id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18479 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.5-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. Fatal Python error: Segmentation fault Current thread 0x00000001ffc5df00 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, 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All rights reserved. How to cite UCSF ChimeraX > open /Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM- > QC/DATA/BRD9/M-26709/StrAnalysis-M26709(BRD9).cxs format session Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half1_map.mrc as #1.1, grid size 300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half2_map.mrc as #1.2, grid size 300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_local_filtered_map.mrc as #1.3, grid size 300,300,300, pixel 0.65, shown at level 0.0246, step 1, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_unsharpened_map.mrc as #1.4, grid size 300,300,300, pixel 0.65, shown at level 0.028, step 1, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc as #1.5, grid size 300,300,300, pixel 0.65, shown at level 0.0338, step 1, values float32 Opened Gaussian_local_filtered_map.mrc as #1.6, grid size 300,300,300, pixel 0.65, shown at level 0.0285, step 1, values float32 Opened Gaussian_unsharpened_map.mrc as #1.7, grid size 300,300,300, pixel 0.65, shown at level 0.0282, step 1, values float32 Opened final_unsharp_EMreadyOUT.mrc as #2.1, grid size 300,300,300, pixel 0.65, shown at level 4.81, step 1, values float32 Opened EMready_Maps as #2.2, grid size 300,300,300, pixel 0.65, shown at level 4.5, step 1, values float32 opened ChimeraX session > open /Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM- > QC/DATA/BRD9/M-26709/CryoEM_QC-M26709.cxs format session Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half1_map.mrc as #1.1, grid size 300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half2_map.mrc as #1.2, grid size 300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_local_filtered_map.mrc as #1.3, grid size 300,300,300, pixel 0.65, shown at level 0.0246, step 1, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_unsharpened_map.mrc as #1.4, grid size 300,300,300, pixel 0.65, shown at level 0.028, step 1, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc as #1.5, grid size 300,300,300, pixel 0.65, shown at level 0.0338, step 1, values float32 Opened Gaussian_local_filtered_map.mrc as #1.6, grid size 300,300,300, pixel 0.65, shown at level 0.0285, step 1, values float32 Opened Gaussian_unsharpened_map.mrc as #1.7, grid size 300,300,300, pixel 0.65, shown at level 0.0282, step 1, values float32 Opened final_unsharp_EMreadyOUT.mrc as #2.1, grid size 300,300,300, pixel 0.65, shown at level 4.81, step 1, values float32 Opened EMready_Maps as #2.2, grid size 300,300,300, pixel 0.65, shown at level 4.08, step 1, values float32 opened ChimeraX session > show #!1.6 models > hide #!5 models > hide #!2.2 models > show #!2.2 models > hide #!2 models > show #!1.7 models > hide #!1.7 models > show #!1.7 models > hide #!1.6 models > show #!1.6 models > hide #!1.7 models > color #1.6 #d6d6d6ff models > color #1.6 #ebebebff models > color #1.6 #d6d6d6ff models > lighting flat > lighting soft > lighting full > lighting shadows false > lighting shadows true > lighting full > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > lighting simple > lighting soft > volume #1.6 level 0.02726 > save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1263 > supersample 4 > show #!2.1 models > hide #!2.1 models > show #!2.1 models > hide #!1.6 models > hide #!2.1 models > show #!1.6 models > hide #!1.6 models > show #!1.7 models > hide #!2 models > show #!1.6 models > hide #!1.7 models > fitmap #5.2 inMap#1.6 Expected a keyword > fitmap #5.2 inMap #1.6 Fit molecule schrodinger_relaxed_with_rotamer_corrected.pdb (#5.2) to map Gaussian_local_filtered_map.mrc (#1.6) using 16233 atoms average map value = 2.48e-19, steps = 652 shifted from previous position = 32.3 rotated from previous position = 22.2 degrees atoms outside contour = 16233, contour level = 0.027265 Position of schrodinger_relaxed_with_rotamer_corrected.pdb (#5.2) relative to Gaussian_local_filtered_map.mrc (#1.6) coordinates: Matrix rotation and translation 0.93565187 -0.15830921 -0.31542632 64.40958566 0.11186587 0.98069697 -0.16037296 -107.24352394 0.33472615 0.11476782 0.93530035 -87.17093173 Axis 0.36398764 -0.86009595 0.35741846 Axis point 357.21288153 -0.00000000 33.78486496 Rotation angle (degrees) 22.20697265 Shift along axis 84.52751343 > show #!5 models > fitmap #5.2 inMap #1.6 Fit molecule schrodinger_relaxed_with_rotamer_corrected.pdb (#5.2) to map Gaussian_local_filtered_map.mrc (#1.6) using 16233 atoms average map value = 2.48e-19, steps = 144 shifted from previous position = 0.00707 rotated from previous position = 0.121 degrees atoms outside contour = 16233, contour level = 0.027265 Position of schrodinger_relaxed_with_rotamer_corrected.pdb (#5.2) relative to Gaussian_local_filtered_map.mrc (#1.6) coordinates: Matrix rotation and translation 0.93530406 -0.15724230 -0.31698764 64.48169295 0.11038925 0.98079281 -0.16080942 -107.06117498 0.33618525 0.11541368 0.93469736 -87.32017575 Axis 0.36441148 -0.86170815 0.35307695 Axis point 355.38830202 0.00000000 33.25914596 Rotation angle (degrees) 22.27168615 Shift along axis 84.92261543 > show #!5.2 models > hide #!5.1 models > show #!5.1 models > show #!2 models > hide #!2 models > hide #!5.2 models > show #!5.2 models > select add #5.2 16233 atoms, 16405 bonds, 8 pseudobonds, 1020 residues, 3 models selected > ui mousemode right ""translate selected models"" > view matrix models > #5.2,0.9353,-0.15724,-0.31699,12.334,0.11039,0.98079,-0.16081,85.765,0.33619,0.11541,0.9347,-9.9527 > view matrix models > #5.2,0.9353,-0.15724,-0.31699,31.751,0.11039,0.98079,-0.16081,79.217,0.33619,0.11541,0.9347,-5.824 > view matrix models > #5.2,0.9353,-0.15724,-0.31699,30.154,0.11039,0.98079,-0.16081,85.427,0.33619,0.11541,0.9347,-3.5056 > fitmap #5.2 inMap #1.6 Fit molecule schrodinger_relaxed_with_rotamer_corrected.pdb (#5.2) to map Gaussian_local_filtered_map.mrc (#1.6) using 16233 atoms average map value = 0.02531, steps = 208 shifted from previous position = 10.6 rotated from previous position = 22.4 degrees atoms outside contour = 10058, contour level = 0.027265 Position of schrodinger_relaxed_with_rotamer_corrected.pdb (#5.2) relative to Gaussian_local_filtered_map.mrc (#1.6) coordinates: Matrix rotation and translation 0.99999867 -0.00036713 0.00159068 -0.08863738 0.00036638 0.99999982 0.00047471 -0.07580690 -0.00159085 -0.00047412 0.99999862 0.18892049 Axis -0.27906254 0.93572596 0.21573369 Axis point 119.44333269 0.00000000 56.77798040 Rotation angle (degrees) 0.09740463 Shift along axis -0.00544259 > hide sel atoms > select #5.2/I 115 atoms, 120 bonds, 1 residue, 1 model selected > show sel atoms > select #5.2/I 115 atoms, 120 bonds, 1 residue, 1 model selected > color sel orange > color zone #1.6 near #5.2@C /I distance 5 > color zone #1.6 near #5.2@C /I distance 6 > hide #!5.1 models > hide #!5.2 models > color zone #1.6 near #5.2@C /I distance 4 > color zone #1.6 near #5.2@C /I distance 5 > lighting shadows true intensity 0.5 > lighting flat > lighting soft > color zone #1.6 near #5.2@C /I distance 5.5 > color zone #1.6 near #5.2@C /I distance 6 > save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1263 > supersample 3 > show #!5.1 models > hide #!1.6 models > show #!2 models > hide #!2.2 models > show #!2.2 models > volume #2.2 level 2.064 > undo > volume #2.2 level 4.28 > volume #2.2 color white > lighting soft > lighting shadows true intensity 0.5 > lighting flat > lighting soft > show #!5.2 models > show #!1.6 models > color #1.6 #d6d6d6ff models > ui mousemode right select > select clear > hide #5.1.4 models > hide #5.1.5 models > hide #5.1.3 models > ui windowfill toggle > select #5.2/I 115 atoms, 120 bonds, 1 residue, 1 model selected > select #5.2/I 115 atoms, 120 bonds, 1 residue, 1 model selected > color sel byhetero > select #5.2/I 115 atoms, 120 bonds, 1 residue, 1 model selected > hide sel h Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > select #5.2/I 115 atoms, 120 bonds, 1 residue, 1 model selected > hide sel H Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > select #5.2/I 115 atoms, 120 bonds, 1 residue, 1 model selected > select sel H Expected a keyword > select clear > select #5.2/I:1@H521 1 atom, 1 residue, 1 model selected > hide sel atoms > select #5.2/I:1@H522 1 atom, 1 residue, 1 model selected > select #5.2/I:1@H523 1 atom, 1 residue, 1 model selected > select add #5.2/I:1@H522 2 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H541 3 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H542 4 atoms, 1 residue, 1 model selected > select #5.2/I:1@H541 1 atom, 1 residue, 1 model selected > select add #5.2/I:1@H542 2 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H523 3 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H522 4 atoms, 1 residue, 1 model selected > hide sel atoms > ui windowfill toggle > hide #!2 models > hide #!1.6 models > select clear > select #5.2/I:1@H531 1 atom, 1 residue, 1 model selected > select add #5.2/I:1@H532 2 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H1_2 3 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H1_3 4 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H1_1 5 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H533 6 atoms, 1 residue, 1 model selected > select add #5.2/I:1@HC49 7 atoms, 1 residue, 1 model selected > select add #5.2/I:1@HC40 8 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H442 9 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H433 10 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H431 