id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17969 Crash moving window between screens 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. 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""com.apple.CoreFoundation"", ""size"" : 5500928, ""uuid"" : ""df489a59-b4f6-32b8-9bb4-9b832960aa52"", ""path"" : ""\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation"", ""name"" : ""CoreFoundation"", ""CFBundleVersion"" : ""3502.1.401"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6834032640, ""CFBundleShortVersionString"" : ""6.9"", ""CFBundleIdentifier"" : ""com.apple.Foundation"", ""size"" : 14586624, ""uuid"" : ""e8f6a451-0acc-3e05-b18f-fec6618ce44a"", ""path"" : ""\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation"", ""name"" : ""Foundation"", ""CFBundleVersion"" : ""3502.1.401"" } ], ""sharedCache"" : { ""base"" : 6805913600, ""size"" : 5047205888, ""uuid"" : ""d7397d7f-8df9-3920-81a7-c0a144be9c51"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=4.4G written=193.2M(4%) resident=2618K(0%) swapped_out=190.7M(4%) unallocated=4.2G(96%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nCG image 208K 11 \nColorSync 640K 32 \nCoreAnimation 2464K 111 \nCoreGraphics 64K 4 \nCoreUI image data 2128K 21 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 3.6G 116 \nMALLOC guard page 288K 18 \nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 736K 46 \nStack 234.5M 47 \nStack Guard 56.0M 1 \nVM_ALLOCATE 430.7M 408 \nVM_ALLOCATE (reserved) 160.0M 2 reserved VM address space (unallocated)\n__AUTH 5521K 697 \n__AUTH_CONST 77.4M 944 \n__CTF 824 1 \n__DATA 34.2M 1092 \n__DATA_CONST 37.0M 1110 \n__DATA_DIRTY 2778K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 646.4M 160 \n__OBJC_RO 61.4M 1 \n__OBJC_RW 2396K 1 \n__TEXT 1.3G 1117 \n__TEXT (graphics) 11.2M 13 \n__TPRO_CONST 128K 2 \ndyld private memory 3360K 29 \nmapped file 283.7M 73 \npage table in kernel 2618K 1 \nshared memory 3760K 29 \n=========== ======= ======= \nTOTAL 6.9G 6444 \nTOTAL, minus reserved VM space 6.7G 6444 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""556647c35ef89b3806408c99b5701d85537eb44e"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""67d07cd6a7affa169ae21f45"", ""factorPackIds"" : { }, ""deploymentId"" : 240000002 }, { ""rolloutId"" : ""670e9bd77a111748a97092a1"", ""factorPackIds"" : { ""SIRI_TTS_DEVICE_TRAINING"" : ""67d07fb744f1a3655d87002b"" }, ""deploymentId"" : 240000016 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== 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 > open > /Users/gaurideak/Desktop/H2AZ-H2BV_Summary_Folder/Final_Structure/v28_for_thesis/TbH2AZ-H2BV_v29.2.pdb TbH2AZ-H2BV_v29.2.pdb title: The H2A.Z-H2B.V nucleosome core particle from trypanosoma brucei [more info...] Chain information for TbH2AZ-H2BV_v29.2.pdb #1 --- Chain | Description A E | T. brucei Histone H3 B F | T. brucei Histone H4 C G | T. brucei Histone H2A.Z D H | T. brucei Histone H2B.V I | Widom 601 145 bp DNA (143-mer ordered and built) J | Widom 601 145 bp DNA (143-mer ordered and built) > open > /Users/gaurideak/Desktop/Computational/TbH2AZ-H2BV_Model_Building/J381_H2AZ_H2BV/zflip/cryosparc_P121_J381_007_volume_map_zflip.mrc Opened cryosparc_P121_J381_007_volume_map_zflip.mrc as #2, grid size 304,304,304, pixel 0.829, shown at level 0.0171, step 2, values float32 > open > /Users/gaurideak/Desktop/Computational/TbH2AZ-H2BV_Model_Building/J381_H2AZ_H2BV/zflip/cryosparc_P121_J410_map_sharp_bfact80_zflip.mrc Opened cryosparc_P121_J410_map_sharp_bfact80_zflip.mrc as #3, grid size 304,304,304, pixel 0.829, shown at level 0.0229, step 