.py"", line 1580, in _surfaceChosen self._update_position_label_text() File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/segmentations/ui/orthoplanes.py"", line 764, in _update_position_label_text dicom_data = self.view.drawing.parent.data.dicom_data ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'MRCGrid' object has no attribute 'dicom_data' AttributeError: 'MRCGrid' object has no attribute 'dicom_data' File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/segmentations/ui/orthoplanes.py"", line 764, in _update_position_label_text dicom_data = self.view.drawing.parent.data.dicom_data ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/segmentations/ui/orthoplanes.py"", line 1580, in _surfaceChosen self._update_position_label_text() File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/segmentations/ui/orthoplanes.py"", line 764, in _update_position_label_text dicom_data = self.view.drawing.parent.data.dicom_data ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'MRCGrid' object has no attribute 'dicom_data' AttributeError: 'MRCGrid' object has no attribute 'dicom_data' File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/segmentations/ui/orthoplanes.py"", line 764, in _update_position_label_text dicom_data = self.view.drawing.parent.data.dicom_data ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/segmentations/ui/orthoplanes.py"", line 1580, in _surfaceChosen self._update_position_label_text() File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/segmentations/ui/orthoplanes.py"", line 764, in _update_position_label_text dicom_data = self.view.drawing.parent.data.dicom_data ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'MRCGrid' object has no attribute 'dicom_data' AttributeError: 'MRCGrid' object has no attribute 'dicom_data' File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/segmentations/ui/orthoplanes.py"", line 764, in _update_position_label_text dicom_data = self.view.drawing.parent.data.dicom_data ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. > close session > open /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3954_006_volume_map.mrc Opened cryosparc_P9_J3954_006_volume_map.mrc as #1, grid size 324,324,324, pixel 1.22, shown at level 0.0183, step 2, values float32 > volume #1 level 0.03022 > ui tool show ""Segment Map"" > volume #1 level 0.06089 Segmenting cryosparc_P9_J3954_006_volume_map.mrc, density threshold 0.060885 Showing 17 region surfaces 1782 watershed regions, grouped to 17 regions Showing cryosparc_P9_J3954_006_volume_map.seg - 17 regions, 17 surfaces > select #2.4 1 model selected Saving 1 regions to mrc file... Opened cryosparc_P9_J3954_006_volume_map_region_2128.mrc as #3, grid size 42,45,72, pixel 1.22, shown at step 1, values float32 Wrote cryosparc_P9_J3954_006_volume_map_region_2128.mrc > volume resample #3 onGrid #1 Opened cryosparc_P9_J3954_006_volume_map_region_2128.mrc resampled as #4, grid size 324,324,324, pixel 1.22, shown at step 1, values float32 > save > /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3954_006_volume_map_region_2128.mrc > models #4 > volume #1 level 0.07315 > close session > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V2_holo- > coot-2.pdb Summary of feedback from opening /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V2_holo- coot-2.pdb --- warnings | Duplicate atom serial number found: 8964 Duplicate atom serial number found: 8965 Duplicate atom serial number found: 8966 Duplicate atom serial number found: 8967 Duplicate atom serial number found: 8968 26 messages similar to the above omitted Chain information for V2_holo-coot-2.pdb #1 --- Chain | Description A | No description available B | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V3_holo- > coot-2.pdb Summary of feedback from opening /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V3_holo- coot-2.pdb --- warnings | Duplicate atom serial number found: 8964 Duplicate atom serial number found: 8965 Duplicate atom serial number found: 8966 Duplicate atom serial number found: 8967 Duplicate atom serial number found: 8968 26 messages similar to the above omitted Chain information for V3_holo-coot-2.pdb #2 --- Chain | Description A | No description available B | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V4_holo- > coot-3.pdb Summary of feedback from opening /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V4_holo- coot-3.pdb --- warnings | Duplicate atom serial number found: 8965 Duplicate atom serial number found: 8966 Duplicate atom serial number found: 8967 Duplicate atom serial number found: 8968 Duplicate atom serial number found: 8969 30 messages similar to the above omitted Chain information for V4_holo-coot-3.pdb #3 --- Chain | Description A | No description available B | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V5_holo- > coot-1.pdb Summary of feedback from opening /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V5_holo- coot-1.pdb --- warnings | Duplicate atom serial number found: 8965 Duplicate atom serial number found: 8966 Duplicate atom serial number found: 8967 Duplicate atom serial number found: 8968 Duplicate atom serial number found: 8969 17 messages similar to the above omitted Chain information for V5_holo-coot-1.pdb #4 --- Chain | Description A | No description available B | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V6_holo- > coot-1.pdb Summary of feedback from opening /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V6_holo- coot-1.pdb --- warnings | Duplicate atom serial number found: 8965 Duplicate atom serial number found: 8966 Duplicate atom serial number found: 8967 Duplicate atom serial number found: 8968 Duplicate atom serial number found: 8969 20 messages similar to the above omitted Chain information for V6_holo-coot-1.pdb #5 --- Chain | Description A | No description available B | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V7_holo- > coot-2.pdb Chain information for V7_holo-coot-2.pdb #6 --- Chain | Description A | No description available B | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V9_holo- > coot-0.pdb Summary of feedback from opening /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V9_holo- coot-0.pdb --- warnings | Duplicate atom serial number found: 8965 Duplicate atom serial number found: 8966 Duplicate atom serial number found: 8967 Duplicate atom serial number found: 8968 Duplicate atom serial number found: 8969 24 messages similar to the above omitted Chain information for V9_holo-coot-0.pdb #7 --- Chain | Description A | No description available B | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V10_holo- > coot-1.pdb Chain information for V10_holo-coot-1.pdb #8 --- Chain | Description A | No description available B | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V11_holo- > coot-1.pdb Summary of feedback from opening /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V11_holo- coot-1.pdb --- warnings | Duplicate atom serial number found: 8965 Duplicate atom serial number found: 8966 Duplicate atom serial number found: 8967 Duplicate atom serial number found: 8968 Duplicate atom serial number found: 8969 29 messages similar to the above omitted Chain information for V11_holo-coot-1.pdb #9 --- Chain | Description A | No description available B | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V12_holo- > coot-3.pdb Chain information for V12_holo-coot-3.pdb #10 --- Chain | Description A | No description available B | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V14_holo- > coot-1.pdb Summary of feedback from opening /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V14_holo- coot-1.pdb --- warnings | Duplicate atom serial number found: 8964 Duplicate atom serial number found: 8965 Duplicate atom serial number found: 8966 Duplicate atom serial number found: 8967 Duplicate atom serial number found: 8968 28 messages similar to the above omitted Chain information for V14_holo-coot-1.pdb #11 --- Chain | Description A | No description available B | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V15_holo- > coot-1.pdb Summary of feedback from opening /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V15_holo- coot-1.pdb --- warnings | Duplicate atom serial number found: 8965 Duplicate atom serial number found: 8966 Duplicate atom serial number found: 8968 Duplicate atom serial number found: 8969 Duplicate atom serial number found: 8970 20 messages similar to the above omitted Chain information for V15_holo-coot-1.pdb #12 --- Chain | Description A | No description available B | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V17_holo- > coot-3.pdb Summary of feedback from opening /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V17_holo- coot-3.pdb --- warnings | Duplicate atom serial number found: 8965 Duplicate atom serial number found: 8966 Duplicate atom serial number found: 8967 Duplicate atom serial number found: 8968 Duplicate atom serial number found: 8969 22 messages similar to the above omitted Chain information for V17_holo-coot-3.pdb #13 --- Chain | Description A | No description available B | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V18_holo- > coot-1.pdb Summary of feedback from opening /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V18_holo- coot-1.pdb --- warnings | Duplicate atom serial number found: 8965 Duplicate atom serial number found: 8966 Duplicate atom serial number found: 8967 Duplicate atom serial number found: 8968 Duplicate atom serial number found: 8969 24 messages similar to the above omitted Chain information for V18_holo-coot-1.pdb #14 --- Chain | Description A | No description available B | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V19_holo- > coot-6.pdb Summary of feedback from opening /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V19_holo- coot-6.pdb --- warnings | Duplicate atom serial number found: 8965 Duplicate atom serial number found: 8966 Duplicate atom serial number found: 8967 Duplicate atom serial number found: 8968 Duplicate atom serial number found: 8969 26 messages similar to the above omitted Chain information for V19_holo-coot-6.pdb #15 --- Chain | Description A | No description available B | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V21_holo- > coot-2.pdb Summary of feedback from opening /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V21_holo- coot-2.pdb --- warnings | Duplicate atom serial