11 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H432 12 atoms, 1 residue, 1 model selected > select add #5.2/I:1@HC42 13 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H441 14 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H372 15 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H371 16 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H382 17 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H381 18 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H8_2 19 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H153 20 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H9_2 21 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H8_1 22 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H6_2 23 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H6_1 24 atoms, 1 residue, 1 model selected > select add #5.2/I:1@HC4 25 atoms, 1 residue, 1 model selected > hide sel atoms > select add #5.2/I:1@HC46 26 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H211 27 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H213 28 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H212 29 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H311 30 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H313 31 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H312 32 atoms, 1 residue, 1 model selected > select add #5.2/I:1@HC18 33 atoms, 1 residue, 1 model selected > select add #5.2/I:1@HC16 34 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H293 35 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H292 36 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H291 37 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H253 38 atoms, 1 residue, 1 model selected > select add #5.2/I:1@C25 39 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H251 40 atoms, 1 residue, 1 model selected > select subtract #5.2/I:1@C25 39 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H252 40 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H112 41 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H321 42 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H341 43 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H342 44 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H351 45 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H443 46 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H9_1 47 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H151 48 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H152 49 atoms, 1 residue, 1 model selected > hide sel atoms > select add #5.2/I:1@HC23 50 atoms, 1 residue, 1 model selected > hide sel atoms > select add #5.2/I:1@H111 51 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H322 52 atoms, 1 residue, 1 model selected > select add #5.2/I:1@HC50 53 atoms, 1 residue, 1 model selected > select add #5.2/I:1@H352 54 atoms, 1 residue, 1 model selected > hide sel atoms > show #!1.6 models > show #!2 models > ui windowfill toggle > show #!1.4 models > hide #!1.4 models > show #!1.4 models > hide #!2 models > hide #!2.2 models > show #!1.3 models > hide #!1.4 models > hide #!1.6 models > hide #!1.3 models > show #!1.3 models > show #!1.6 models > hide #!1.6 models > show #!1.6 models > show #!1.7 models > hide #!1.6 models > show #!1.6 models > hide #!1.7 models > show #!2.2 models > hide #!1.3 models > volume #1.6 level 0.02546 > volume #2.2 level 4.161 > ui windowfill toggle Drag select of 1.6 Gaussian_local_filtered_map.mrc , 36 residues Drag select of 1.6 Gaussian_local_filtered_map.mrc , 2.2 EMready_Maps , 1020 residues, 56 atoms, 61 bonds Drag select of 2.2 EMready_Maps , 172 atoms, 1018 residues, 26 pseudobonds, 167 bonds Drag select of 2.2 EMready_Maps , 172 atoms, 1016 residues, 26 pseudobonds, 167 bonds > select clear Drag select of 2.2 EMready_Maps , 172 atoms, 1018 residues, 26 pseudobonds, 167 bonds > ui mousemode right ""translate selected models"" > ui mousemode right select > select clear Drag select of 1.6 Gaussian_local_filtered_map.mrc , 56 atoms, 1018 residues, 61 bonds > ui mousemode right ""translate selected models"" > view matrix models > #1.6,1,0,0,-16.312,0,1,0,90.607,0,0,1,47.123,#5.2,1,-0.00036713,0.0015907,-16.401,0.00036638,1,0.00047471,90.531,-0.0015908,-0.00047412,1,47.312 > ui mousemode right select > select clear > ui windowfill toggle > hide #!1 models > hide #!5.2 models > undo > hide #!5.2 models > ui windowfill toggle > save /Users/tarunnarwani/Pictures/Image1.jpg width 1920 height 850 > supersample 4 > ui windowfill toggle > hide #!2 models > hide #!5.1 models > show #!5.2 models > show #!1 models > ui windowfill toggle > save /Users/tarunnarwani/Pictures/Image1.jpg width 1920 height 850 > supersample 4 > ui windowfill toggle > show #!5.1 models > hide #!5.2 models > hide #!1.6 models > show #!2 models > hide #!2.2 models > show #!2.1 models > hide #!2.1 models > show #!2.2 models > hide #3 models > volume #2.2 level 3.939 > lighting shadows true intensity 0.5 > lighting shadows false > lighting soft > lighting flat > lighting soft > volume #2.1 level 4.777 > volume #2.2 step 2 > volume #2.2 step 1 > select #5.1/I:1@N57 1 atom, 1 residue, 1 model selected > select clear > select #2.2 2 models selected > select clear > select #5.1/B:62@OH 1 atom, 1 residue, 1 model selected > select up 12 atoms, 12 bonds, 1 residue, 1 model selected > select #5.1/B 1337 atoms, 1376 bonds, 42 pseudobonds, 171 residues, 4 models selected > select #5.1/B 1337 atoms, 1376 bonds, 42 pseudobonds, 171 residues, 4 models selected > hide sel atoms > select #5.1/C 825 atoms, 847 bonds, 109 pseudobonds, 101 residues, 3 models selected > hide sel atoms > select clear > ui windowfill toggle > select #2.2 2 models selected > select clear > save /Users/tarunnarwani/Pictures/Image1.jpg width 1920 height 850 > supersample 4 > ui windowfill toggle > fitmap #5.2 inMap #1.6 Fit molecule schrodinger_relaxed_with_rotamer_corrected.pdb (#5.2) to map Gaussian_local_filtered_map.mrc (#1.6) using 16233 atoms average map value = 0.02531, steps = 28 shifted from previous position = 0.00877 rotated from previous position = 0.0068 degrees atoms outside contour = 9226, contour level = 0.025461 Position of schrodinger_relaxed_with_rotamer_corrected.pdb (#5.2) relative to Gaussian_local_filtered_map.mrc (#1.6) coordinates: Matrix rotation and translation 0.99999881 -0.00040674 0.00148637 -0.07764102 0.00040609 0.99999982 0.00043444 -0.06917223 -0.00148654 -0.00043383 0.99999880 0.17950003 Axis -0.27116477 0.92845541 0.25385077 Axis point 120.29893784 0.00000000 51.89437557 Rotation angle (degrees) 0.09173041 Shift along axis 0.00239640 > show #!5.2 models > show #!1.4 models > hide #!1.4 models > show #!1.3 models > fitmap #5.1 inMap #1.3 Fit molecule DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb (#5.1) to map DDB1-DCAF16-BRD9_AMPH-26709-010-04_local_filtered_map.mrc (#1.3) using 8099 atoms average map value = 0.04491, steps = 40 shifted from previous position = 0.0244 rotated from previous position = 0.0515 degrees atoms outside contour = 1826, contour level = 0.024647 Position of DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb (#5.1) relative to DDB1-DCAF16-BRD9_AMPH-26709-010-04_local_filtered_map.mrc (#1.3) coordinates: Matrix rotation and translation 0.99999975 -0.00041862 -0.00056256 0.08661369 0.00041881 0.99999985 0.00035071 -0.08006894 0.00056241 -0.00035095 0.99999978 -0.02480425 Axis -0.44743420 -0.71737671 0.53401620 Axis point 49.33028395 0.00000000 158.26863156 Rotation angle (degrees) 0.04492490 Shift along axis 0.00543979 > fitmap #5.1 inMap #1.5 Fit molecule DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb (#5.1) to map DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc (#1.5) using 8099 atoms average map value = 0.1535, steps = 28 shifted from previous position = 0.0166 rotated from previous position = 0.0267 degrees atoms outside contour = 1204, contour level = 0.033787 Position of DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb (#5.1) relative to DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc (#1.5) coordinates: Matrix rotation and translation 0.99999969 -0.00029605 -0.00073344 0.08979761 0.00029600 0.99999995 -0.00006562 -0.01650503 0.00073346 0.00006540 0.99999973 -0.07136704 Axis 0.08254430 -0.92415452 0.37299445 Axis point 95.33653629 0.00000000 122.83775369 Rotation angle (degrees) 0.04547248 Shift along axis -0.00395404 > hide #!1.3 models > show #!1.3 models > hide #!1.3 models > show #!1.5 models > hide #!1.5 models > show #!1.6 models > hide #!1.6 models > show #!1.6 models > hide #!1.6 models > show #!1.4 models > show #!1.6 models > hide #!1.6 models > show #!1.6 models > hide #!1.6 models > show #!1.5 models > hide #!1.5 models > hide #!1.4 models > show #!1.4 models > show #!1.5 models > volume #1.5 level 0.05162 > fitmap #5.1 inMap #1.5 Fit molecule DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb (#5.1) to map DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc (#1.5) using 8099 atoms average map value = 0.1535, steps = 40 shifted from previous position = 0.013 rotated from previous position = 0.0195 degrees atoms outside contour = 1959, contour level = 0.051617 Position of DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb (#5.1) relative to DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc (#1.5) coordinates: Matrix rotation and translation 0.99999978 0.00000255 -0.00066430 0.05792100 -0.00000250 1.00000000 0.00008443 -0.01270232 0.00066430 -0.00008443 0.99999978 -0.05454194 Axis -0.12607893 -0.99201304 -0.00377292 Axis point 82.10293260 0.00000000 88.20845195 Rotation angle (degrees) 0.03836801 Shift along axis 0.00550403 > measure mapstats #1.5 Map DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc #1.5, minimum -0.618, maximum 0.9837, mean -0.0002284, SD 