2, values float32 > open > /Users/gaurideak/Desktop/Computational/TbH2AZ-H2BV_Model_Building/J381_H2AZ_H2BV/zflip/cryosparc_P121_J408_map_sharp_deepemhance_zflip.mrc Opened cryosparc_P121_J408_map_sharp_deepemhance_zflip.mrc as #4, grid size 304,304,304, pixel 0.829, shown at level 0.000929, step 2, values float32 > volume #2 level 0.03007 > volume #3 level 0.03474 > volume #4 level 0.03757 > hide atoms > show cartoons > volume #4 step 1 > volume #3 step 1 > volume #2 step 1 > transparency 50 > hide #!2 models > hide #!3 models > volume #4 level 0.0422 > hide #!4 models > show #!3 models > volume #3 level 0.05579 > hide #!3 models > show #!2 models > volume #2 level 0.02805 > ui tool show ""Command Line Interface"" > color #1/A,E blue > color #1/B,F green > color #1/C,G #ee9b00 > color #1/D,H #f395ab > color #1/I,J light grey > set bgColor white > undo > color #1/I,J light grey > graphics silhouettes true width 1.5 > graphics silhouettes true width 1 > lighting soft > graphics silhouettes true width 1.5 > open > /Users/gaurideak/Desktop/Computational/TbH2AZ-H2BV_Model_Building/TbH2AZ-H2BV_NCP_starting_model_truncated.pdb Chain information for TbH2AZ-H2BV_NCP_starting_model_truncated.pdb #5 --- Chain | Description A E | No description available B F | No description available C G | No description available D H | No description available I | No description available J | No description available > hide atoms > show cartoons > color #5 light green > show atoms > style stick Changed 23929 atom styles > volume #2 level 0.02453 > volume #2 level 0.0356 > volume #2 level 0.02906 > volume #2 level 0.02503 > volume #2 level 0.021 > color #2 #F8DD9A > color #1 orange > color #1 blue > color #5 light grey > color #1 cornflower blue > transparency 0.5 > transparency 50 > transparency 90 > transparency 70 > volume #2 level 0.03762 > ui tool show ""Side View"" > hide #!2 models > show #!2 models > hide #1 models > show #1 models > hide #!2 models > show #!2 models > hide #!2 models > ui tool show ""Surface Zone"" > ui mousemode right select > select #1/C:161 11 atoms, 11 bonds, 1 residue, 1 model selected > select #1/C:161 11 atoms, 11 bonds, 1 residue, 1 model selected > select #1/C:160 7 atoms, 7 bonds, 1 residue, 1 model selected Alignment identifier is 1/C > select #1/C:161 11 atoms, 11 bonds, 1 residue, 1 model selected > select #1/C:161-170 87 atoms, 88 bonds, 10 residues, 1 model selected > surface zone #2 nearAtoms #1 distance 4.97 > surface zone #2 nearAtoms sel distance 4.97 > show #!2 models > hide all atoms > hide all cartoons > show sel atoms > select #1/C:160-170 94 atoms, 96 bonds, 11 residues, 1 model selected > show sel atoms > select #1/C:159-170 101 atoms, 103 bonds, 12 residues, 1 model selected > show sel atoms > surface zone #2 nearAtoms sel distance 4.81 > surface zone #2 nearAtoms sel distance 2.58 > volume #2 level 0.03033 > surface zone #2 nearAtoms sel distance 2.93 > select clear > select #5/c 872 atoms, 881 bonds, 112 residues, 1 model selected Alignment identifier is 5/C > select #5/C:160 7 atoms, 7 bonds, 1 residue, 1 model selected > select #5/C:160-173 119 atoms, 121 bonds, 14 residues, 1 model selected > show sel atoms > style sel stick Changed 119 atom styles > color sel byhetero > color #5 coral > select clear > hide #5 models > hide #1 models > show #5 models > select #5/C:159 7 atoms, 6 bonds, 1 residue, 1 model selected > select #5/C:159 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select clear No atoms selected for zoning > show #1 models No atoms selected for zoning > select #1/C:159 