number found: 8964 Duplicate atom serial number found: 8965 Duplicate atom serial number found: 8966 Duplicate atom serial number found: 8967 Duplicate atom serial number found: 8968 23 messages similar to the above omitted Chain information for V21_holo-coot-2.pdb #16 --- Chain | Description A | No description available B | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V23_holo- > coot-2.pdb Chain information for V23_holo-coot-2.pdb #17 --- Chain | Description A | No description available B | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V25_holo- > coot-2.pdb Summary of feedback from opening /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V25_holo- coot-2.pdb --- warnings | Duplicate atom serial number found: 8964 Duplicate atom serial number found: 8965 Duplicate atom serial number found: 8966 Duplicate atom serial number found: 8967 Duplicate atom serial number found: 8968 30 messages similar to the above omitted Chain information for V25_holo-coot-2.pdb #18 --- Chain | Description A | No description available B | No description available Computing secondary structure > select #1/A:59, 60, 78, 79,49, 51, 394, 395,49, 394, 395,272, 273, 274, > 275,113, 114, 136,277, 278, 329, 330, 331,274, 275, 276, 277, 301,256, 257, > 258,100, 101, 102, 103, 104,100, 101, 102, 103,285, 298, 299,291, 292, 293, > 294,299, 300, 301, 302,49, 50, 51, 388, 389, 390,59, 60, 78, 79,80, 81 983 atoms, 1091 bonds, 45 residues, 1 model selected > hide #2-18 target m > select #1/A:59, 60, 78, 79,49, 51, 394, 395,49, 394, 395,272, 273, 274, > 275,113, 114, 136,277, 278, 329, 330, 331,274, 275, 276, 277, 301,256, 257, > 258,100, 101, 102, 103, 104,100, 101, 102, 103,285, 298, 299,291, 292, 293, > 294,299, 300, 301, 302,49, 50, 51, 388, 389, 390,59, 60, 78, 79,80, 81 983 atoms, 1091 bonds, 45 residues, 1 model selected > select #8/A:100, 101, 102, 103,256, 257, 258,261, 271, 272, 273,26, 27, 28, > 41,275, 276, 332, 333,275, 276, 333,49, 50, 51, 388, 389, 390,48, 50, 386, > 387, 399,385, 386, 387,291, 292, 293, 294,277, 278, 329, 330, 331,275, 276, > 333,113, 114, 136,15, 16, 17,25, 26, 274, 332,25, 26, 332,26, 274, 332,272, > 273, 274,272, 273, 274, 275,273, 333,337, 338, 388,337, 388,382, 383, > 384,49, 389, 390, 392, 393,49, 394, 395,49, 51, 394, 395,56, 57, 254,59, 60, > 78, 79,61, 81, 250,80, 81 1459 atoms, 1618 bonds, 67 residues, 1 model selected > show #8 models > hide #1 models > select > #1/A:15,21-29,39-67,69-84,96-101,105-112,249-261,272-293,295-312,327-340,386-400 3255 atoms, 3639 bonds, 151 residues, 1 model selected > hide #8 models > show #1 models > show #2-18 target m > ui tool show Matchmaker > matchmaker #2-18 to #1 & sel matrix Nucleic Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V3_holo-coot-2.pdb, chain A (#2), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.380 angstroms; (across all 151 pairs: 0.413) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V4_holo-coot-3.pdb, chain A (#3), sequence alignment score = 604 RMSD between 151 pruned atom pairs is 0.322 angstroms; (across all 151 pairs: 0.322) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V5_holo-coot-1.pdb, chain A (#4), sequence alignment score = 604 RMSD between 151 pruned atom pairs is 0.445 angstroms; (across all 151 pairs: 0.445) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V6_holo-coot-1.pdb, chain A (#5), sequence alignment score = 604 RMSD between 151 pruned atom pairs is 0.365 angstroms; (across all 151 pairs: 0.365) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V7_holo-coot-2.pdb, chain A (#6), sequence alignment score = 604 RMSD between 151 pruned atom pairs is 0.323 angstroms; (across all 151 pairs: 0.323) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V9_holo-coot-0.pdb, chain A (#7), sequence alignment score = 604 RMSD between 151 pruned atom pairs is 0.325 angstroms; (across all 151 pairs: 0.325) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V10_holo-coot-1.pdb, chain A (#8), sequence alignment score = 604 RMSD between 151 pruned atom pairs is 0.364 angstroms; (across all 151 pairs: 0.364) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V11_holo-coot-1.pdb, chain A (#9), sequence alignment score = 604 RMSD between 151 pruned atom pairs is 0.374 angstroms; (across all 151 pairs: 0.374) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V12_holo-coot-3.pdb, chain A (#10), sequence alignment score = 604 RMSD between 151 pruned atom pairs is 0.367 angstroms; (across all 151 pairs: 0.367) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V14_holo-coot-1.pdb, chain A (#11), sequence alignment score = 604 RMSD between 149 pruned atom pairs is 0.402 angstroms; (across all 151 pairs: 0.464) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V15_holo-coot-1.pdb, chain A (#12), sequence alignment score = 604 RMSD between 151 pruned atom pairs is 0.359 angstroms; (across all 151 pairs: 0.359) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V17_holo-coot-3.pdb, chain A (#13), sequence alignment score = 604 RMSD between 149 pruned atom pairs is 0.351 angstroms; (across all 151 pairs: 0.441) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V18_holo-coot-1.pdb, chain A (#14), sequence alignment score = 604 RMSD between 151 pruned atom pairs is 0.367 angstroms; (across all 151 pairs: 0.367) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V19_holo-coot-6.pdb, chain A (#15), sequence alignment score = 604 RMSD between 151 pruned atom pairs is 0.488 angstroms; (across all 151 pairs: 0.488) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V21_holo-coot-2.pdb, chain A (#16), sequence alignment score = 604 RMSD between 151 pruned atom pairs is 0.445 angstroms; (across all 151 pairs: 0.445) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V23_holo-coot-2.pdb, chain A (#17), sequence alignment score = 604 RMSD between 151 pruned atom pairs is 0.368 angstroms; (across all 151 pairs: 0.368) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V25_holo-coot-2.pdb, chain A (#18), sequence alignment score = 604 RMSD between 151 pruned atom pairs is 0.430 angstroms; (across all 151 pairs: 0.430) > select 178904 atoms, 198000 bonds, 10136 residues, 18 models selected > hide sel target a > select #1/C 31 atoms, 31 residues, 1 model selected > select #1-18/C 542 atoms, 542 residues, 18 models selected > show sel target ab > style sel sphere Changed 542 atom styles > hide #2-18 target m > hide #1 models > show #1 models > show #2 models > hide #1 models > show #1 models > hide #1 models > show #3 models > hide #3 models > show #4 models > hide #4 models > show #5 models > hide #5 models > show #6 models > hide #6 models > show #7 models > hide #7 models > show #8 models > hide #8 models > show #9 models > hide #9 models > show #10 models > hide #10 models > show #11 models > show #12 models > show #13 models > hide #13 models > show #13 models > hide #13 models > show #14 models > hide #14 models > show #15 models > show #16 models > show #17 models > hide #17 models > show #18 models > select #1-18/C/7 542 atoms, 542 residues, 18 models selected > select #1-18/C:7 18 atoms, 18 residues, 18 models selected > select #1-18/C:4 18 atoms, 18 residues, 18 models selected > select #1-18/C:24 12 atoms, 12 residues, 12 models selected > select clear > hide #2 models > hide #11 models > hide #12 models > hide #15 models > hide #16 models > hide #18 models > show #1 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #3 models > show #2 models > show #4 models > show #5 models > hide #5 models > show #5 models > show #6 models > show #7 models > show #8 models > show #9 models > show #10 models > show #11 models > show #12 models > show #13 models > show #14 models > show #15 models > show #16 models > show #17 models > show #18 models > set bgColor white > select #1-18/A 161316 atoms, 180684 bonds, 7506 residues, 18 models selected > ui tool show ""Color Actions"" > color sel light slate gray > select #1-18/B 17046 atoms, 17316 bonds, 2088 residues, 18 models selected > ui tool show ""Color Actions"" > color sel plum > surface sel > surface hidePatches (#!1-18 & sel) > select #1/B 947 atoms, 962 bonds, 116 residues, 1 model selected > surface (#!1 & sel) > surface hidePatches (#!1 & sel) > surface (#!1 & sel) > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for V2_holo-coot-2.pdb_B SES surface #1.1: minimum, -9.82, mean 5.09, maximum 22.28 To also show corresponding color key, enter the above coulombic command and add key true > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > surface hidePatches (#!1 & sel) > select #1-18/C:1 7 atoms, 7 residues, 7 models selected > select #1-18/A:50,389,390 1188 atoms, 1314 bonds, 54 residues, 18 models selected > cartoon hide sel > show sel target ab > hide (sel-residues & (protein|nucleic)) target a > cartoon hide sel-residues > show (sel-residues & backbone) target ab > hide sel target a > hide (sel-residues & (protein|nucleic)) target a > cartoon hide sel-residues > show (sel-residues & backbone) target ab > hide (sel-residues & (protein|nucleic)) target a > cartoon hide sel-residues > show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab > show (sel-residues & sidechain) target ab > hide (sel-residues & (protein|nucleic)) target a > cartoon hide sel-residues > show (sel-residues & backbone) target ab > hide sel target a > hide (sel-residues & (protein|nucleic)) target a > cartoon hide sel-residues > show (sel-residues & backbone) target ab > nucleotides sel atoms > style nucleic & sel stick Changed 1188 atom styles > select #1-18/A:7 360 atoms, 378 bonds, 18 residues, 18 models selected > select #1-18/A:50,389,390 1188 atoms, 1314 bonds, 54 residues, 18 models selected > color sel red > select #6/A:392 22 atoms, 24 bonds, 1 residue, 1 model selected > select #15/A:393 20 atoms, 21 bonds, 1 residue, 1 model selected > select #3/C:68@MG 1 atom, 1 residue, 1 model selected > select up 35 atoms, 35 residues, 1 model selected > select #1-18/C:7 18 atoms, 18 residues, 18 models selected > ui tool show ""Selection Inspector"" > size sel atomRadius 0.7 Changed 18 atom radii > color sel red > select #1-18/A:50,389,390 1188 atoms, 1314 bonds, 54 residues, 18 models selected > ui tool show ""Color Actions"" > color sel brown > color sel coral > color sel orange > color sel coral > color sel tomato > color sel coral > select #14/C:80@MG 1 atom, 1 residue, 1 model selected > select add #13/C:7@MG 2 atoms, 