0.01979, RMS 0.01979 > measure mapstats #1.4 Map DDB1-DCAF16-BRD9_AMPH-26709-010-04_unsharpened_map.mrc #1.4, minimum -0.06459, maximum 0.1527, mean -0.0002284, SD 0.004562, RMS 0.004568 > fitmap #5.1 inMap #1.5 Fit molecule DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb (#5.1) to map DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc (#1.5) using 8099 atoms average map value = 0.1535, steps = 44 shifted from previous position = 0.01 rotated from previous position = 0.00612 degrees atoms outside contour = 1959, contour level = 0.051617 Position of DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb (#5.1) relative to DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc (#1.5) coordinates: Matrix rotation and translation 0.99999976 -0.00009341 -0.00069344 0.06935420 0.00009344 0.99999999 0.00004760 -0.01070345 0.00069343 -0.00004766 0.99999976 -0.05495719 Axis -0.06791780 -0.98875810 0.13320880 Axis point 79.01021253 0.00000000 99.84512464 Rotation angle (degrees) 0.04018274 Shift along axis -0.00144804 > fitmap #5.1 inMap #1.4 Fit molecule DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb (#5.1) to map DDB1-DCAF16-BRD9_AMPH-26709-010-04_unsharpened_map.mrc (#1.4) using 8099 atoms average map value = 0.04366, steps = 44 shifted from previous position = 0.0167 rotated from previous position = 0.0238 degrees atoms outside contour = 2489, contour level = 0.028037 Position of DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb (#5.1) relative to DDB1-DCAF16-BRD9_AMPH-26709-010-04_unsharpened_map.mrc (#1.4) coordinates: Matrix rotation and translation 0.99999973 -0.00041544 -0.00060533 0.09005454 0.00041562 0.99999987 0.00029471 -0.07560695 0.00060521 -0.00029496 0.99999977 -0.03497916 Axis -0.37265894 -0.76503607 0.52520960 Axis point 62.98367676 0.00000000 152.38017056 Rotation angle (degrees) 0.04533038 Shift along axis 0.00591103 > fitmap #5.1 inMap #2.2 Fit molecule DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb (#5.1) to map EMready_Maps (#2.2) using 8099 atoms average map value = 5.396, steps = 40 shifted from previous position = 0.0258 rotated from previous position = 0.0492 degrees atoms outside contour = 1841, contour level = 3.939 Position of DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb (#5.1) relative to EMready_Maps (#2.2) coordinates: Matrix rotation and translation 0.99999873 -0.00095513 -0.00127197 0.20736724 0.00095547 0.99999951 0.00026985 -0.12373672 0.00127171 -0.00027106 0.99999915 -0.07722232 Axis -0.16762293 -0.78825778 0.59207452 Axis point 68.77375787 0.00000000 165.20808818 Rotation angle (degrees) 0.09244556 Shift along axis 0.01705556 > fitmap #5.1 inMap #2.1 Fit molecule DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb (#5.1) to map final_unsharp_EMreadyOUT.mrc (#2.1) using 8099 atoms average map value = 8.94, steps = 36 shifted from previous position = 0.0103 rotated from previous position = 0.0193 degrees atoms outside contour = 1568, contour level = 4.7773 Position of DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb (#5.1) relative to final_unsharp_EMreadyOUT.mrc (#2.1) coordinates: Matrix rotation and translation 0.99999874 -0.00067755 -0.00143404 0.20192690 0.00067809 0.99999970 0.00037363 -0.11415728 0.00143379 -0.00037460 0.99999890 -0.08365712 Axis -0.22957660 -0.87993219 0.41594943 Axis point 64.05481872 0.00000000 143.84235556 Rotation angle (degrees) 0.09336790 Shift along axis 0.01929585 > measure mapstats #2.1 Map final_unsharp_EMreadyOUT.mrc #2.1, minimum -0.1337, maximum 18.67, mean 0.0002461, SD 0.702, RMS 0.702 > measure mapstats #2.2 Map EMready_Maps #2.2, minimum -0.1027, maximum 9.086, mean 0.0006311, SD 0.5525, RMS 0.5525 > open /Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM- > QC/DATA/BRD9/M-26709/CryoEM_QC-M26709.cxs format session Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half1_map.mrc as #1.1, grid size 300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half2_map.mrc as #1.2, grid size 300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_local_filtered_map.mrc as #1.3, grid size 300,300,300, pixel 0.65, shown at level 0.0246, step 1, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_unsharpened_map.mrc as #1.4, grid size 300,300,300, pixel 0.65, shown at level 0.028, step 1, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc as #1.5, grid size 300,300,300, pixel 0.65, shown at level 0.0338, step 1, values float32 Opened Gaussian_local_filtered_map.mrc as #1.6, grid size 300,300,300, pixel 0.65, shown at level 0.0285, step 1, values float32 Opened Gaussian_unsharpened_map.mrc as #1.7, grid size 300,300,300, pixel 0.65, shown at level 0.0282, step 1, values float32 Opened final_unsharp_EMreadyOUT.mrc as #2.1, grid size 300,300,300, pixel 0.65, shown at level 4.81, step 1, values float32 Opened EMready_Maps as #2.2, grid size 300,300,300, pixel 0.65, shown at level 4.08, step 1, values float32 opened ChimeraX session > hide #5.1.5 models > hide #5.1.4 models > hide #5.1.3 models > hide #3 models > show #!2.1 models > hide #!2.2 models > show #!2.2 models > hide #!2.1 models > color #2.2 #ffffff79 models > color #2.2 #ffffff78 models > open /Users/tarunnarwani/Documents/StructurePG_TJR/ChimeraX/PreQC- > Proteros_SMARCA2_40272set.cxs format session Opened AMPH-38945-001_screening.mrc as #1.1, grid size 256,256,256, pixel 0.914, shown at level 0.127, step 1, values float32 Opened AMPH-39541-001_screening.mrc as #1.2, grid size 256,256,256, pixel 0.914, shown at level 0.203, step 1, values float32 Opened AMPH-39576-003_screening.mrc as #1.3, grid size 256,256,256, pixel 0.914, shown at level 0.121, step 1, values float32 Opened AMPH-40272-003_screening.mrc as #1.4, grid size 256,256,256, pixel 0.914, shown at level 0.224, step 1, values float32 Opened AMPH-38945-001_screening.mrc gaussian as #5, grid size 256,256,256, pixel 0.914, shown at step 1, values float32 Opened AMPH-39541-001_screening.mrc gaussian as #6, grid size 256,256,256, pixel 0.914, shown at level 0.173, step 1, values float32 Opened AMPH-39576-003_screening.mrc gaussian as #7, grid size 256,256,256, pixel 0.914, shown at step 1, values float32 Opened AMPH-40272-003_screening.mrc gaussian as #8, grid size 256,256,256, pixel 0.914, shown at step 1, values float32 opened ChimeraX session > show #!8 models > hide #!7 models > show #!7 models > volume #!7-8 style surface > volume #!7-8 showOutlineBox false > hide #!8 models > show #!3 models > hide #!3 models > volume #7 level 0.2814 > volume #8 change image level -0.01811,0 level 0.1172,0.8 level 0.6057,1 > volume #8 level 0.05563 > volume #8 level 0.05659 > volume #1.4 level 0.3053 > volume #1.4 level 0.2353 Drag select of 1.4 AMPH-40272-003_screening.mrc > select clear > volume #5 level -0.01558,0 level 0.09931,0.8 level 0.5854,1 > volume #5 style surface > volume #5 level 0.3267 > volume #5 level 0.1177 > show #2 models > show #!6 models > hide #!5 models > hide #2 models > volume #6 level 0.2989 > volume #6 level 0.1818 > volume #6 level 0.1669 > volume #6 level 0.1699 > open /Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM- > QC/DATA/BRD9/M-26709/CryoEM_QC-M26709.cxs format session Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half1_map.mrc as #1.1, grid size 300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half2_map.mrc as #1.2, grid size 300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_local_filtered_map.mrc as #1.3, grid size 300,300,300, pixel 0.65, shown at level 0.0246, step 1, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_unsharpened_map.mrc as #1.4, grid size 300,300,300, pixel 0.65, shown at level 0.028, step 1, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc as #1.5, grid size 300,300,300, pixel 0.65, shown at level 0.0338, step 1, values float32 Opened Gaussian_local_filtered_map.mrc as #1.6, grid size 300,300,300, pixel 0.65, shown at level 0.0285, step 1, values float32 Opened Gaussian_unsharpened_map.mrc as #1.7, grid size 300,300,300, pixel 0.65, shown at level 0.0282, step 1, values float32 Opened final_unsharp_EMreadyOUT.mrc as #2.1, grid size 300,300,300, pixel 0.65, shown at level 4.81, step 1, values float32 Opened EMready_Maps as #2.2, grid size 300,300,300, pixel 0.65, shown at level 4.08, step 1, values float32 opened ChimeraX session > hide #5.1.3 models > hide #5.1.4 models > hide #5.1.5 models > hide #3 models > select #5.1/I 56 atoms, 61 bonds, 1 residue, 1 model selected > surface zone #2.2 nearAtoms sel distance 5 > surface zone #2.2 nearAtoms sel distance 3.5 > volume gaussian #2.2 bfactor 200 Opened EMready_Maps gaussian as #4, grid size 300,300,300, pixel 0.65, shown at step 1, values float32 > surface zone #3 nearAtoms sel distance 3.5 No surfaces specified > hide #!4 models > show #!4 models > surface zone #4 nearAtoms sel distance 3.5 > show #!2.2 models > hide #!4 models > close #4 > color #2.2 #ffffff80 models > color #2.2 #ffffff5d models > color #2.2 #ffffff5e models > select #5.1/B:173 6 atoms, 5 bonds, 1 residue, 1 model selected > select add #5.1/B:175 12 atoms, 10 bonds, 2 residues, 1 model selected > select add #5.1/B:174 19 atoms, 16 bonds, 3 residues, 1 model selected > hide sel atoms > select clear > surface zone #4 nearAtoms sel distance 3 No surfaces specified > surface zone #2.2 nearAtoms sel distance 3 No atoms specified > select #5.1/I 56 atoms, 61 bonds, 1 residue, 1 model selected > surface zone #2.2 nearAtoms sel distance 3 > select #5.1/B,C 2162 atoms, 2223 bonds, 173 pseudobonds, 272 residues, 4 models selected > select #5.1/B,C 2162 atoms, 2223 bonds, 173 pseudobonds, 272 residues, 4 models selected > color sel light gray > select #5.1/B,C 2162 atoms, 2223 bonds, 173 pseudobonds, 272 residues, 4 models selected > color sel gray > select #5.1/B,C 2162 atoms, 2223 bonds, 173 pseudobonds, 