2 residues, 2 models selected > ui tool show Distances > distance #14/C:80@MG #13/C:7@MG Distance between V18_holo-coot-1.pdb #14/C MG 80 MG and V17_holo-coot-3.pdb #13/C MG 7 MG: 14.313Å > select #10/C:80@MG 1 atom, 1 residue, 1 model selected > select add #12/C:7@MG 2 atoms, 2 residues, 2 models selected > distance #10/C:80@MG #12/C:7@MG Distance between V12_holo-coot-3.pdb #10/C MG 80 MG and V15_holo-coot-1.pdb #12/C MG 7 MG: 12.866Å > hide #!1-18 target m > show #!1 models > show #!2 models > show #!3 models > show #!4 models > show #!5 models > show #!6 models > hide #!6 models > show #!6 models > show #!7 models > show #!8 models > show #!9 models > show #!10 models > hide #!10 models > show #!10 models > show #!11 models > show #!12 models > hide #!12 models > show #!12 models > show #!13 models > show #!14 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > select #6/C:24@MG 1 atom, 1 residue, 1 model selected > select add #6/C:75@MG 2 atoms, 2 residues, 1 model selected > distance #6/C:24@MG #6/C:75@MG Distance between V7_holo-coot-2.pdb #6/C MG 24 MG and MG 75 MG: 6.929Å > select #10/C:84@MG 1 atom, 1 residue, 1 model selected > select add #6/C:24@MG 2 atoms, 2 residues, 2 models selected > distance #10/C:84@MG #6/C:24@MG Distance between V12_holo-coot-3.pdb #10/C MG 84 MG and V7_holo-coot-2.pdb #6/C MG 24 MG: 3.368Å > select #6/C:24@MG 1 atom, 1 residue, 1 model selected > select add #5/C:7@MG 2 atoms, 2 residues, 2 models selected > distance #6/C:24@MG #5/C:7@MG Distance between V7_holo-coot-2.pdb #6/C MG 24 MG and V6_holo-coot-1.pdb #5/C MG 7 MG: 7.527Å > select #9/C:4@MG 1 atom, 1 residue, 1 model selected > select add #12/C:7@MG 2 atoms, 2 residues, 2 models selected > distance #9/C:4@MG #12/C:7@MG Distance between V11_holo-coot-1.pdb #9/C MG 4 MG and V15_holo-coot-1.pdb #12/C MG 7 MG: 9.036Å > ~distance #6/C:24@MG #6/C:75@MG > ~distance #9/C:4@MG #12/C:7@MG > ~distance #14/C:80@MG #13/C:7@MG > ~distance #10/C:84@MG #6/C:24@MG > ~distance #6/C:24@MG #5/C:7@MG > ~distance #10/C:80@MG #12/C:7@MG > select #1-18/A:50,389,390 1188 atoms, 1314 bonds, 54 residues, 18 models selected > ui tool show ""Color Actions"" > color sel tomato > color sel chocolate > color sel fire brick > color sel coral > color sel goldenrod > color (#!1-14 & sel) #ff2600ff > color sel sienna > color sel cyan > color sel medium blue > color sel cornflower blue > select #1-18/C:7 18 atoms, 18 residues, 18 models selected > color (#!1-14 & sel) blue > color sel red > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/pdb_models_YTZ/holoES- > pretRNA-5mM-Ca/Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb Chain information for Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb #19 --- Chain | Description A | No description available B | No description available C | No description available E | No description available Computing secondary structure > select up 542 atoms, 542 residues, 18 models selected > select up 178904 atoms, 198000 bonds, 10136 residues, 18 models selected > select > #1/A:15,21-29,39-67,69-84,96-101,105-112,249-261,272-293,295-312,327-340,386-400 3255 atoms, 3639 bonds, 151 residues, 1 model selected > ui tool show Matchmaker > matchmaker #19 to #1 & sel matrix Nucleic Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with Ternary_pretRNA_5mM_Ca- coot-7_real_space_refined_018.pdb, chain A (#19), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.728 angstroms; (across all 151 pairs: 0.766) > select #19 12016 atoms, 13315 bonds, 661 residues, 1 model selected > hide sel target a > select #19/C 1889 atoms, 2107 bonds, 89 residues, 1 model selected > hide #19 models > show #19 models > hide #19 models > show #19 models > color sel yellow > select #19/D 30 atoms, 30 residues, 1 model selected > show sel target ab > hide #19 models > show #19 models > hide #19 models > show #19 models > select #10/C:84@MG 1 atom, 1 residue, 1 model selected > select clear > select #10/C:84@MG 1 atom, 1 residue, 1 model selected > select add #11/A:390@OP2 2 atoms, 2 residues, 2 models selected > distance #10/C:84@MG #11/A:390@OP2 Distance between V12_holo-coot-3.pdb #10/C MG 84 MG and V14_holo-coot-1.pdb #11/A A 390 OP2: 3.278Å > select #10/C:84@MG 1 atom, 1 residue, 1 model selected > select #19/D:5@CA 1 atom, 1 residue, 1 model selected > select add #10/C:84@MG 2 atoms, 2 residues, 2 models selected > distance #19/D:5@CA #10/C:84@MG Distance between Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb #19/D CA 5 CA and V12_holo-coot-3.pdb #10/C MG 84 MG: 6.302Å > select #10/C:84@MG 1 atom, 1 residue, 1 model selected > select add #19/D:30@CA 2 atoms, 2 residues, 2 models selected > distance #10/C:84@MG #19/D:30@CA Distance between V12_holo-coot-3.pdb #10/C MG 84 MG and Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb #19/D CA 30 CA: 7.802Å > hide #19 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > select #13/C:24@MG 1 atom, 1 residue, 1 model selected > select #9/C:24@MG 1 atom, 1 residue, 1 model selected > select add #10/C:84@MG 2 atoms, 2 residues, 2 models selected > distance #9/C:24@MG #10/C:84@MG Distance between V11_holo-coot-1.pdb #9/C MG 24 MG and V12_holo-coot-3.pdb #10/C MG 84 MG: 3.570Å > select #10/C:84@MG 1 atom, 1 residue, 1 model selected > hide #!1-14 target m > show #!12 models > show #19 models > hide #19 models > show #19 models > hide #19 models > hide #!12 models > show #!10 models > show #19 models > select #19/C:0 20 atoms, 21 bonds, 1 residue, 1 model selected > select #19/C:1 23 atoms, 25 bonds, 1 residue, 1 model selected > select add #19/C:0 43 atoms, 46 bonds, 2 residues, 1 model selected > hide #19 models > show #!1-18 target m > select #10/C:80@MG 1 atom, 1 residue, 1 model selected > select clear > show #19 models > hide #19 models > show #19 models > hide #19 models > show #19 models > hide #19 models > select #1-18/ Expected an objects specifier or a keyword > select #1-18 178904 atoms, 198000 bonds, 2 pseudobonds, 10136 residues, 19 models selected > select #1-18/C 542 atoms, 1 pseudobond, 542 residues, 19 models selected > ui tool show ""Color Actions"" > color sel forest green > select #1-18/C:7 18 atoms, 18 residues, 18 models selected > ui tool show ""Color Actions"" > color sel dark red > color sel maroon > color sel dark red > ui tool show ""Selection Inspector"" > ~distance #10/C:84@MG #11/A:390@OP2 > ~distance #19/D:5@CA #10/C:84@MG > ~distance #9/C:24@MG #10/C:84@MG > ~distance #10/C:84@MG #19/D:30@CA > select #10/C:84@MG 1 atom, 1 residue, 1 model selected > select add #17/C:87@MG 2 atoms, 2 residues, 2 models selected > select #1-18/C 542 atoms, 542 residues, 18 models selected > ui tool show ""Selection Inspector"" > size sel atomRadius 0.7 Changed 542 atom radii > select #13/C:22@MG 1 atom, 1 residue, 1 model selected > select #1-18/C:9 16 atoms, 16 residues, 16 models selected [deleted to fit within ticket limits] > color sel #5e5e5e9f > color sel #5e5e5e9d > color sel #5e5e5e9b > color sel #5e5e5e99 > color sel #5e5e5e97 > color sel #5e5e5e93 > color sel #5e5e5e91 > color sel #5e5e5e8f > color sel #5e5e5e8d > color sel #5e5e5e8a > color sel #5e5e5e87 > color sel #5e5e5e85 > color sel #5e5e5e82 > color sel #5e5e5e80 > color sel #5e5e5e7f > color sel #5e5e5e7d > color sel #5e5e5e7c > color sel #5e5e5e7b [Repeated 1 time(s)] > color sel #5e5e5e7a [Repeated 1 time(s)] > color sel #5e5e5e78 > color sel #5e5e5e77 > color sel #5e5e5e76 > color sel #5e5e5e75 > color sel #5e5e5e74 [Repeated 1 time(s)] > color sel #5e5e5e73 [Repeated 2 time(s)] > color sel #5e5e5e72 [Repeated 3 time(s)] > color sel #5e5e5e71 > color sel #5e5e5e70 [Repeated 1 time(s)] > color sel #5e5e5e6f [Repeated 1 time(s)] > color sel #5e5e5e6e > color sel #5e5e5e6d [Repeated 1 time(s)] > color sel #5e5e5e6c [Repeated 2 time(s)] > color sel #5e5e5e6b [Repeated 2 time(s)] > color sel #5e5e5e6a [Repeated 1 time(s)] > color sel #5e5e5e69 [Repeated 4 time(s)] > color sel #5e5e5e68 [Repeated 2 time(s)] > color sel #5e5e5e67 [Repeated 2 time(s)] > color sel #5e5e5e66 [Repeated 2 time(s)] > color sel #5e5e5e65 [Repeated 4 time(s)] > color sel #5e5e5e64 [Repeated 2 time(s)] > color sel #5e5e5e63 [Repeated 1 time(s)] > color sel #5e5e5e64 > color sel #5e5e5e65 > color sel #5e5e5e67 > color sel #5e5e5e68 > color sel #5e5e5e6a > color sel #5e5e5e6c > color sel #5e5e5e6d > color sel #5e5e5e6e > color sel #5e5e5e70 > color sel #5e5e5e71 > color sel #5e5e5e72 > color sel #5e5e5e74 > color sel #5e5e5e75 > color sel #5e5e5e77 > color sel #5e5e5e79 > color sel #5e5e5e7a > color sel #5e5e5e7b > color sel #5e5e5e7c > color sel #5e5e5e7d > color sel #5e5e5e7e [Repeated 1 time(s)] > color sel #5e5e5e7f [Repeated 1 time(s)] > color sel #5e5e5e80 > color sel #5e5e5e84 [Repeated 1 time(s)] > color sel #5e5e5e86 > color sel #5e5e5e87 > color sel #5e5e5e89 > color sel #5e5e5e8a > color sel #5e5e5e8b [Repeated 1 time(s)] > color sel #5e5e5e8c > color sel #5e5e5e8d > color sel #5e5e5e8e > color sel #5e5e5e8f > color sel #5e5e5e90 > color sel #5e5e5e91 > color sel #5e5e5e93 > color sel #5e5e5e95 > color sel #5e5e5e96 > color sel #5e5e5e99 > color sel #5e5e5e9c > color sel #5e5e5e9f > color sel #5e5e5ea2 > color sel #5e5e5ea4 > color sel #5e5e5ea5 > color sel #5e5e5ea6 > color sel #5e5e5ea7 > color sel #5e5e5ea8 > color sel #5e5e5eaa > color sel #5e5e5eae > color sel #5e5e5eb1 > color sel #5e5e5eb5 > color sel #5e5e5ebc > color sel #5e5e5ec2 > color sel #5e5e5ec4 > color sel #5e5e5ec6 [Repeated 1 time(s)] > color sel #5e5e5ec7 > color sel #5e5e5ec8 [Repeated 1 time(s)] > color sel #5e5e5ec9 > color sel #5e5e5ecd > color sel #5e5e5ecf > color sel #5e5e5ed6 > color sel #5e5e5edd > color sel #5e5e5ee2 > color sel #5e5e5ee4 > color sel #5e5e5ee5 > color sel #5e5e5ee6 [Repeated 1 time(s)] > color sel #5e5e5ee7 > color sel #5e5e5ee8 > color sel #5e5e5ee9 > color sel #5e5e5eeb > color sel #5e5e5eed > color sel #5e5e5ef0 > color sel #5e5e5ef4 > color sel #5e5e5ef8 > color sel #5e5e5efb > color sel #5e5e5efd > color sel #5e5e5eff [Repeated 1 time(s)] > color sel #4c4c4cff [Repeated 1 time(s)] > color sel #4d4d4dff > color sel #4e4e4eff [Repeated 1 time(s)] > color sel #4f4f4fff > color sel #505050ff > color sel #515151ff [Repeated 1 time(s)] > color sel #525252ff [Repeated 1 time(s)] > color sel #535353ff > color sel #545454ff [Repeated 2 time(s)] > color sel #555555ff > color sel #565656ff [Repeated 1 time(s)] > color sel #575757ff > color sel #595959ff > color sel #5a5a5aff > color sel #5b5b5bff > color sel #5c5c5cff > color sel #5d5d5dff > color sel #5e5e5eff > color sel #5f5f5fff > color sel #616161ff > color sel #636363ff > color sel #656565ff > color sel #696969ff > color sel #6b6b6bff > color sel #717171ff > color sel #767676ff > color sel #7a7a7aff > color sel #7d7d7dff > color sel #808080ff > color sel #848484ff > color sel #868686ff > color sel #878787ff > color sel #898989ff > color sel #8b8b8bff > color sel #8c8c8cff > color sel #8f8f8fff > color sel #909090ff > color sel #929292ff > color sel #939393ff > color sel #949494ff [Repeated 1 time(s)] > color sel #959595ff [Repeated 3 time(s)] > color sel #969696ff > color sel #979797ff > color sel #989898ff [Repeated 1 time(s)] > color sel #999999ff [Repeated 1 time(s)] > color sel #9a9a9aff [Repeated 1 time(s)] > color sel #9b9b9bff > color sel #9c9c9cff [Repeated 1 time(s)] > color sel #9d9d9dff [Repeated 1 time(s)] > color sel #9e9e9eff > color sel #9f9f9fff > color sel #a0a0a0ff > color sel #a1a1a1ff > color sel #a3a3a3ff > color sel #a4a4a4ff > color sel #a6a6a6ff > color sel #a7a7a7ff > color sel #a8a8a8ff > color sel #aaaaaaff > color sel #abababff > color sel #acacacff > color sel #aeaeaeff > color sel #b0b0b0ff > color sel #b1b1b1ff > color sel #b2b2b2ff > color sel #b3b3b3ff > color sel #b4b4b4ff [Repeated 1 time(s)] > color sel #b5b5b5ff > color sel #b6b6b6ff [Repeated 1 time(s)] > color sel #b7b7b7ff [Repeated 5 time(s)] > color sel #b8b8b8ff [Repeated 4 time(s)] > color sel #b7b7b7ff [Repeated 1 time(s)] > color sel #b6b6b6ff > color sel #b5b5b5ff > color sel #b3b3b3ff > color sel #afafafff > color sel #a4a4a4ff > color sel #989898ff > color sel #8f8f8fff > color sel #878787ff > color sel #828282ff > color sel #7c7c7cff > color sel #767676ff > color sel #727272ff > color sel #6d6d6dff > color sel #686868ff > color sel #646464ff > color sel #606060ff > color sel #5b5b5bff > color sel #585858ff > color sel #535353ff > color sel #4f4f4fff > color sel #4c4c4cff > color sel #4a4a4aff > color sel #474747ff > color sel #454545ff > color sel #444444ff > color sel #424242ff > color sel #404040ff > color sel #3f3f3fff > color sel #3d3d3dff > color sel #3b3b3bff > color sel #3a3a3aff > color sel #383838ff > color sel #373737ff [Repeated 1 time(s)] > color sel #363636ff > color sel #353535ff > color sel #343434ff > color sel #333333ff > color sel #313131ff [Repeated 1 time(s)] > color sel #303030ff > color sel #2f2f2fff [Repeated 3 time(s)] > color sel #2e2e2eff [Repeated 2 time(s)] > color sel #2d2d2dff [Repeated 2 time(s)] > color sel #2e2e2eff > color sel #303030ff > color sel #343434ff > color sel #393939ff > color sel #3d3d3dff > color sel #434343ff > color sel #4a4a4aff > color sel #4d4d4dff > color sel #515151ff > color sel #525252ff > color sel #535353ff > color sel #545454ff > color sel #555555ff > color sel #565656ff > color sel #575757ff > color sel #585858ff [Repeated 1 time(s)] > color sel #595959ff > color sel #5a5a5aff > color sel #5c5c5cff > color sel #5e5e5eff > color sel #5f5f5fff > color sel #606060ff > color sel #616161ff [Repeated 1 time(s)] > color sel #626262ff [Repeated 3 time(s)] > color sel #636363ff [Repeated 1 time(s)] > color sel #646464ff [Repeated 2 time(s)] > color sel #656565ff [Repeated 1 time(s)] > color sel #666666ff [Repeated 2 time(s)] > color sel #676767ff [Repeated 1 time(s)] > color sel #686868ff [Repeated 1 time(s)] > color sel #696969ff > color sel #6a6a6aff > color sel #6b6b6bff [Repeated 1 time(s)] > color sel #6a6a6aff > color sel #686868ff > color sel #676767ff > color sel #666666ff > color sel #646464ff [Repeated 1 time(s)] > color sel #626262ff > color sel #616161ff > color sel #5f5f5fff [Repeated 1 time(s)] > color sel #5e5e5eff > color sel #5d5d5dff [Repeated 1 time(s)] > color sel #5c5c5cff [Repeated 1 time(s)] > color sel #5b5b5bff [Repeated 2 time(s)] > color sel #5a5a5aff [Repeated 1 time(s)] > color sel #595959ff [Repeated 2 time(s)] > color sel #585858ff [Repeated 2 time(s)] > color sel #575757ff [Repeated 1 time(s)] > color sel #565656ff [Repeated 1 time(s)] > color sel #555555ff [Repeated 1 time(s)] > color sel #545454ff [Repeated 2 time(s)] > color sel #535353ff [Repeated 1 time(s)] > color sel #525252ff [Repeated 1 time(s)] > color sel #515151ff > color sel #505050ff [Repeated 1 time(s)] > color sel #4f4f4fff [Repeated 2 time(s)] > color sel #4e4e4eff > color sel #4d4d4dff [Repeated 2 time(s)] > color sel #4c4c4cff [Repeated 1 time(s)] > color sel #4b4b4bff [Repeated 2 time(s)] > color sel #4a4a4aff [Repeated 2 time(s)] > color sel #494949ff [Repeated 2 time(s)] > color sel #484848ff [Repeated 3 time(s)] > color sel #474747ff [Repeated 3 time(s)] > color sel #464646ff [Repeated 2 time(s)] > color sel #454545ff [Repeated 5 time(s)] > color sel #464646ff > color sel #474747ff > color sel #494949ff > color sel #4b4b4bff > color sel #4c4c4cff > color sel #4d4d4dff > color sel #4e4e4eff > color sel #505050ff > color sel #515151ff [Repeated 1 time(s)] > color sel #525252ff [Repeated 2 time(s)] > color sel #535353ff [Repeated 1 time(s)] > color sel #545454ff [Repeated 2 time(s)] > color sel #555555ff [Repeated 1 time(s)] > color sel #565656ff > color sel #575757ff > color sel #585858ff [Repeated 1 time(s)] > color sel #595959ff [Repeated 2 time(s)] > color sel #5a5a5aff [Repeated 2 time(s)] > color sel #5b5b5bff > color sel #5c5c5cff > color sel #5f5f5fff > color sel #606060ff > color sel #626262ff > color sel #646464ff > color sel #656565ff > color sel #676767ff > color sel #696969ff > color sel #6a6a6aff > color sel #6c6c6cff > color sel #6e6e6eff > color sel #6f6f6fff > color sel #717171ff > color sel #737373ff > color sel #757575ff > color sel #767676ff > color sel #787878ff > color sel #797979ff > color sel #7a7a7aff > color sel #7b7b7bff > color sel #7c7c7cff > color sel #7d7d7dff > color sel #7f7f7fff > color sel #808080ff > color sel #848484ff > color sel #858585ff > color sel #878787ff > color sel #898989ff > color sel #8a8a8aff > color sel #8c8c8cff > color sel #8e8e8eff > color sel #8f8f8fff > color sel #919191ff > color sel #929292ff > color sel #949494ff > color sel #969696ff > color sel #979797ff > color sel #989898ff > color sel #999999ff [Repeated 2 time(s)] > color sel #989898ff > color sel #949494ff > color sel #8a8a8aff > color sel #838383ff > color sel #7d7d7dff > color sel #7a7a7aff > color sel #777777ff > color sel #747474ff > color sel #717171ff > color sel #6f6f6fff > color sel #6d6d6dff > color sel #6b6b6bff > color sel #696969ff > color sel #676767ff > color sel #666666ff > color sel #646464ff > color sel #636363ff > color sel #616161ff > color sel #606060ff > color sel #5f5f5fff > color sel #5e5e5eff [Repeated 2 time(s)] > color sel #5d5d5dff [Repeated 4 time(s)] > color sel #5c5c5cff [Repeated 1 time(s)] > color sel #5b5b5bff [Repeated 1 time(s)] > color sel #5a5a5aff [Repeated 2 time(s)] > color sel #595959ff [Repeated 1 time(s)] > color sel #585858ff [Repeated 3 time(s)] > color sel #575757ff [Repeated 3 time(s)] > color sel #565656ff [Repeated 3 time(s)] > color sel #555555ff [Repeated 2 time(s)] > color sel #565656ff > color sel #575757ff > color sel #585858ff > color sel #5a5a5aff > color sel #5b5b5bff > color sel #5c5c5cff > color sel #5d5d5dff > color sel #5e5e5eff [Repeated 2 time(s)] > color sel #5f5f5fff > select #10/C:84@MG 1 atom, 1 residue, 1 model selected > select add #17/C:87@MG 2 atoms, 2 residues, 2 models selected > distance #10/C:84@MG #17/C:87@MG Distance between V12_holo-coot-3.pdb #10/C MG 84 MG and V23_holo-coot-2.pdb #17/C MG 87 MG: 3.390Å > select #10/C:84@MG 1 atom, 1 residue, 1 model selected > select add #19/C:1@O3' 2 atoms, 2 residues, 2 models selected > distance #10/C:84@MG #19/C:1@O3' Distance between V12_holo-coot-3.pdb #10/C MG 84 MG and Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb #19/C G 1 O3': 7.687Å > select #10/C:84@MG 1 atom, 1 residue, 1 model selected > select add #19/D:5@CA 2 atoms, 2 residues, 2 models selected > select #19/D:5@CA 1 atom, 1 residue, 1 model selected > select add #10/C:84@MG 2 atoms, 2 residues, 2 models selected > distance #19/D:5@CA #10/C:84@MG Distance between Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb #19/D CA 5 CA and V12_holo-coot-3.pdb #10/C MG 84 MG: 6.681Å > select #10/C:84@MG 1 atom, 1 residue, 1 model selected > select add #19/D:6@CA 2 atoms, 2 residues, 2 models selected > distance #10/C:84@MG #19/D:6@CA Distance between V12_holo-coot-3.pdb #10/C MG 84 MG and Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb #19/D CA 6 CA: 2.783Å > select #10/C:84@MG 1 atom, 1 residue, 1 model selected > select add #3/C:24@MG 2 atoms, 2 residues, 2 models selected > distance #10/C:84@MG #3/C:24@MG Distance between V12_holo-coot-3.pdb #10/C MG 84 MG and V4_holo-coot-3.pdb #3/C MG 24 MG: 3.250Å > select #17/C:87@MG 1 atom, 1 residue, 1 model selected > select add #19/D:6@CA 2 atoms, 2 residues, 2 models selected > distance #17/C:87@MG #19/D:6@CA Distance between V23_holo-coot-2.pdb #17/C MG 87 MG and Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb #19/D CA 6 CA: 5.916Å > select #17/C:87@MG 1 atom, 1 residue, 1 model selected > select add #19/C:1@O3' 2 atoms, 2 residues, 2 models selected > distance #17/C:87@MG #19/C:1@O3' Distance between V23_holo-coot-2.pdb #17/C MG 87 MG and Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb #19/C G 1 O3': 4.880Å > select #17/C:87@MG 1 atom, 1 residue, 1 model selected > select add #19/D:5@CA 2 atoms, 2 residues, 2 models selected > distance #17/C:87@MG #19/D:5@CA Distance between V23_holo-coot-2.pdb #17/C MG 87 MG and Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb #19/D CA 5 CA: 6.174Å > select #17/C:87@MG 1 atom, 1 residue, 1 model selected > select add #19/C:1@OP1 2 atoms, 2 residues, 2 models selected > distance #17/C:87@MG #19/C:1@OP1 Distance between V23_holo-coot-2.pdb #17/C MG 87 MG and Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb #19/C G 1 OP1: 6.874Å > select #19/D:5@CA 1 atom, 1 residue, 1 model selected > select add #19/C:1@OP1 2 atoms, 2 residues, 1 model selected > distance #19/D:5@CA #19/C:1@OP1 Distance between Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb #19/D CA 5 CA and /C G 1 OP1: 2.234Å > select #19/D:7@CA 1 atom, 1 residue, 1 model selected > select add #19/C:1@OP2 2 atoms, 2 residues, 1 model selected > distance #19/D:7@CA #19/C:1@OP2 Distance between Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb #19/D CA 7 