272 residues, 4 models selected > color sel light gray > color #5.1 darkgrey > color #5.1 #929292ff > color #5.1 #929292a4 > color #5.1 #929292ff > select #5.1/I 56 atoms, 61 bonds, 1 residue, 1 model selected > color sel orange > select #5.1/I 56 atoms, 61 bonds, 1 residue, 1 model selected > color sel byhetero > select #5.1/B:58 6 atoms, 5 bonds, 1 residue, 1 model selected > select #5.1/B:58 6 atoms, 5 bonds, 1 residue, 1 model selected > color sel byhetero > select #5.1/B:58 6 atoms, 5 bonds, 1 residue, 1 model selected > label sel > label sel bgColor yellow > show #5.1.4 models > ui mousemode right label > label delete residues > select #5.1/B:58 6 atoms, 5 bonds, 1 residue, 1 model selected > label sel > label sel bgColor yellow > ui mousemode right ""move label"" > ui mousemode right select > select clear > ui windowfill toggle > save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 885 > supersample 4 > open /Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM- > QC/DATA/BRD9/M-26709/StrAnalysis-M26709(BRD9).cxs format session Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half1_map.mrc as #1.1, grid size 300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half2_map.mrc as #1.2, grid size 300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_local_filtered_map.mrc as #1.3, grid size 300,300,300, pixel 0.65, shown at level 0.0246, step 1, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_unsharpened_map.mrc as #1.4, grid size 300,300,300, pixel 0.65, shown at level 0.028, step 1, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc as #1.5, grid size 300,300,300, pixel 0.65, shown at level 0.0338, step 1, values float32 Opened Gaussian_local_filtered_map.mrc as #1.6, grid size 300,300,300, pixel 0.65, shown at level 0.0285, step 1, values float32 Opened Gaussian_unsharpened_map.mrc as #1.7, grid size 300,300,300, pixel 0.65, shown at level 0.0282, step 1, values float32 Opened final_unsharp_EMreadyOUT.mrc as #2.1, grid size 300,300,300, pixel 0.65, shown at level 4.81, step 1, values float32 Opened EMready_Maps as #2.2, grid size 300,300,300, pixel 0.65, shown at level 4.5, step 1, values float32 opened ChimeraX session > open /Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM- > QC/DATA/BRD9/M-26709/CryoEM_QC-M26709.cxs format session Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half1_map.mrc as #1.1, grid size 300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half2_map.mrc as #1.2, grid size 300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_local_filtered_map.mrc as #1.3, grid size 300,300,300, pixel 0.65, shown at level 0.0246, step 1, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_unsharpened_map.mrc as #1.4, grid size 300,300,300, pixel 0.65, shown at level 0.028, step 1, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc as #1.5, grid size 300,300,300, pixel 0.65, shown at level 0.0338, step 1, values float32 Opened Gaussian_local_filtered_map.mrc as #1.6, grid size 300,300,300, pixel 0.65, shown at level 0.0285, step 1, values float32 Opened Gaussian_unsharpened_map.mrc as #1.7, grid size 300,300,300, pixel 0.65, shown at level 0.0282, step 1, values float32 Opened final_unsharp_EMreadyOUT.mrc as #2.1, grid size 300,300,300, pixel 0.65, shown at level 4.81, step 1, values float32 Opened EMready_Maps as #2.2, grid size 300,300,300, pixel 0.65, shown at level 4.08, step 1, values float32 opened ChimeraX session > hide #3 models > hide #5.1.5 models > hide #5.1.3 models > ui mousemode right ""move label"" > label bgColor color gray Invalid ""bgColor"" argument: Expected 'none' or a color > label bgColor gray > label bgColor light gray > select #5.1/B:173,191 17 atoms, 15 bonds, 2 residues, 1 model selected > select #5.1/B:173,191 /C:216,188 33 atoms, 29 bonds, 12 pseudobonds, 4 residues, 3 models selected > select #5.1/B:173,191 /C:216,188 33 atoms, 29 bonds, 12 pseudobonds, 4 residues, 3 models selected > color sel maroon > select #5.1/B:173,191 /C:216,188 33 atoms, 29 bonds, 12 pseudobonds, 4 residues, 3 models selected > color sel byhetero > select #5.1/B:173,191 /C:216,188 33 atoms, 29 bonds, 12 pseudobonds, 4 residues, 3 models selected > label sel bgColor light yellow > select #5.1/B:58 6 atoms, 5 bonds, 1 residue, 1 model selected > label sel bgColor yellow > ui mousemode right select > select clear > select #2.2 2 models selected > select #5.1/I:1@C15 1 atom, 1 residue, 1 model selected > select up 56 atoms, 61 bonds, 1 residue, 1 model selected > select down 1 atom, 1 residue, 1 model selected > select add #5.1/I:1@C21 2 atoms, 2 bonds, 1 residue, 1 model selected > select add #5.1/I:1@N57 3 atoms, 2 bonds, 1 residue, 1 model selected > select add #5.1/I:1@C44 4 atoms, 3 bonds, 1 residue, 1 model selected > color sel maroon > color sel byhetero > select clear > save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1263 > supersample 3 > open /Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM- > QC/DATA/BRD9/M-26709/CryoEM_QC-M26709.cxs format session Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half1_map.mrc as #1.1, grid size 300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half2_map.mrc as #1.2, grid size 300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_local_filtered_map.mrc as #1.3, grid size 300,300,300, pixel 0.65, shown at level 0.0246, step 1, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_unsharpened_map.mrc as #1.4, grid size 300,300,300, pixel 0.65, shown at level 0.028, step 1, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc as #1.5, grid size 300,300,300, pixel 0.65, shown at level 0.0338, step 1, values float32 Opened Gaussian_local_filtered_map.mrc as #1.6, grid size 300,300,300, pixel 0.65, shown at level 0.0285, step 1, values float32 Opened Gaussian_unsharpened_map.mrc as #1.7, grid size 300,300,300, pixel 0.65, shown at level 0.0282, step 1, values float32 Opened final_unsharp_EMreadyOUT.mrc as #2.1, grid size 300,300,300, pixel 0.65, shown at level 4.81, step 1, values float32 Opened EMready_Maps as #2.2, grid size 300,300,300, pixel 0.65, shown at level 4.08, step 1, values float32 opened ChimeraX session > ui tool show ""Model-map Q-Score"" > style #5.2 stick Changed 16233 atom styles > color #5.2 byhetero > transparency #2.2 60 > qscore #5.2 toVolume #2.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false > assignAttr false Overall mean Q-Score: 0.64 > qscore #5.2 toVolume #2.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false > assignAttr false Overall mean Q-Score: 0.64 > qscore #5.2 toVolume #2.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false > assignAttr false Overall mean Q-Score: 0.64 > qscore #5.2/C toVolume #2.2 When the ""qscore"" command is called with ""useGui True"", the analysis will be run on the entire model. > ui tool show ""Model-map Q-Score"" > transparency #2.2 60 Overall mean Q-Score: 0.64 > select #5.1/C:140 7 atoms, 7 bonds, 1 residue, 1 model selected > select clear > select #5.1/C:171 7 atoms, 7 bonds, 1 residue, 1 model selected > select #5.1/C:225 8 atoms, 7 bonds, 1 residue, 1 model selected > select clear > select #5.1/C:239 10 atoms, 9 bonds, 1 residue, 1 model selected > qscore #5.2 toVolume #2.2 useGui false pointsPerShell 5 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false > assignAttr false Overall mean Q-Score: 0.65 > qscore #5.2 toVolume #2.2 useGui false pointsPerShell 5 shellRadiusStep > 0.100 maxShellRadius 2.50 referenceGaussianSigma 0.75 logDetails false > assignAttr false Overall mean Q-Score: 0.74 > qscore #5.2 toVolume #2.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.75 logDetails false > assignAttr false Overall mean Q-Score: 0.69 > qscore #5.2 toVolume #2.2 useGui false pointsPerShell 4 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.75 logDetails false > assignAttr false Overall mean Q-Score: 0.69 > qscore #5.2 toVolume #2.2 useGui false pointsPerShell 4 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.75 logDetails false > assignAttr false Overall mean Q-Score: 0.69 > qscore #5.2 toVolume #2.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.75 logDetails false > assignAttr false Overall mean Q-Score: 0.69 > qscore #5.2 toVolume #2.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.75 logDetails false > assignAttr false Overall mean Q-Score: 0.69 > qscore #5.2 toVolume #2.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.75 logDetails false > assignAttr false Overall mean Q-Score: 0.69 > qscore #5.2 toVolume #2.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.50 referenceGaussianSigma 0.75 logDetails false > assignAttr false Overall mean Q-Score: 0.74 > qscore #5.2 toVolume #2.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.75 logDetails false > assignAttr false Overall mean Q-Score: 0.69 > open /Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM- > QC/DATA/BRD9/M-26709/CryoEM_QC-M26709.cxs format session Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half1_map.mrc as #1.1, grid size 300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half2_map.mrc as #1.2, grid size 300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_local_filtered_map.mrc as #1.3, grid size 300,300,300, pixel 0.65, shown at level 0.0246, step 1, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_unsharpened_map.mrc as #1.4, grid size 300,300,300, pixel 0.65, shown at level 0.028, step 1, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc as #1.5, grid size 300,300,300, pixel 0.65, shown at level 0.0338, step 1, values float32 Opened Gaussian_local_filtered_map.mrc as #1.6, grid size 300,300,300, pixel 0.65, shown at level 0.0285, step 1, values float32 Opened Gaussian_unsharpened_map.mrc as #1.7, grid size 300,300,300, pixel 0.65, shown at level 0.0282, step 1, values float32 Opened final_unsharp_EMreadyOUT.mrc as #2.1, grid size 300,300,300, pixel 0.65, shown at level 4.81, step 1, values float32 Opened EMready_Maps as #2.2, grid size 300,300,300, pixel 0.65, shown at level 4.08, step 1, values float32 opened ChimeraX session > ui tool show ""Ramachandran Plot"" > hide #3 models > show #3 models > hide #5.1.5 models > hide #5.1.3 models > show #5.1.5 models > hide #5.1.5 models Drag select of 1 atoms, 1 bonds > select clear > hide #!2.2 models > ui mousemode right label > label #5.1/C:157 > label #5.1/C:156 > label #5.1/B:62 > label #5.1/C:160 > label #5.1/C:157 > show #!2.2 models > hide #!2.2 models > undo > hide #!2.2 models > ui mousemode right ""move label"" > select #5.1/B:58 6 atoms, 5 bonds, 1 residue, 1 model selected > select #5.1/B:58 6 atoms, 5 bonds, 1 residue, 1 model selected > label sel color green > select #5.1/B:58 6 atoms, 5 bonds, 1 residue, 1 model selected > label sel bgColor yellow > show #!2.2 models > ui mousemode right select > select clear > hide #3 models > show #3 models > show #5.1.5 models > hide #5.1.5 models > show #5.1.5 models > hide sel > ui mousemode right label > label #5.1/C:167 > label #5.1/B:196 > select #5.1/C:167 /B:196 16 atoms, 14 bonds, 4 pseudobonds, 2 residues, 2 models selected > select #5.1/C:167 /B:196 16 atoms, 14 bonds, 4 pseudobonds, 2 residues, 2 models selected > label sel color orange > select #5.1/C:167 /B:196 16 atoms, 14 bonds, 4 pseudobonds, 2 residues, 2 models selected > label sel bgColor light yellow > ui mousemode right ""move label"" > ui mousemode right select > select clear Drag select of 2.2 EMready_Maps > select clear > ui mousemode right ""move label"" > ui windowfill toggle > save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 885 > supersample 4 > ui windowfill toggle > open /Users/tarunnarwani/Library/CloudStorage/OneDrive- > AmphistaLTD/Proteros/SOW-8_C1943/AMPH-26709/DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb title: DDB1-DCAF16-BRD9 In complex with ligand AMPH-26709-010-04 [more info...] Chain information for DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb #4 --- Chain | Description A | No description available B | No description available C | No description available Non-standard residues in DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb #4 --- INX — (INX) ZN — (ZN) 21 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > color #4 #ff9300ff > color #4 #ff2600ff > select #4 8099 atoms, 8271 bonds, 8 pseudobonds, 1020 residues, 3 models selected > hide sel atoms > select #4/I 56 atoms, 61 bonds, 1 residue, 1 model selected > show sel atoms > color #4 bychain > select #4/B:191 11 atoms, 10 bonds, 1 residue, 1 model selected > select #4/B:191,62 23 atoms, 22 bonds, 2 residues, 1 model selected > select #4/B:191,54 25 atoms, 25 bonds, 2 residues, 1 model selected > select #4/B:191,52 19 atoms, 17 bonds, 2 residues, 1 model selected > select #4/B:191,53 16 atoms, 14 bonds, 2 residues, 1 model selected > select #4/B:191,55 20 atoms, 18 bonds, 2 residues, 1 model selected > select #4/B:191,55 20 atoms, 18 bonds, 2 residues, 1 model selected > show sel atoms > select #4/B:191,55 20 atoms, 18 bonds, 2 residues, 1 model selected > show sel atoms > color sel red > select #4/B:191,55 20 atoms, 18 bonds, 2 residues, 1 model selected > show sel atoms > color sel byhetero > select #5.1/B:191,55 20 atoms, 18 bonds, 2 residues, 1 model selected > show sel atoms > color #4 mediumslateblue > color #4 #7b68ee3a > color #4 #7b68ee8b > color #4 #7b68ee74 > color #4 #7b68ee73 > select #4/B:191,55 20 atoms, 18 bonds, 2 residues, 1 model selected > show sel atoms > color sel red > select #4/B:191,55 20 atoms, 18 bonds, 2 residues, 1 model selected > show sel atoms > color sel byhetero > ui mousemode right select > ui mousemode right ""move label"" > hide #!5.1 models > show #!5.1 models > hide #!5.1 models > show #!5.1 models > color #4 bychain > select #4/B:191,55 20 atoms, 18 bonds, 2 residues, 1 model selected > show sel atoms > color sel red > select #4/B:191,55 20 atoms, 18 bonds, 2 residues, 1 model selected > show sel atoms > color sel byhetero > ui mousemode right label > hide #!2.2 models > label #5.1/B:55 > ui mousemode right ""move label"" > ui mousemode right label > label delete residues > label sel color orange > label sel bgColor gray > ui mousemode right ""move label"" > ui mousemode right select > select clear Drag select of 1 pseudobonds > select add #5.1/C:163@CZ 1 atom, 7 pseudobonds, 1 residue, 3 models selected > select subtract #5.1/C:163 1 pseudobond, 1 model selected Drag select of 2 pseudobonds Drag select of 6 pseudobonds > hide sel > select clear > hide sel > select clear > hide sel > select clear Drag select of 1 pseudobonds > hide sel > select clear > hide sel > ui mousemode right label > ui mousemode right ""move label"" > ui mousemode right select > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 14 atoms, 15 bonds, 1 residue, 1 model selected > hide sel > select clear > select #5.1/B:196 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #5.1/C:166 15 atoms, 13 bonds, 2 residues, 1 model selected > select #5.1/C:167@CG 1 atom, 1 residue, 1 model selected > select #5.1/C:166 7 atoms, 6 bonds, 1 residue, 1 model selected > select ~sel & ##selected 8092 atoms, 8265 bonds, 257 pseudobonds, 1019 residues, 6 models selected > select up 8094 atoms, 8265 bonds, 257 pseudobonds, 1020 residues, 6 models selected > select ~sel & ##selected 5 atoms, 6 bonds, 1 residue, 1 model selected > select #5.1/C:167 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #5.1/B:196 16 atoms, 14 bonds, 2 residues, 1 model selected > hide sel > select #5.1/C:163 11 atoms, 11 bonds, 1 residue, 1 model selected > hide sel > select #5.1/B:173 6 atoms, 5 bonds, 1 residue, 1 model selected > select add #5.1/B:174 13 atoms, 11 bonds, 2 residues, 1 model selected > hide sel > show #!2.2 models > select clear > hide sel > select #4/B:55@OE1 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 1 model selected > select ~sel & ##selected 8090 atoms, 8263 bonds, 8 pseudobonds, 1019 residues, 3 models selected > select ~sel & ##selected 9 atoms, 8 bonds, 1 residue, 1 model selected > color #4 mediumslateblue > select #4/B:191,55 20 atoms, 18 bonds, 2 residues, 1 model selected > show sel atoms > color sel red > color #4 bychain > select #4/B:191,55 20 atoms, 18 bonds, 2 residues, 1 model selected > show sel atoms > color sel red > select #4/B:191,55 20 atoms, 18 bonds, 2 residues, 1 model selected > show sel atoms > color sel byhetero > select clear > color #2.2 #ffffff00 models > color #2.2 #ffffff14 models > color #2.2 #ffffff20 models > color #2.2 #ffffff1f models > hide #!2.2 models > show #!2.1 models > hide #!2.1 models > show #!2.2 models > hide #!2.2 models > show #!2.2 models > lighting flat > lighting soft > select #2.2 2 models selected > hide #!2.2 models > select #5.1/B:180 4 atoms, 3 bonds, 1 residue, 1 model selected > hide sel > select #4/B:55@NE2 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #5.1/B:191 20 atoms, 18 bonds, 2 residues, 2 models selected > select subtract #5.1/B:191 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 11 atoms, 9 bonds, 2 residues, 1 model selected > select up 20 atoms, 18 bonds, 2 residues, 1 model selected > show #!2.2 models > ui mousemode right ""move label"" > select #5.1/B:58 6 atoms, 5 bonds, 1 residue, 1 model selected > select #5.1/B:58 6 atoms, 5 bonds, 1 residue, 1 model selected > label sel color green > label sel bgColor yellow > ui mousemode right select > select clear > ui windowfill toggle > save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 885 > supersample 4 > ui windowfill toggle > open /Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM- > QC/DATA/BRD9/M-26709/CryoEM_QC-M26709.cxs format session Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half1_map.mrc as #1.1, grid size 300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half2_map.mrc as #1.2, grid size 300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_local_filtered_map.mrc as #1.3, grid size 300,300,300, pixel 0.65, shown at level 0.0246, step 1, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_unsharpened_map.mrc as #1.4, grid size 300,300,300, pixel 0.65, shown at level 0.028, step 1, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc as #1.5, grid size 300,300,300, pixel 0.65, shown at level 0.0338, step 1, values float32 Opened Gaussian_local_filtered_map.mrc as #1.6, grid size 300,300,300, pixel 0.65, shown at level 0.0285, step 1, values float32 Opened Gaussian_unsharpened_map.mrc as #1.7, grid size 300,300,300, pixel 0.65, shown at level 0.0282, step 1, values float32 Opened final_unsharp_EMreadyOUT.mrc as #2.1, grid size 300,300,300, pixel 0.65, shown at level 4.81, step 1, values float32 Opened EMready_Maps as #2.2, grid size 300,300,300, pixel 0.65, shown at level 4.08, step 1, values float32 opened ChimeraX session > color #2.2 #ffffff00 models > hide #!2.2 models > hide #3 models > hide #5.1.3 models > hide #5.1.4 models > hide #5.1.5 models > select #5.1/I:1@C25 1 atom, 1 residue, 1 model selected > select up 56 atoms, 61 bonds, 1 residue, 1 model selected > select down 1 atom, 1 residue, 1 model selected > select add #5.1/I:1@O27 2 atoms, 2 bonds, 1 residue, 1 model selected > select add #5.1/I:1@C28 3 atoms, 8 bonds, 1 residue, 1 model selected > select add #5.1/C:222@OH 4 atoms, 16 bonds, 2 residues, 1 model selected > select add #5.1/C:160 15 atoms, 27 bonds, 3 residues, 1 model selected > select add #5.1/I:1@C19 16 atoms, 27 bonds, 3 residues, 1 model selected > select add #5.1/I:1@C21 17 atoms, 28 bonds, 3 residues, 1 model selected > select subtract #5.1/I:1@C19 16 atoms, 28 bonds, 3 residues, 1 model selected > select add #5.1/I:1@C12 17 