CA and /C G 1 OP2: 2.625Å > ~distance #10/C:84@MG #17/C:87@MG > ~distance #19/D:5@CA #10/C:84@MG > ~distance #10/C:84@MG #19/C:1@O3' > ~distance #19/D:7@CA #19/C:1@OP2 > ~distance #17/C:87@MG #19/C:1@O3' > ~distance #19/D:5@CA #19/C:1@OP1 > ~distance #17/C:87@MG #19/C:1@OP1 > ~distance #10/C:84@MG #19/D:6@CA > ~distance #17/C:87@MG #19/D:5@CA > ~distance #10/C:84@MG #3/C:24@MG > ~distance #17/C:87@MG #19/D:6@CA > color sel #5f5f5fff > color sel #5f5f5ffe > color sel #5f5f5ffd [Repeated 3 time(s)] > color sel #5f5f5ffc [Repeated 1 time(s)] > color sel #5f5f5ffb [Repeated 1 time(s)] > color sel #5f5f5ffa [Repeated 1 time(s)] > color sel #5f5f5ff9 [Repeated 1 time(s)] > color sel #5f5f5ff8 > color sel #5f5f5ff7 > color sel #5f5f5ff6 > color sel #5f5f5ff5 > color sel #5f5f5ff3 > color sel #5f5f5ff2 > color sel #5f5f5ff1 > color sel #5f5f5ff0 > color sel #5f5f5fee > color sel #5f5f5fec > color sel #5f5f5feb > color sel #5f5f5fea > color sel #5f5f5fe9 [Repeated 3 time(s)] > color sel #5f5f5fe8 [Repeated 2 time(s)] > color sel #5f5f5fe7 [Repeated 6 time(s)] > select #19/C 1889 atoms, 2107 bonds, 89 residues, 1 model selected > lighting simple > lighting soft > lighting full > lighting soft > lighting simple > lighting soft > lighting simple > color sel #5f5f5fe7 > color sel #5f5f5fe6 > color sel #5f5f5fe3 > color sel #5f5f5fe2 > color sel #5f5f5fe1 [Repeated 1 time(s)] > color sel #5f5f5fe0 > color sel #5f5f5fdf [Repeated 2 time(s)] > color sel #5f5f5fde [Repeated 1 time(s)] > color sel #5f5f5fdd > color sel #5f5f5fdc > color sel #5f5f5fda > color sel #5f5f5fd8 > color sel #5f5f5fd6 > color sel #5f5f5fd4 > color sel #5f5f5fd2 > color sel #5f5f5fd1 > color sel #5f5f5fd0 > color sel #5f5f5fcf > color sel #5f5f5fcd > color sel #5f5f5fcc > color sel #5f5f5fca > color sel #5f5f5fc9 > color sel #5f5f5fc7 > color sel #5f5f5fc5 > color sel #5f5f5fc1 > color sel #5f5f5fbf > color sel #5f5f5fbd > color sel #5f5f5fbb > color sel #5f5f5fba > color sel #5f5f5fb8 > color sel #5f5f5fb5 > color sel #5f5f5fb4 > color sel #5f5f5fb1 > color sel #5f5f5fb0 > color sel #5f5f5fae [Repeated 2 time(s)] > color sel #5f5f5fad > color sel #5f5f5fac > color sel #5f5f5fab > color sel #5f5f5fa9 > color sel #5f5f5fa7 > color sel #5f5f5fa3 > color sel #5f5f5f9f > color sel #5f5f5f9b > color sel #5f5f5f99 > color sel #5f5f5f96 [Repeated 3 time(s)] > color sel #5f5f5f95 > color sel #5f5f5f94 > color sel #5f5f5f93 > color sel #5f5f5f92 > color sel #5f5f5f90 > color sel #5f5f5f8f > color sel #5f5f5f8e > color sel #5f5f5f8d > color sel #5f5f5f8c [Repeated 1 time(s)] > color sel #5f5f5f8b > color sel #5f5f5f89 > color sel #5f5f5f88 [Repeated 1 time(s)] > color sel #5f5f5f87 > color sel #5f5f5f85 > color sel #5f5f5f84 [Repeated 1 time(s)] > color sel #5f5f5f83 [Repeated 2 time(s)] > color sel #5f5f5f84 > color sel #5f5f5f87 > color sel #5f5f5f8d > color sel #5f5f5f95 > color sel #5f5f5f99 > color sel #5f5f5f9d > color sel #5f5f5f9f > color sel #5f5f5fa1 > color sel #5f5f5fa3 > color sel #5f5f5fa4 > color sel #5f5f5fa5 [Repeated 2 time(s)] > color sel #5f5f5fa6 > color sel #5f5f5fa8 > color sel #5f5f5fab > color sel #5f5f5fad > color sel #5f5f5fae > color sel #5f5f5faf [Repeated 2 time(s)] > color sel #5f5f5fb1 > color sel #5f5f5fb2 > color sel #5f5f5fb5 > color sel #5f5f5fb6 > color sel #5f5f5fb7 [Repeated 1 time(s)] > color sel #5f5f5fb8 [Repeated 2 time(s)] > color sel #5f5f5fb9 [Repeated 1 time(s)] > color sel #5f5f5fbb > color sel #5f5f5fbd > color sel #5f5f5fc1 > color sel #5f5f5fc7 > color sel #5f5f5fcc > color sel #5f5f5fcf > color sel #5f5f5fd0 > color sel #5f5f5fce > color sel #5f5f5fc2 > color sel #5f5f5fb8 > color sel #5f5f5fb2 > color sel #5f5f5fb1 [Repeated 1 time(s)] > color sel #5f5f5fb0 > color sel #5f5f5fad > color sel #5f5f5fab > color sel #5f5f5fa9 > color sel #5f5f5fa5 > color sel #5f5f5fa3 > select #19/D:30@CA 1 atom, 1 residue, 1 model selected > select add #19/D:5@CA 2 atoms, 2 residues, 1 model selected > color sel #404040ff > select #19/D:7@CA 1 atom, 1 residue, 1 model selected > select #19/D:7@CA 1 atom, 1 residue, 1 model selected > color sel #404040ff > color sel #3f3f3fff > color sel #3e3e3eff > color sel #3d3d3dff [Repeated 4 time(s)] > color sel #3c3c3cff [Repeated 2 time(s)] > color sel #3d3d3dff [Repeated 1 time(s)] > select #19/D:6@CA 1 atom, 1 residue, 1 model selected > select add #19/D:1@CA 2 atoms, 2 residues, 1 model selected > select add #19/D:3@CA 3 atoms, 3 residues, 1 model selected > color sel #4f8f00ff > color sel #005493ff > select clear > save > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/apo_holo_analysis/ions/ions_holo_new_core_aa_models_ternary_comp.cxs > hide #19 models > save ions_core_holo.png supersample 3 transparentBackground true > lighting simple > lighting soft > lighting simple > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > ui tool show ""Side View"" > lighting soft > lighting simple > lighting soft > save ions_core_holo_2.png supersample 3 transparentBackground true > select #10/C:84@MG 1 atom, 1 residue, 1 model selected > select add #11/A:390@OP2 2 atoms, 2 residues, 2 models selected > distance #10/C:84@MG #11/A:390@OP2 Distance between V12_holo-coot-3.pdb #10/C MG 84 MG and V14_holo-coot-1.pdb #11/A A 390 OP2: 3.278Å > select #6/C:24@MG 1 atom, 1 residue, 1 model selected > select add #6/A:390@OP2 2 atoms, 2 residues, 1 model selected > distance #6/C:24@MG #6/A:390@OP2 Distance between V7_holo-coot-2.pdb #6/C MG 24 MG and /A A 390 OP2: 4.213Å > select #6/C:24@MG 1 atom, 1 residue, 1 model selected > select #10/C:84@MG 1 atom, 1 residue, 1 model selected > select clear > select #17/C:87@MG 1 atom, 1 residue, 1 model selected > select add #11/A:390@OP2 2 atoms, 2 residues, 2 models selected > distance #17/C:87@MG #11/A:390@OP2 Distance between V23_holo-coot-2.pdb #17/C MG 87 MG and V14_holo-coot-1.pdb #11/A A 390 OP2: 4.350Å > ~distance #6/C:24@MG #6/A:390@OP2 > ~distance #10/C:84@MG #11/A:390@OP2 > ~distance #17/C:87@MG #11/A:390@OP2 > select clear > lighting simple > toolshed show > select #18/C:24@MG 1 atom, 1 residue, 1 model selected > select add #11/A:390@OP2 2 atoms, 2 residues, 2 models selected > distance #18/C:24@MG #11/A:390@OP2 Distance between V25_holo-coot-2.pdb #18/C MG 24 MG and V14_holo-coot-1.pdb #11/A A 390 OP2: 4.140Å > select #17/A:50@OP2 1 atom, 1 residue, 1 model selected > select add #9/C:4@MG 2 atoms, 2 residues, 2 models selected > distance #17/A:50@OP2 #9/C:4@MG Distance between V23_holo-coot-2.pdb #17/A A 50 OP2 and V11_holo-coot-1.pdb #9/C MG 4 MG: 5.979Å > select #11/A:390@OP2 1 atom, 1 residue, 1 model selected > select add #10/C:84@MG 2 atoms, 2 residues, 2 models selected > distance #11/A:390@OP2 #10/C:84@MG Distance between V14_holo-coot-1.pdb #11/A A 390 OP2 and V12_holo-coot-3.pdb #10/C MG 84 MG: 3.278Å > select #17/C:87@MG 1 atom, 1 residue, 1 model selected > select add #10/C:84@MG 2 atoms, 2 residues, 2 models selected > distance #17/C:87@MG #10/C:84@MG Distance between V23_holo-coot-2.pdb #17/C MG 87 MG and V12_holo-coot-3.pdb #10/C MG 84 MG: 3.390Å > select #10/C:84@MG 1 atom, 1 residue, 1 model selected > select add #17/C:87@MG 2 atoms, 2 residues, 2 models selected > select #10/C:84@MG 1 atom, 1 residue, 1 model selected > select #10/C:84@MG 1 atom, 1 residue, 1 model selected > color sel lime > color sel purple > ~distance #11/A:390@OP2 #10/C:84@MG > ~distance #17/A:50@OP2 #9/C:4@MG > ~distance #17/C:87@MG #10/C:84@MG > ~distance #18/C:24@MG #11/A:390@OP2 > select clear > select #7/C:24@MG 1 atom, 1 residue, 1 model selected > select add #7/A:390@C5' 2 atoms, 2 residues, 1 model selected > distance #7/C:24@MG #7/A:390@C5' Distance between V9_holo-coot-0.pdb #7/C MG 24 MG and /A A 390 C5': 5.156Å > select clear > select #7/C:24@MG 1 atom, 1 residue, 1 model selected > select add #11/A:390@OP2 2 atoms, 2 residues, 2 models selected > distance #7/C:24@MG #11/A:390@OP2 Distance between V9_holo-coot-0.pdb #7/C MG 24 MG and V14_holo-coot-1.pdb #11/A A 390 OP2: 4.308Å > select #3/C:24@MG 1 atom, 1 residue, 1 model selected > select add #11/A:390@OP2 2 atoms, 2 residues, 2 models selected > distance #3/C:24@MG #11/A:390@OP2 Distance between V4_holo-coot-3.pdb #3/C MG 24 MG and V14_holo-coot-1.pdb #11/A A 390 OP2: 4.180Å > select #13/C:24@MG 1 atom, 1 residue, 1 model selected > select #11/A:390@OP2 1 atom, 1 residue, 1 model selected > select add #13/C:24@MG 2 atoms, 2 residues, 2 models selected > distance #11/A:390@OP2 #13/C:24@MG Distance between V14_holo-coot-1.pdb #11/A A 390 OP2 and V17_holo-coot-3.pdb #13/C MG 24 MG: 4.168Å > select #4/C:24@MG 1 atom, 1 residue, 1 model selected > select add #11/A:390@OP2 2 atoms, 2 residues, 2 models selected > distance #4/C:24@MG #11/A:390@OP2 Distance between V5_holo-coot-1.pdb #4/C MG 24 MG and V14_holo-coot-1.pdb #11/A A 390 OP2: 4.683Å > ~distance #7/C:24@MG #7/A:390@C5' > ~distance #4/C:24@MG #11/A:390@OP2 > ~distance #3/C:24@MG #11/A:390@OP2 > ~distance #7/C:24@MG #11/A:390@OP2 > ~distance #11/A:390@OP2 #13/C:24@MG > select clear > save ions_core_holo_2.png supersample 3 transparentBackground true > save > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/apo_holo_analysis/ions/ions_holo_new_core_aa_models.cxs > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V1_Mg- > coot-1.pdb Chain information for V1_Mg-coot-1.pdb #20 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V2_Mg- > coot-1.pdb Chain information for V2_Mg-coot-1.pdb #21 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V3_Mg- > coot-2.pdb Chain information for V3_Mg-coot-2.pdb #22 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V4_Mg- > coot-2.pdb Chain information for V4_Mg-coot-2.pdb #23 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V5_Mg- > coot-1.pdb Chain information for V5_Mg-coot-1.pdb #24 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V6_Mg- > coot-1.pdb Chain information for V6_Mg-coot-1.pdb #25 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V7_Mg- > coot-2.pdb Chain information for V7_Mg-coot-2.pdb #26 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V8_Mg- > coot-2.pdb Chain information for V8_Mg-coot-2.pdb #27 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V9_Mg- > coot-3.pdb Chain information for V9_Mg-coot-3.pdb #28 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V10_Mg- > coot-3.pdb Chain information for V10_Mg-coot-3.pdb #29 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V11_Mg- > coot-2.pdb Chain information for V11_Mg-coot-2.pdb #30 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V12_real_space_refined_011-coot-0.pdb Chain information for V12_real_space_refined_011-coot-0.pdb #31 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V13_Mg- > coot-2.pdb Chain information for V13_Mg-coot-2.pdb #32 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V13_Mg- > coot-3_6.pdb Chain information for V13_Mg-coot-3_6.pdb #33 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V14_Mg- > coot-1.pdb Chain information for V14_Mg-coot-1.pdb #34 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V15_Mg- > coot-2.pdb Chain information for V15_Mg-coot-2.pdb #35 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V16_Mg- > coot-1.pdb Chain information for V16_Mg-coot-1.pdb #36 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V17_Mg- > coot-2.pdb Chain information for V17_Mg-coot-2.pdb #37 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V18_Mg- > coot-1.pdb Chain information for V18_Mg-coot-1.pdb #38 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V19_Mg- > coot-3.pdb Chain information for V19_Mg-coot-3.pdb #39 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V20_Mg- > coot-2.pdb Chain information for V20_Mg-coot-2.pdb #40 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V21_Mg_real_space_refined_002-coot-1.pdb Chain information for V21_Mg_real_space_refined_002-coot-1.pdb #41 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V22_Mg_6sig.pdb Chain information for V22_Mg_6sig.pdb #42 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V22_Mg_real_space_refined_002-coot-1.pdb Chain information for V22_Mg_real_space_refined_002-coot-1.pdb #43 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V23_Mg_6sig.pdb Chain information for V23_Mg_6sig.pdb #44 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V23_Mg- > coot-1.pdb Chain information for V23_Mg-coot-1.pdb #45 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V24_6sig.pdb Chain information for V24_6sig.pdb #46 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V24_Mg- > coot-6.pdb Chain information for V24_Mg-coot-6.pdb #47 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V25_Mg- > coot-1.pdb Chain information for V25_Mg-coot-1.pdb #48 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V26_Mg- > coot-1.pdb Chain information for V26_Mg-coot-1.pdb #49 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V27_Mg- > coot-2.pdb Chain information for V27_Mg-coot-2.pdb #50 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V28_Mg- > coot-1.pdb Chain information for V28_Mg-coot-1.pdb #51 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V29_Mg- > coot-2.pdb Chain information for V29_Mg-coot-2.pdb #52 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V30_Mg- > coot-3.pdb Chain information for V30_Mg-coot-3.pdb #53 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V31_Mg- > coot-3.pdb Chain information for V31_Mg-coot-3.pdb #54 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V32_Mg- > coot-2.pdb Chain information for V32_Mg-coot-2.pdb #55 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V33_Mg- > coot-2.pdb Chain information for V33_Mg-coot-2.pdb #56 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V34_Mg- > coot-3.pdb Chain information for V34_Mg-coot-3.pdb #57 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V35_Mg- > coot-2.pdb Chain information for V35_Mg-coot-2.pdb #58 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V36_Mg- > coot-1.pdb Chain information for V36_Mg-coot-1.pdb #59 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V37_Mg- > coot-1.pdb Chain information for V37_Mg-coot-1.pdb #60 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V38_Mg- > coot-1.pdb Chain information for V38_Mg-coot-1.pdb #61 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V39_Mg_real_space_refined_002-coot-0.pdb Chain information for V39_Mg_real_space_refined_002-coot-0.pdb #62 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V40_Mg_real_space_refined_003-coot-0_aligned.pdb Chain information for V40_Mg_real_space_refined_003-coot-0_aligned.pdb #63 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V40_Mg_real_space_refined_003-coot-0.pdb Chain information for V40_Mg_real_space_refined_003-coot-0.pdb #64 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V41_Mg_real_space_refined_003-coot-0.pdb Chain information for V41_Mg_real_space_refined_003-coot-0.pdb #65 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V42_Mg_real_space_refined_003-coot-0.pdb Chain information for V42_Mg_real_space_refined_003-coot-0.pdb #66 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V43_Mg_real_space_refined_001-coot-0.pdb Chain information for V43_Mg_real_space_refined_001-coot-0.pdb #67 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V44_Mg_real_space_refined_003-coot-0.pdb Chain information for V44_Mg_real_space_refined_003-coot-0.pdb #68 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V45_Mg- > coot-3.pdb Chain information for V45_Mg-coot-3.pdb #69 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V46_Mg- > coot-2.pdb Chain information for V46_Mg-coot-2.pdb #70 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V47_Mg- > coot-4.pdb Chain information for V47_Mg-coot-4.pdb #71 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V48_Mg- > coot-1.pdb Chain information for V48_Mg-coot-1.pdb #72 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V49_Mg- > coot-2.pdb Chain information for V49_Mg-coot-2.pdb #73 --- Chain | Description A | No description available Computing secondary structure [Repeated 53 time(s)] > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/apo_conf/V1_holo_set_noprot- > coot-2.pdb Chain information for V1_holo_set_noprot-coot-2.pdb #74 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/apo_conf/V8_holo_no_prot_a- > coot-4.pdb Summary of feedback from opening /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/apo_conf/V8_holo_no_prot_a- coot-4.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 ASN B 10 GLN B 19 1 10 Start residue of secondary structure not found: HELIX 2 2 ALA B 54 GLU B 70 1 17 Start residue of secondary structure not found: HELIX 3 3 GLN B 87 ALA B 89 1 3 Start residue of secondary structure not found: HELIX 4 4 TYR B 94 LYS B 107 1 14 Start residue of secondary structure not found: SHEET 1 1 1 PHE B 28 ASP B 34 0 2 messages similar to the above omitted Chain information for V8_holo_no_prot_a-coot-4.pdb #75 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/apo_conf/V13_holo_set_noapo- > coot-3.pdb Summary of feedback from opening /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/apo_conf/V13_holo_set_noapo- coot-3.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 ASN B 10 GLN B 19 1 10 Start residue of secondary structure not found: HELIX 2 2 ALA B 54 GLU B 70 1 17 Start residue of secondary structure not found: HELIX 3 3 GLN B 87 ALA B 89 1 3 Start residue of secondary structure not found: HELIX 4 4 TYR B 94 LYS B 107 1 14 Start residue of secondary structure not found: SHEET 1 1 1 PHE B 28 ASP B 34 0 2 messages similar to the above omitted Chain information for V13_holo_set_noapo-coot-3.pdb #76 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/apo_conf/V20_holo_no_prot- > coot-1.pdb Chain information for V20_holo_no_prot-coot-1.pdb #77 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/apo_conf/V22_holo_no_prot- > coot-1.pdb Chain information for V22_holo_no_prot-coot-1.pdb #78 --- Chain | Description A | No description available > open > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/apo_conf/V24_holo_no_prot- > coot-3.pdb Chain information for V24_holo_no_prot-coot-3.pdb #79 --- Chain | Description A | No description available Computing secondary structure [Repeated 5 time(s)] > select > #1/A:15,21-29,39-67,69-84,96-101,105-112,249-261,272-293,295-312,327-340,386-400 3255 atoms, 3639 bonds, 151 residues, 1 model selected > ui tool show Matchmaker > matchmaker #20-49,51-79#!50 to #1 & sel matrix Nucleic Computing secondary structure [Repeated 60 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V1_Mg-coot-1.pdb, chain A (#20), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.460 angstroms; (across all 151 pairs: 0.510) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V2_Mg-coot-1.pdb, chain A (#21), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.443 angstroms; (across all 151 pairs: 0.490) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V3_Mg-coot-2.pdb, chain A (#22), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.478 angstroms; (across all 151 pairs: 0.530) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V4_Mg-coot-2.pdb, chain A (#23), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.470 angstroms; (across all 151 pairs: 0.515) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V5_Mg-coot-1.pdb, chain A (#24), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.472 angstroms; (across all 151 pairs: 0.521) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V6_Mg-coot-1.pdb, chain A (#25), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.469 angstroms; (across all 151 pairs: 0.519) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V7_Mg-coot-2.pdb, chain A (#26), sequence alignment score = 604 RMSD between 148 pruned atom pairs is 0.517 angstroms; (across all 151 pairs: 0.622) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V8_Mg-coot-2.pdb, chain A (#27), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.465 angstroms; (across all 151 pairs: 0.504) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V9_Mg-coot-3.pdb, chain A (#28), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.490 angstroms; (across all 151 pairs: 0.523) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V10_Mg-coot-3.pdb, chain A (#29), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.491 angstroms; (across all 151 pairs: 0.532) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V11_Mg-coot-2.pdb, chain A (#30), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.480 angstroms; (across all 151 pairs: 0.536) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V12_real_space_refined_011-coot-0.pdb, chain A (#31), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.523 angstroms; (across all 151 pairs: 0.559) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V13_Mg-coot-2.pdb, chain A (#32), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.504 