atoms, 29 bonds, 3 residues, 1 model selected > select add #5.1/I:1@C15 18 atoms, 32 bonds, 3 residues, 1 model selected > select add #5.1/I:1@C18 19 atoms, 37 bonds, 3 residues, 1 model selected > select add #5.1/C:161 30 atoms, 50 bonds, 4 residues, 1 model selected > contacts sel distanceOnly 3.4 9 distances > contacts sel distanceOnly 3.5 18 distances > show #3 models > undo > select add #5.1/C:215 42 atoms, 62 bonds, 5 residues, 1 model selected > contacts sel distanceOnly 3.5 23 distances > open /Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM- > QC/DATA/BRD9/M-26709/CryoEM_QC-M26709.cxs format session Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half1_map.mrc as #1.1, grid size 300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half2_map.mrc as #1.2, grid size 300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_local_filtered_map.mrc as #1.3, grid size 300,300,300, pixel 0.65, shown at level 0.0246, step 1, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_unsharpened_map.mrc as #1.4, grid size 300,300,300, pixel 0.65, shown at level 0.028, step 1, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc as #1.5, grid size 300,300,300, pixel 0.65, shown at level 0.0338, step 1, values float32 Opened Gaussian_local_filtered_map.mrc as #1.6, grid size 300,300,300, pixel 0.65, shown at level 0.0285, step 1, values float32 Opened Gaussian_unsharpened_map.mrc as #1.7, grid size 300,300,300, pixel 0.65, shown at level 0.0282, step 1, values float32 Opened final_unsharp_EMreadyOUT.mrc as #2.1, grid size 300,300,300, pixel 0.65, shown at level 4.81, step 1, values float32 Opened EMready_Maps as #2.2, grid size 300,300,300, pixel 0.65, shown at level 4.08, step 1, values float32 opened ChimeraX session > color #2.2 #ffffff00 models > ui mousemode right label > ui mousemode right select > select #2.2 2 models selected > select #2.2 2 models selected > select clear > hide #!2.2 models > select #5.1/B:174 7 atoms, 6 bonds, 1 residue, 1 model selected > select clear > color sel teal > select clear > color sel teal > select #5.1/C:169@CD1 1 atom, 1 residue, 1 model selected > color sel teal > select clear > ui tool show ""Side View"" > ui mousemode right ""move label"" > ui mousemode right select > select ~sel & ##selected 139 pseudobonds, 1 model selected > select ~sel 24332 atoms, 24676 bonds, 265 pseudobonds, 2040 residues, 31 models selected > select clear > color sel yellow > color sel light yellow > color sel palegreen yellow Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > select clear > color sel darkred yellow Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color sel lightblue orange Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color sel orange > color sel light yellow > show #!2.2 models > select clear > ui windowfill toggle > ui mousemode right ""move label"" > ui windowfill toggle > save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301 > supersample 3 > view > hide #!2.2 models > ui mousemode right label > label #5.1/C:158 > undo > ui mousemode right ""move label"" > hide #3 models > hide #5.1.5 models > show #5.1.5 models > hide #5.1.3 models > show #5.1.3 models > hide #!2.2 models > ui mousemode right label > ui mousemode right select > select clear > ui mousemode right ""move label"" > ui mousemode right label > ui mousemode right select > select #5.1/C:158 10 atoms, 10 bonds, 1 residue, 1 model selected > select #5.1/C:158 10 atoms, 10 bonds, 1 residue, 1 model selected > label sel bgColor lightblue white Expected a keyword > select #5.1/C:158 10 atoms, 10 bonds, 1 residue, 1 model selected > label sel bgColor white > select #5.1/C:158 10 atoms, 10 bonds, 1 residue, 1 model selected > label sel light yellow Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a keyword > select #5.1/C:158 10 atoms, 10 bonds, 1 residue, 1 model selected > label sel bgColor light yellow > select #5.1/C:158 10 atoms, 10 bonds, 1 residue, 1 model selected > label sel color green > ui mousemode right ""move label"" > ui mousemode right select > select clear > hide sel > save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301 > supersample 3 > select #5.1/B:173 6 atoms, 5 bonds, 1 residue, 1 model selected > select #5.1/B:178 6 atoms, 5 bonds, 1 residue, 1 model selected > ui mousemode right ""tape measure"" > marker segment #4 position 101.6,120.9,65.37 toPosition 106,122,63.79 color > yellow radius 0.1 label 4.839 labelHeight 0.4839 labelColor yellow > marker segment #4 position 101.6,120.9,65.37 toPosition 105.9,122.2,65.29 > color yellow radius 0.1 label 4.542 labelHeight 0.4542 labelColor yellow > marker segment #4 position 101.6,120.9,65.37 toPosition 105.2,122,64.93 > color yellow radius 0.1 label 3.836 labelHeight 0.3836 labelColor yellow > show #!2.2 models > hide #!4 models > ui mousemode right ""move label"" > ui mousemode right select > hide #!2.2 models > select #5.1/I:1@C40 1 atom, 1 residue, 1 model selected > select add #5.1/I:1@N39 2 atoms, 1 residue, 1 model selected > select add #5.1/I:1@C38 3 atoms, 1 residue, 1 model selected > select add #5.1/I:1@O48 4 atoms, 4 bonds, 1 residue, 1 model selected > select add #5.1/I:1@N57 5 atoms, 7 bonds, 1 residue, 1 model selected > select add #5.1/I:1@C54 6 atoms, 10 bonds, 1 residue, 1 model selected > select add #5.1/I:1@C52 7 atoms, 11 bonds, 1 residue, 1 model selected > select add #5.1/I:1@F55 8 atoms, 11 bonds, 1 residue, 1 model selected > contacts sel distanceOnly 3.5 No distances > contacts sel distanceOnly 4 2 distances > contacts sel distanceOnly 4 2 distances > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > hide #5.1.5 models > hide #5.1.3 models > show #3 models > hide #3 models > show #3 models > show #5.1.3 models > hide #5.1.3 models > show #5.1.3 models > select clear > select #5.1/B:54 14 atoms, 15 bonds, 1 residue, 1 model selected > select #5.1/B:54 14 atoms, 15 bonds, 1 residue, 1 model selected > select clear > select #5.1/B:55 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > show #!5.2 models > hide #!5.2 models > show #!5.2 models > hide #!5.2 models > ui mousemode right ""move label"" > ui mousemode right select > select clear Drag select of 2 residues > select clear > ui mousemode right ""move label"" > show #!2.2 models > save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301 > supersample 3 > ui mousemode right select > select #2.2 2 models selected > select #5.1/C:158 10 atoms, 10 bonds, 1 residue, 1 model selected > select #5.1/C:158 10 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > save /Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM- > QC/DATA/BRD9/M-26709/CryoEM_QC-M26709.cxs Taking snapshot of stepper: DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb > open ""/Users/tarunnarwani/Documents/StructurePG_TJR/ChimeraX/Picture > Sandbox- BRD9 images.cxs"" Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half1_map.mrc as #1.1, grid size 300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half2_map.mrc as #1.2, grid size 300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_local_filtered_map.mrc as #1.3, grid size 300,300,300, pixel 0.65, shown at level 0.0246, step 1, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_unsharpened_map.mrc as #1.4, grid size 300,300,300, pixel 0.65, shown at level 0.028, step 1, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc as #1.5, grid size 300,300,300, pixel 0.65, shown at level 0.0338, step 1, values float32 Opened Gaussian_local_filtered_map.mrc as #1.6, grid size 300,300,300, pixel 0.65, shown at level 0.0285, step 1, values float32 Opened Gaussian_unsharpened_map.mrc as #1.7, grid size 300,300,300, pixel 0.65, shown at level 0.0282, step 1, values float32 Opened final_unsharp_EMreadyOUT.mrc as #2.1, grid size 300,300,300, pixel 0.65, shown at level 4.81, step 1, values float32 Opened EMready_Maps as #2.2, grid size 300,300,300, pixel 0.65, shown at level 3.28, step 1, values float32 opened ChimeraX session > graphics silhouettes false > select #5.2/I 115 atoms, 120 bonds, 1 residue, 1 model selected > graphics selection sil Expected a keyword > graphics selection silhoutte Expected a keyword > select clear > select #5.2/I 115 atoms, 120 bonds, 1 residue, 1 model selected > graphics silhouettes true > graphics silhouettes false > graphics selection silhoutte true Expected a keyword > graphics selection silhouettes true Expected a keyword > graphics silhouettes true color orange depthJump 1.5 > select clear > select #5.2/I 115 atoms, 120 bonds, 1 residue, 1 model selected > graphics selection color black width 5 > graphics selection color black width 1 > graphics selection color black width 1.5 > graphics selection color black width 3 > graphics selection color black width 2 > graphics selection color black width 1 > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > select clear > graphics selection color black width 1 > select #5.2/I 115 atoms, 120 bonds, 1 residue, 1 model selected > graphics selection color black width 1 > select clear > select #5.2/I 115 atoms, 120 bonds, 1 residue, 1 model selected > open ""/Users/tarunnarwani/Documents/StructurePG_TJR/ChimeraX/Picture > Sandbox- BRD9 images.cxs"" format session Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half1_map.mrc as #1.1, grid size 300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half2_map.mrc as #1.2, grid size 300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_local_filtered_map.mrc as #1.3, grid size 300,300,300, pixel 0.65, shown at level 0.0246, step 1, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_unsharpened_map.mrc as #1.4, grid size 300,300,300, pixel 0.65, shown at level 0.028, step 1, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc as #1.5, grid size 300,300,300, pixel 0.65, shown at level 0.0338, step 