angstroms; (across all 151 pairs: 0.540) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V13_Mg-coot-3_6.pdb, chain A (#33), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.504 angstroms; (across all 151 pairs: 0.540) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V14_Mg-coot-1.pdb, chain A (#34), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.477 angstroms; (across all 151 pairs: 0.534) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V15_Mg-coot-2.pdb, chain A (#35), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.461 angstroms; (across all 151 pairs: 0.518) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V16_Mg-coot-1.pdb, chain A (#36), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.452 angstroms; (across all 151 pairs: 0.506) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V17_Mg-coot-2.pdb, chain A (#37), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.439 angstroms; (across all 151 pairs: 0.502) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V18_Mg-coot-1.pdb, chain A (#38), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.461 angstroms; (across all 151 pairs: 0.498) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V19_Mg-coot-3.pdb, chain A (#39), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.458 angstroms; (across all 151 pairs: 0.496) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V20_Mg-coot-2.pdb, chain A (#40), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.458 angstroms; (across all 151 pairs: 0.520) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V21_Mg_real_space_refined_002-coot-1.pdb, chain A (#41), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.480 angstroms; (across all 151 pairs: 0.525) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V22_Mg_6sig.pdb, chain A (#42), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.449 angstroms; (across all 151 pairs: 0.508) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V22_Mg_real_space_refined_002-coot-1.pdb, chain A (#43), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.449 angstroms; (across all 151 pairs: 0.508) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V23_Mg_6sig.pdb, chain A (#44), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.495 angstroms; (across all 151 pairs: 0.534) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V23_Mg-coot-1.pdb, chain A (#45), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.495 angstroms; (across all 151 pairs: 0.534) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V24_6sig.pdb, chain A (#46), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.487 angstroms; (across all 151 pairs: 0.552) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V24_Mg-coot-6.pdb, chain A (#47), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.487 angstroms; (across all 151 pairs: 0.552) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V25_Mg-coot-1.pdb, chain A (#48), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.465 angstroms; (across all 151 pairs: 0.518) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V26_Mg-coot-1.pdb, chain A (#49), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.491 angstroms; (across all 151 pairs: 0.546) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V28_Mg-coot-1.pdb, chain A (#51), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.514 angstroms; (across all 151 pairs: 0.557) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V29_Mg-coot-2.pdb, chain A (#52), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.486 angstroms; (across all 151 pairs: 0.512) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V30_Mg-coot-3.pdb, chain A (#53), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.427 angstroms; (across all 151 pairs: 0.470) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V31_Mg-coot-3.pdb, chain A (#54), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.462 angstroms; (across all 151 pairs: 0.524) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V32_Mg-coot-2.pdb, chain A (#55), sequence alignment score = 604 RMSD between 149 pruned atom pairs is 0.454 angstroms; (across all 151 pairs: 0.624) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V33_Mg-coot-2.pdb, chain A (#56), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.472 angstroms; (across all 151 pairs: 0.515) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V34_Mg-coot-3.pdb, chain A (#57), sequence alignment score = 604 RMSD between 149 pruned atom pairs is 0.539 angstroms; (across all 151 pairs: 0.609) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V35_Mg-coot-2.pdb, chain A (#58), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.538 angstroms; (across all 151 pairs: 0.577) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V36_Mg-coot-1.pdb, chain A (#59), sequence alignment score = 604 RMSD between 149 pruned atom pairs is 0.505 angstroms; (across all 151 pairs: 0.589) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V37_Mg-coot-1.pdb, chain A (#60), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.476 angstroms; (across all 151 pairs: 0.520) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V38_Mg-coot-1.pdb, chain A (#61), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.462 angstroms; (across all 151 pairs: 0.509) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V39_Mg_real_space_refined_002-coot-0.pdb, chain A (#62), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.495 angstroms; (across all 151 pairs: 0.539) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V40_Mg_real_space_refined_003-coot-0_aligned.pdb, chain A (#63), sequence alignment score = 604 RMSD between 149 pruned atom pairs is 0.522 angstroms; (across all 151 pairs: 0.591) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V40_Mg_real_space_refined_003-coot-0.pdb, chain A (#64), sequence alignment score = 604 RMSD between 149 pruned atom pairs is 0.526 angstroms; (across all 151 pairs: 0.595) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V41_Mg_real_space_refined_003-coot-0.pdb, chain A (#65), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.484 angstroms; (across all 151 pairs: 0.540) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V42_Mg_real_space_refined_003-coot-0.pdb, chain A (#66), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.482 angstroms; (across all 151 pairs: 0.526) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V43_Mg_real_space_refined_001-coot-0.pdb, chain A (#67), sequence alignment score = 604 RMSD between 149 pruned atom pairs is 0.513 angstroms; (across all 151 pairs: 0.602) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V44_Mg_real_space_refined_003-coot-0.pdb, chain A (#68), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.507 angstroms; (across all 151 pairs: 0.549) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V45_Mg-coot-3.pdb, chain A (#69), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.494 angstroms; (across all 151 pairs: 0.546) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V46_Mg-coot-2.pdb, chain A (#70), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.436 angstroms; (across all 151 pairs: 0.490) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V47_Mg-coot-4.pdb, chain A (#71), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.564 angstroms; (across all 151 pairs: 0.596) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V48_Mg-coot-1.pdb, chain A (#72), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.468 angstroms; (across all 151 pairs: 0.523) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V49_Mg-coot-2.pdb, chain A (#73), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.461 angstroms; (across all 151 pairs: 0.529) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V1_holo_set_noprot- coot-2.pdb, chain A (#74), sequence alignment score = 604 RMSD between 149 pruned atom pairs is 0.402 angstroms; (across all 151 pairs: 0.464) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V8_holo_no_prot_a-coot-4.pdb, chain A (#75), sequence alignment score = 604 RMSD between 149 pruned atom pairs is 0.486 angstroms; (across all 151 pairs: 0.562) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V13_holo_set_noapo- coot-3.pdb, chain A (#76), sequence alignment score = 604 RMSD between 151 pruned atom pairs is 0.491 angstroms; (across all 151 pairs: 0.491) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V20_holo_no_prot-coot-1.pdb, chain A (#77), sequence alignment score = 604 RMSD between 151 pruned atom pairs is 0.442 angstroms; (across all 151 pairs: 0.442) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V22_holo_no_prot-coot-1.pdb, chain A (#78), sequence alignment score = 604 RMSD between 149 pruned atom pairs is 0.357 angstroms; (across all 151 pairs: 0.438) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V24_holo_no_prot-coot-3.pdb, chain A (#79), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.494 angstroms; (across all 151 pairs: 0.557) Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V27_Mg-coot-2.pdb, chain A (#50), sequence alignment score = 604 RMSD between 150 pruned atom pairs is 0.544 angstroms; (across all 151 pairs: 0.594) > select #20-79/A 537720 atoms, 602280 bonds, 25020 residues, 60 models selected > color sel dim gray > hide sel target a > select #20-79/A:50,389,390 3960 atoms, 4380 bonds, 180 residues, 60 models selected > cartoon hide sel > show sel target ab > nucleotides sel atoms > style nucleic & sel stick Changed 3960 atom styles > hide (sel-residues & (protein|nucleic)) target a > cartoon hide sel-residues > show (sel-residues & backbone) target ab > ui tool show ""Color Actions"" > color sel cornflower blue > hide #19#!1-18 target m > select #20/C:1@O 1 atom, 1 residue, 1 model selected > select add #42/B:67@MG 2 atoms, 2 residues, 2 models selected > select add #61/B:65@MG 3 atoms, 3 residues, 3 models selected > select add #65/B:44@MG 4 atoms, 4 residues, 4 models selected > hide sel target a > select #30/B:61@MG 1 atom, 1 residue, 1 model selected > select add #69/B:62@MG 2 atoms, 2 residues, 2 models selected > hide sel target a > select #20-79/B 2199 atoms, 1 pseudobond, 2199 residues, 56 models selected > ui tool show ""Selection Inspector"" > size sel atomRadius 0.7 Changed 2199 atom radii > select clear > select #46/B:66@MG 1 atom, 1 residue, 1 model selected > select add #75/A:390@O3' 2 atoms, 2 residues, 2 models selected > distance #46/B:66@MG #75/A:390@O3' Distance between V24_6sig.pdb #46/B MG 66 MG and V8_holo_no_prot_a-coot-4.pdb #75/A A 390 O3': 5.502Å > close #42 > close #44 > close #46 > select #20-79/B 2062 atoms, 1 pseudobond, 2062 residues, 53 models selected > close #33 > close #63 > select #20-79/B:7 50 atoms, 50 residues, 50 models selected > select #75/C:7@MG 1 atom, 1 residue, 1 model selected > select add #69/B:7@MG 2 atoms, 2 residues, 2 models selected > select add #68/B:7@MG 3 atoms, 3 residues, 3 models selected > select add #55/B:7@MG 4 atoms, 4 residues, 4 models selected > select #20-79/B 1987 atoms, 1 pseudobond, 1987 residues, 51 models selected > select #20-79/C 187 atoms, 187 residues, 6 models selected > ui tool show ""Selection Inspector"" > size sel atomRadius 0.7 Changed 187 atom radii > select #20-79/B:7 50 atoms, 50 residues, 50 models selected > ui tool show ""Color Actions"" > color sel #941100ff > select #20-79/C:7 5 atoms, 5 residues, 5 models selected > ui tool show ""Color Actions"" > select #20-79/C:7 5 atoms, 5 residues, 5 models selected > ui tool show ""Color Actions"" > color sel #4f8f00ff > color sel #941100ff > select #20-79/B 1987 atoms, 1 pseudobond, 1987 residues, 51 models selected > ui tool show ""Color Actions"" > color sel forest green > select #20-79/C 187 atoms, 187 residues, 6 models selected > ui tool show ""Color Actions"" > color sel forest green > select #20-79/C:7 5 atoms, 5 residues, 5 models selected > ui tool show ""Color Actions"" > select #20-79/B:7 50 atoms, 50 residues, 50 models selected > ui tool show ""Color Actions"" > color sel #945200ff > color sel #941100ff > select #20-79/C:7 5 atoms, 5 residues, 5 models selected > ui tool show ""Color Actions"" > color sel #945200ff > color sel #941100ff > select clear > select #20-79/B:57 21 atoms, 21 residues, 21 models selected > select #20-79/B:57,66 35 atoms, 35 residues, 25 models selected > select clear > select #65/B:41@MG 1 atom, 1 residue, 1 model selected > select add #39/B:64@MG 2 atoms, 2 residues, 2 models selected > select add #41/B:62@MG 3 atoms, 3 residues, 3 models selected > select add #43/B:63@MG 4 atoms, 4 residues, 4 models selected > select subtract #43/B:63@MG 3 atoms, 3 residues, 3 models selected > select add #43/B:63@MG 4 atoms, 4 residues, 4 models selected > select subtract #41/B:62@MG 3 atoms, 3 residues, 3 models selected > select add #31/B:58@MG 4 atoms, 4 residues, 4 models selected > select add #30/B:57@MG 5 atoms, 5 residues, 5 models selected > select subtract #31/B:58@MG 4 atoms, 4 residues, 4 models selected > select subtract #65/B:41@MG 3 atoms, 3 residues, 3 models selected > select add #65/B:41@MG 4 atoms, 4 residues, 4 models selected > select add #31/B:58@MG 5 atoms, 5 residues, 5 models selected > select subtract #31/B:58@MG 4 atoms, 4 residues, 4 models selected > select subtract #39/B:64@MG 3 atoms, 3 residues, 3 models selected > select add #39/B:64@MG 4 atoms, 4 residues, 4 models selected > select add #38/B:61@MG 5 atoms, 5 residues, 5 models selected > select add #36/B:60@MG 6 atoms, 6 residues, 6 models selected > select subtract #43/B:63@MG 5 atoms, 5 residues, 5 models selected > select add #43/B:63@MG 6 atoms, 6 residues, 6 models selected > hide sel target a > select #26/B:49@MG 1 atom, 1 residue, 1 model selected > select add #31/B:58@MG 2 atoms, 2 residues, 2 models selected > select add #41/B:62@MG 3 atoms, 3 residues, 3 models selected > select add #34/B:59@MG 4 atoms, 4 residues, 4 models selected > hide sel target a > select #43/B:65@MG 1 atom, 1 residue, 1 model selected > select add #30/B:60@MG 2 atoms, 2 residues, 2 models selected > show #19 models > hide #19 models > show #19 models > hide #19 models > show #19 models > hide #19 models > show #19 models > hide #19 models > show #19 models > hide #19 models > show #19 models > hide #19 models > show #19 models > hide #19 models > show #19 models > hide #19 models > select #50/B:64@MG 1 atom, 1 residue, 1 model selected > select add #35/B:62@MG 2 atoms, 2 residues, 2 models selected > select add #51/B:68@MG 3 atoms, 3 residues, 3 models selected > select add #69/B:57@MG 4 atoms, 4 residues, 4 models selected > select add #62/B:45@MG 5 atoms, 5 residues, 5 models selected > select add #64/B:42@MG 6 atoms, 6 residues, 6 models selected > select add #27/B:54@MG 7 atoms, 7 residues, 7 models selected > select add #59/B:66@MG 8 atoms, 8 residues, 8 models selected > hide sel target a > show sel target ab > show #19 models > hide #19 models > show #19 models > hide #19 models > show #19 models > hide #19 models > show #19 models > hide #19 models > show #19 models > hide #19 models > show #19 models > hide #19 models > select #21/B:38@MG 1 atom, 1 residue, 1 model selected > select add #30/B:38@MG 2 atoms, 2 residues, 2 models selected > select add #26/B:38@MG 3 atoms, 3 residues, 3 models selected > select #26/B:38@MG 1 atom, 1 residue, 1 model selected > select add #59/B:64@MG 2 atoms, 2 residues, 2 models selected > distance #26/B:38@MG #59/B:64@MG Distance between V7_Mg-coot-2.pdb #26/B MG 38 MG and V36_Mg-coot-1.pdb #59/B MG 64 MG: 9.452Å > select #26/B:38@MG 1 atom, 1 residue, 1 model selected > select add #23/B:7@MG 2 atoms, 2 residues, 2 models selected > distance #26/B:38@MG #23/B:7@MG Distance between V7_Mg-coot-2.pdb #26/B MG 38 MG and V4_Mg-coot-2.pdb #23/B MG 7 MG: 8.150Å > select #26/B:38@MG 1 atom, 1 residue, 1 model selected > select add #21/B:38@MG 2 atoms, 2 residues, 2 models selected > select add #30/B:38@MG 3 atoms, 3 residues, 3 models selected > hide sel target a > select #36/B:38@MG 1 atom, 1 residue, 1 model selected > select add #59/B:38@MG 2 atoms, 2 residues, 2 models selected > hide sel target a > select add #62/B:30@MG 3 atoms, 3 residues, 3 models selected > select #53/B:65@MG 1 atom, 1 residue, 1 model selected > select #75/A:390@O3' 1 atom, 1 residue, 1 model selected > select add #24/B:50@MG 2 atoms, 2 residues, 2 models selected > distance #75/A:390@O3' #24/B:50@MG Distance between V8_holo_no_prot_a-coot-4.pdb #75/A A 390 O3' and V5_Mg- coot-1.pdb #24/B MG 50 MG: 5.771Å > select #24/B:50@MG 1 atom, 1 residue, 1 model selected > select #47/B:66@MG 1 atom, 1 residue, 1 model selected > select add #34/B:61@MG 2 atoms, 2 residues, 2 models selected > select add #32/B:60@MG 3 atoms, 3 residues, 3 models selected > select add #24/B:50@MG 4 atoms, 4 residues, 4 models selected > select add #53/B:65@MG 5 atoms, 5 residues, 5 models selected > select add #48/B:69@MG 6 atoms, 6 residues, 6 models selected > select add #36/B:61@MG 7 atoms, 7 residues, 7 models selected > select #47/B:66@MG 1 atom, 1 residue, 1 model selected > select add #55/B:62@MG 2 atoms, 2 residues, 2 models selected > distance #47/B:66@MG #55/B:62@MG Distance between V24_Mg-coot-6.pdb #47/B MG 66 MG and V32_Mg-coot-2.pdb #55/B MG 62 MG: 5.257Å > save > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/apo_holo_analysis/ions/ions_apo_holo_new_core_aa_models.cxs > select #43/B:65@MG 1 atom, 1 residue, 1 model selected > select add #58/B:4@MG 2 atoms, 2 residues, 2 models selected > distance #43/B:65@MG #58/B:4@MG Distance between V22_Mg_real_space_refined_002-coot-1.pdb #43/B MG 65 MG and V35_Mg-coot-2.pdb #58/B MG 4 MG: 9.512Å > select #43/B:65@MG 1 atom, 1 residue, 1 model selected > select add #30/B:60@MG 2 atoms, 2 residues, 2 models selected > hide sel target a > save > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/apo_holo_analysis/ions/ions_apo_holo_new_core_aa_models.cxs > select #59/B:64@MG 1 atom, 1 residue, 1 model selected > select clear > select #48/B:30@MG 1 atom, 1 residue, 1 model selected > select add #75/C:7@MG 2 atoms, 2 residues, 2 models selected > distance #48/B:30@MG #75/C:7@MG Distance between V25_Mg-coot-1.pdb #48/B MG 30 MG and V8_holo_no_prot_a- coot-4.pdb #75/C MG 7 MG: 7.041Å > select #48/B:30@MG 1 atom, 1 residue, 1 model selected > select add #58/A:389@OP1 2 atoms, 2 residues, 2 models selected > distance #48/B:30@MG #58/A:389@OP1 Distance between V25_Mg-coot-1.pdb #48/B MG 30 MG and V35_Mg-coot-2.pdb #58/A A 389 OP1: 2.362Å > select #69/B:30@MG 1 atom, 1 residue, 1 model selected > select add #65/B:30@MG 2 atoms, 2 residues, 2 models selected > select add #48/B:30@MG 3 atoms, 3 residues, 3 models selected > select add #41/B:30@MG 4 atoms, 4 residues, 4 models selected > select add #55/B:66@MG 5 atoms, 5 residues, 5 models selected > select add #50/B:30@MG 6 atoms, 6 residues, 6 models selected > color sel blue > select clear > select #39/B:65@MG 1 atom, 1 residue, 1 model selected > select add #75/A:390@O3' 2 atoms, 2 residues, 2 models selected > distance #39/B:65@MG #75/A:390@O3' Distance between V19_Mg-coot-3.pdb #39/B MG 65 MG and V8_holo_no_prot_a- coot-4.pdb #75/A A 390 O3': 4.560Å > select #28/B:40@MG 1 atom, 1 residue, 1 model selected > select #75/A:390@O3' 1 atom, 1 residue, 1 model selected > select add #72/B:40@MG 2 atoms, 2 residues, 2 models selected > distance #75/A:390@O3' #72/B:40@MG Distance between V8_holo_no_prot_a-coot-4.pdb #75/A A 390 O3' and V48_Mg- coot-1.pdb #72/B MG 40 MG: 5.512Å > select #20-79/B:40 33 atoms, 33 residues, 33 models selected > save > /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/apo_holo_analysis/ions/ions_apo_holo_new_core_aa_models.cxs ——— End of log from Wed Sep 17 17:35:30 2025 ——— opened ChimeraX session OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M2 Max OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,6 Model Number: Z1760005VLL/A Chip: Apple M2 Max Total Number of Cores: 12 (8 performance and 4 efficiency) Memory: 64 GB System Firmware Version: 11881.140.96 OS Loader Version: 11881.140.96 Software: System Software Overview: System Version: macOS 15.6.1 (24G90) Kernel Version: Darwin 24.6.0 Time since boot: 1 day, 18 hours, 31 minutes Graphics/Displays: Apple M2 Max: Chipset Model: Apple M2 Max Type: GPU Bus: Built-In Total Number of Cores: 38 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL P2715Q: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported DELL P2715Q: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 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1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 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1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 finufft: 2.4.1 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect assigned normal Window Toolkit all ChimeraX