1, values float32 Opened Gaussian_local_filtered_map.mrc as #1.6, grid size 300,300,300, pixel 0.65, shown at level 0.0285, step 1, values float32 Opened Gaussian_unsharpened_map.mrc as #1.7, grid size 300,300,300, pixel 0.65, shown at level 0.0282, step 1, values float32 Opened final_unsharp_EMreadyOUT.mrc as #2.1, grid size 300,300,300, pixel 0.65, shown at level 4.81, step 1, values float32 Opened EMready_Maps as #2.2, grid size 300,300,300, pixel 0.65, shown at level 3.28, step 1, values float32 opened ChimeraX session > graphics silhouettes false > show #!1.7 models > hide #!1.7 models > show #!1.6 models > hide #!1.6 models > show #!1.5 models > hide #!1.5 models > show #!2 models > select #5.2/C 1660 atoms, 1682 bonds, 101 residues, 1 model selected > select #5.2/C 1660 atoms, 1682 bonds, 101 residues, 1 model selected > color sel black > color zone #2.2 near #5.2@C /I distance 7 > select #5.2/A 11759 atoms, 11864 bonds, 4 pseudobonds, 747 residues, 2 models selected > color sel purple > select #5.2/I 115 atoms, 120 bonds, 1 residue, 1 model selected > color sel orange > color zone #2.2 near #5.2@C /I distance 7 > select clear > color zone #2.2 near #5.2@C /I distance 10 > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting flat > color zone #2.2 near #5.2@C /I distance 15 > hide #!5.2 models > volume #2.2 level 3.388 > volume #2.2 level 4.279 > surface dust #2.2 size 6.5 > save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301 > supersample 3 > graphics silhouettes false > graphics silhouettes true > open /Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM- > QC/DATA/BRD9/M-26709/CryoEM_QC-M26709.cxs format session Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half1_map.mrc as #1.1, grid size 300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half2_map.mrc as #1.2, grid size 300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_local_filtered_map.mrc as #1.3, grid size 300,300,300, pixel 0.65, shown at level 0.0246, step 1, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_unsharpened_map.mrc as #1.4, grid size 300,300,300, pixel 0.65, shown at level 0.028, step 1, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc as #1.5, grid size 300,300,300, pixel 0.65, shown at level 0.0338, step 1, values float32 Opened Gaussian_local_filtered_map.mrc as #1.6, grid size 300,300,300, pixel 0.65, shown at level 0.0285, step 1, values float32 Opened Gaussian_unsharpened_map.mrc as #1.7, grid size 300,300,300, pixel 0.65, shown at level 0.0282, step 1, values float32 Opened final_unsharp_EMreadyOUT.mrc as #2.1, grid size 300,300,300, pixel 0.65, shown at level 4.81, step 1, values float32 Opened EMready_Maps as #2.2, grid size 300,300,300, pixel 0.65, shown at level 4.08, step 1, values float32 opened ChimeraX session > hide #!2.2 models > hide #3 models > hide #!5.1 models > show #!5.2 models > select #5.2/B:178 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > show #!5.1 models > hide #!5.2 models > hide #5.1.3 models > ui mousemode right label > label #5.1/B:178 > ui mousemode right ""move label"" > label bgColor yellow > label bgColor light gray > ui mousemode right distance > distance #5.1/B:178@SG #5.1/I:1@C34 Distance between DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb #5.1/B CYS 178 SG and /I INX 1 C34: 4.542Å > distance #5.1/B:178@SG #5.1/I:1@C35 Distance between DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb #5.1/B CYS 178 SG and /I INX 1 C35: 4.256Å > ui mousemode right ""move label"" > open ""/Users/tarunnarwani/Documents/StructurePG_TJR/ChimeraX/Picture > Sandbox- BRD9 images.cxs"" format session Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half1_map.mrc as #1.1, grid size 300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half2_map.mrc as #1.2, grid size 300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_local_filtered_map.mrc as #1.3, grid size 300,300,300, pixel 0.65, shown at level 0.0246, step 1, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_unsharpened_map.mrc as #1.4, grid size 300,300,300, pixel 0.65, shown at level 0.028, step 1, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc as #1.5, grid size 300,300,300, pixel 0.65, shown at level 0.0338, step 1, values float32 Opened Gaussian_local_filtered_map.mrc as #1.6, grid size 300,300,300, pixel 0.65, shown at level 0.0285, step 1, values float32 Opened Gaussian_unsharpened_map.mrc as #1.7, grid size 300,300,300, pixel 0.65, shown at level 0.0282, step 1, values float32 Opened final_unsharp_EMreadyOUT.mrc as #2.1, grid size 300,300,300, pixel 0.65, shown at level 4.81, step 1, values float32 Opened EMready_Maps as #2.2, grid size 300,300,300, pixel 0.65, shown at level 3.28, step 1, values float32 opened ChimeraX session > graphics silhouettes false > lighting flat > lighting shadows true intensity 0.5 > graphics silhouettes false > lighting flat > graphics silhouettes false > save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301 > supersample 3 > select #5.1/B 1337 atoms, 1376 bonds, 29 pseudobonds, 171 residues, 3 models selected > select #5.1/B 1337 atoms, 1376 bonds, 29 pseudobonds, 171 residues, 3 models selected > show #!5.1 models > hide #!5.2 models > hide #!5.1 models > show #!5.2 models > select #5.2/B 2699 atoms, 2738 bonds, 4 pseudobonds, 171 residues, 2 models selected > select #5.2/B 2699 atoms, 2738 bonds, 4 pseudobonds, 171 residues, 2 models selected > color sel white > save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301 > supersample 3 > undo > select #5.2/C 1660 atoms, 1682 bonds, 101 residues, 1 model selected > color sel white > ui mousemode right select > select clear > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting flat > graphics silhouettes false > select #5.2/C 1660 atoms, 1682 bonds, 101 residues, 1 model selected > color sel light yellow > select clear > select #5.2/C 1660 atoms, 1682 bonds, 101 residues, 1 model selected > color sel yellow > select clear > save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301 > supersample 3 > select #5.2/C 1660 atoms, 1682 bonds, 101 residues, 1 model selected > color sel darkred yellow Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > select #5.2/C 1660 atoms, 1682 bonds, 101 residues, 1 model selected > color sel orange > select clear > save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301 > supersample 3 > select #5.2/B 2699 atoms, 2738 bonds, 4 pseudobonds, 171 residues, 2 models selected > color sel pink > select #5.2/B 2699 atoms, 2738 bonds, 4 pseudobonds, 171 residues, 2 models selected > color sel purple > select #5.2/B 2699 atoms, 2738 bonds, 4 pseudobonds, 171 residues, 2 models selected > color #5.2/B:58 byhetero > select #5.2/I 115 atoms, 120 bonds, 1 residue, 1 model selected > select #5.2/I 115 atoms, 120 bonds, 1 residue, 1 model selected > graphics selection color black > select #5.2/I 115 atoms, 120 bonds, 1 residue, 1 model selected > graphics selection color gray width Missing ""width"" keyword's argument > select #5.2/I 115 atoms, 120 bonds, 1 residue, 1 model selected > graphics selection color gray > select #5.2/I 115 atoms, 120 bonds, 1 residue, 1 model selected > graphics selection color gray width 1.4 > select #5.2/I 115 atoms, 120 bonds, 1 residue, 1 model selected > graphics selection color gray width 2 > select #5.2/I 115 atoms, 120 bonds, 1 residue, 1 model selected > graphics selection color gray width 1 > save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301 > supersample 3 > select #5.2/I 115 atoms, 120 bonds, 1 residue, 1 model selected > graphics selection color gray width 1 > select #5.2/B: black Nothing selected > select #5.2/B: color sel black Expected a keyword > select #5.2/B 2699 atoms, 2738 bonds, 4 pseudobonds, 171 residues, 2 models selected > color sel black > color byhetero > color #5.2/I white > select #5.2/I 115 atoms, 120 bonds, 1 residue, 1 model selected > graphics selection color black width 1 > select #5.2/I 115 atoms, 120 bonds, 1 residue, 1 model selected > color byhetero > save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301 > supersample 3 > color #5.2/B dark green > color byhetero > save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301 > supersample 3 > select clear > select add #5.2/B:179@SG 1 atom, 3 bonds, 1 residue, 1 model selected > label sel > select clear > select #5.2/B:177@SG 1 atom, 1 residue, 1 model selected > ui mousemode right label > label #5.2/B:100 > label #5.2/B:103 > label delete residues > label #5.2/B:177 > label #5.2/B:179 > label #5.2/B:100 > label #5.2/B:103 > select #5.2/I /B:58,100,103,177,179 165 atoms, 166 bonds, 6 residues, 1 model selected > label delete residues > select #5.2/I /B:58,100,103,177,179 Zn Expected a keyword > hide #5.2.2 models > select #5.2/I /B:58,100,103,177,179 165 atoms, 166 bonds, 6 residues, 1 model selected > color #5.2/I black > color #5.2/I byhetero > color #5.2/B light green > color #5.2/B byhetero > select #5.2/I /B:58,100,103,177,179 @CG 115 atoms, 120 bonds, 1 residue, 1 model selected > select #5.2/I /B:58,100,103,177,179 @CB 120 atoms, 120 bonds, 6 residues, 1 model selected > select #5.2/I /B:58,100,103,177,179 @CG 115 atoms, 120 bonds, 1 residue, 1 model selected > select #5.2/I /B:58,100,103,177,179 @CN 115 atoms, 120 bonds, 1 residue, 1 model selected > select #5.2/I /B:58,100,103,177,179 @C 120 atoms, 120 bonds, 6 residues, 1 model selected > select #5.2/I /B:58,100,103,177,179 @CG 115 atoms, 120 bonds, 1 residue, 1 model selected > select #5.2/I /B:58,100,103,177,179 @CB 120 atoms, 120 bonds, 6 residues, 1 model selected > select #5.2/I /B:58,100,103,177,179 @SG 120 atoms, 121 bonds, 6 residues, 1 model selected > select #5.2/I /B:58,100,103,177,179 @C,SG 125 atoms, 121 bonds, 6 residues, 1 model selected > select #5.2/I /B:58,100,103,177,179 165 atoms, 166 bonds, 6 residues, 1 model selected > select #5.2/I /B:58 125 atoms, 130 bonds, 2 residues, 1 model selected > save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301 > supersample 3 > save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301 > supersample 4 > show #!1.7 models > hide #!1.7 models > show #!1.6 models > show #!1.7 models > hide #!1.7 models > show #!1.7 models > hide #!1.6 models > hide #!1.7 models > show #!2 models > color zone #2.2 near #5.2@C /I distance 15 > color #5.2/I orange > color #5.2/C light gray > color zone #2.2 near #5.2@C /I distance 15 > graphics silhouettes true > hide #!5.2 models > select up 352 atoms, 360 bonds, 15 residues, 1 model selected > select down 125 atoms, 130 bonds, 2 residues, 1 model selected > color #5.2/B black > color #5.2/C dark green > color zone #2.2 near #5.2@C /I distance 15 > color #5.2/B purple > color zone #2.2 near #5.2@C /I distance 15 > save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301 > supersample 4 > color #5.2/C purple > color #5.2/B yellow > color #5.2/C light green > color #5.2/I black > color zone #2.2 near #5.2@C /I distance 15 > color #5.2/I dark gray > color #5.2/A purple > color zone #2.2 near #5.2@C /I distance 15 > save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301 > supersample 4 > color #5.2/I purple > color #5.2/C pink > color #5.2/A pink > color zone #2.2 near #5.2@C /I distance 15 > color #5.2/C green > color zone #2.2 near #5.2@C /I distance 15 > color #5.2/C light green > color zone #2.2 near #5.2@C /I distance 15 > save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301 > supersample 4 > color zone #2.2 near #5.2@C /I distance 15 > select #2.2 2 models selected > color zone #2.2 near #5.2@C /I distance 15 > open ""/Users/tarunnarwani/Documents/StructurePG_TJR/ChimeraX/Picture > Sandbox- BRD9 images.cxs"" format session Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half1_map.mrc as #1.1, grid size 300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half2_map.mrc as #1.2, grid size 300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_local_filtered_map.mrc as #1.3, grid size 300,300,300, pixel 0.65, shown at level 0.0246, step 1, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_unsharpened_map.mrc as #1.4, grid size 300,300,300, pixel 0.65, shown at level 0.028, step 1, values float32 Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc as #1.5, grid size 300,300,300, pixel 0.65, shown at level 0.0338, step 1, values float32 Opened Gaussian_local_filtered_map.mrc as #1.6, grid size 300,300,300, pixel 0.65, shown at level 0.0285, step 1, values float32 Opened Gaussian_unsharpened_map.mrc as #1.7, grid size 300,300,300, pixel 0.65, shown at level 0.0282, step 1, values float32 Opened final_unsharp_EMreadyOUT.mrc as #2.1, grid size 300,300,300, pixel 0.65, shown at level 4.81, step 1, values float32 Opened EMready_Maps as #2.2, grid size 300,300,300, pixel 0.65, shown at level 3.28, step 1, values float32 opened ChimeraX session > show #!2 models > hide #!5 models > save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301 > supersample 4 > color #5.2/C green > color zone #2.2 near #5.2@C /I distance 15 > undo > color #5.2/I orange > color #5.2/C green > color zone #2.2 near #5.2@C /I distance 15 > color #5.2/A purple > color zone #2.2 near #5.2@C /I distance 15 > save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301 > supersample 4 > color #5.2/B purple > color #5.2/C gem Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #5.2/C light blue > color #5.2/B light green > color zone #2.2 near #5.2@C /I distance 15 > save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301 > supersample 3 > color #5.2/I purple > color #5.2/A orange > color zone #2.2 near #5.2@C /I distance 15 > save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301 > supersample 4 > color #5.2/B light green > color zone #2.2 near #5.2@C /I distance 15 > color #5.2/B light pink > color zone #2.2 near #5.2@C /I distance 15 > save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301 > supersample 4 > color #5.2/I light green > color #5.2/B purple > color #5.2/C red > color zone #2.2 near #5.2@C /I distance 15 > color #5.2/B purple > color #5.2/C yellow > color #5.2/C red > color #5.2/A yellow > color zone #2.2 near #5.2@C /I distance 15 > save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301 > supersample 4 > hide #!5.2 models > show #!5.2 models > hide #!2 models > graphics silhouettes false > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting flat > graphics silhouettes false > color byhetero > hide #5.2.2 models > select #5.2/I /B:58 125 atoms, 130 bonds, 2 residues, 1 model selected > select #5.2/I /B:58 125 atoms, 130 bonds, 2 residues, 1 model selected > graphics selection color black width 1 > ui mousemode right select > select #5.2/B:1001@ZN 1 atom, 1 residue, 1 model selected > select #5.2/I /B:58 125 atoms, 130 bonds, 2 residues, 1 model selected > graphics selection color black width 1 > select add #5.2/B:1001@ZN 126 atoms, 130 bonds, 3 residues, 1 model selected > select subtract #5.2/B:1001@ZN 125 atoms, 130 bonds, 2 residues, 1 model selected > select add #5.2/B:1001@ZN 126 atoms, 130 bonds, 3 residues, 1 model selected > select add #5.2/B:100@SG 127 atoms, 132 bonds, 4 residues, 1 model selected > select subtract #5.2/B:100@SG 126 atoms, 131 bonds, 3 residues, 1 model selected > select add #5.2/B:100@SG 127 atoms, 131 bonds, 4 residues, 1 model selected > select subtract #5.2/B:100@SG 126 atoms, 131 bonds, 3 residues, 1 model selected > select add #5.2/B:177@SG 127 atoms, 132 bonds, 4 residues, 1 model selected > select subtract #5.2/B:177@SG 126 atoms, 132 bonds, 3 residues, 1 model selected > save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301 > supersample 4 > color #5.2/I orange > color #5.2/I byhetero > color #5.2/I white byhet Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color #5.2/I white > color #5.2/I byhetero > save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301 > supersample 4 > color #5.2/C pink > color #5.2/C darkred pink Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color #5.2/C salmon > color #5.2/I orange > color #5.2/I black > color #5.2/I byhetero > save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301 > supersample 4 > color #5.2/A light green > save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301 > supersample 4 > graphics silhouettes true > save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301 > supersample 4 ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M3 Pro 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: Mac15,6 Model Number: Z1AY0010LB/A Chip: Apple M3 Pro Total Number of Cores: 12 (6 performance and 6 efficiency) Memory: 36 GB System Firmware Version: 11881.121.1 OS Loader Version: 11881.121.1 Software: System Software Overview: System Version: macOS 15.5 (24F74) Kernel Version: Darwin 24.5.0 Time since boot: 39 days, 21 hours, 49 minutes Graphics/Displays: Apple M3 Pro: Chipset Model: Apple M3 Pro Type: GPU Bus: Built-In Total Number of Cores: 18 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal 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 autocommand: 2.2.2 babel: 2.16.0 backports.tarfile: 1.2.0 beautifulsoup4: 4.12.3 biopython: 1.83 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: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-Clipper: 0.24.0 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-Cytoscape: 0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMalign: 0.1.3 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 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-ISOLDE: 1.9 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-LigandRecognizer: 0.2 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 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OpenCommands: 1.2 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PhenixUI: 1.3.7 ChimeraX-PickBlobs: 1.0.1 ChimeraX-PICKLUSTER: 2.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-QScore: 1.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 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-StarMap: 1.2.15 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-TugLigands: 1.1 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 DiffFit: 0.7.0 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 finufft: 2.3.1 fonttools: 4.55.3 fsspec: 2025.3.2 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 importlib_metadata: 8.0.0 importlib_resources: 6.4.0 inflect: 7.3.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jaraco.context: 5.3.0 jaraco.functools: 4.0.1 jaraco.text: 3.12.1 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: 3.10.1 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 MolecularDynamicsViewer: 1.6 more-itertools: 10.3.0 mpmath: 1.3.0 mrcfile: 1.5.0 msgpack: 1.0.8 narwhals: 1.34.1 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: 2.2.4 numpy: 1.26.4 openvr: 1.26.701 ordered-set: 4.1.0 packaging: 23.2 packaging: 24.1 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 platformdirs: 4.2.2 plotly: 6.0.1 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 pyKVFinder: 0.7.3 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 pyqtgraph: 0.13.7 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 Send2Trash: 1.8.3 SEQCROW: 1.8.21 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 sympy: 1.13.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 toml: 0.10.2 tomli: 2.0.1 torch: 2.2.1 tornado: 6.4.2 traitlets: 5.14.3 typeguard: 4.3.0 typing_extensions: 4.12.2 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: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 zipp: 3.19.2 }}} " defect assigned normal Window Toolkit all ChimeraX