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/C:159-170 101 atoms, 103 bonds, 12 residues, 1 model selected > surface zone #2 nearAtoms sel distance 2.44 > volume #2 level 0.03033 > surface zone #2 nearAtoms sel distance 2.93 > surface zone #2 nearAtoms sel distance 2.85 > surface zone #2 nearAtoms sel distance 2.93 > hide #!2 models > show #!2 models > hide #1 models > show #1 models > hide #5 models > select clear > show #1 cartoons > color #1 light grey > select #5/C:159-160 14 atoms, 14 bonds, 2 residues, 1 model selected > select #5/C:159-173 126 atoms, 128 bonds, 15 residues, 1 model selected > color sel blue > select #1/C:159 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/C:159-170 101 atoms, 103 bonds, 12 residues, 1 model selected > color sel blue > color sel #ee9b00 > select clear > show #5 models > hide #!2 models > show #!2 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #!2 models > show #!2 models > hide #5 models > select #1/D:114 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #1/D:132 14 atoms, 12 bonds, 2 residues, 1 model selected Alignment identifier is 1/D > select #1/D:115 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/D:115-137 171 atoms, 172 bonds, 23 residues, 1 model selected > select #1/D:115 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/D:115-137 171 atoms, 172 bonds, 23 residues, 1 model selected > select #1/D:115 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/D:115-136 166 atoms, 167 bonds, 22 residues, 1 model selected > select #1/D:115-116 13 atoms, 12 bonds, 2 residues, 1 model selected > select #1/D:115-135 157 atoms, 158 bonds, 21 residues, 1 model selected > show sel atoms > surface zone #2 nearAtoms sel distance 2.93 > select #1/D:111 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/D:111-134 179 atoms, 182 bonds, 24 residues, 1 model selected > select #1/D:110 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/D:110-129 145 atoms, 147 bonds, 20 residues, 1 model selected > select #1/D:110 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/D:110-130 157 atoms, 160 bonds, 21 residues, 1 model selected > surface zone #2 nearAtoms sel distance 2.93 > show sel atoms > select #1/D:112 7 atoms, 7 bonds, 1 residue, 1 model selected > select #1/D:112-132 154 atoms, 157 bonds, 21 residues, 1 model selected > show sel atoms > surface zone #2 nearAtoms sel distance 2.93 > hide all atoms > hide all cartoons > show sel cartoons > show sel atoms > hide sel cartoons > surface zone #2 nearAtoms sel distance 2.73 > surface zone #2 nearAtoms sel distance 2.58 > show #!3 models > hide #!3 models > color sel #f395ab > select clear > transparency 70 > transparency 50 > transparency 60 > volume #2 level 0.06 > volume #2 level 0.03039 > show #!3 models > hide #!2 models No atoms selected for zoning > select #1/D:112 7 atoms, 7 bonds, 1 residue, 1 model selected > select #1/D:112-132 154 atoms, 157 bonds, 21 residues, 1 model selected > surface zone #3 nearAtoms sel distance 4.97 > surface zone #3 nearAtoms sel distance 5.12 > surface zone #3 nearAtoms sel distance 2.27 > surface zone #3 nearAtoms sel distance 2.21 > surface zone #3 nearAtoms sel distance 2.46 > select clear > volume #2 level 0.03039 > hide #!2 models > volume #3 level 0.065 > volume #3 level 0.06267 > volume #3 level 0.04058 > volume #3 level 0.05686 > select #1/D:66 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/D:66-90 189 atoms, 191 bonds, 25 residues, 1 model selected > select #1/D:65-66 14 atoms, 13 bonds, 2 residues, 1 model selected > select #1/D:65-90 198 atoms, 200 bonds, 26 residues, 1 model selected > surface zone #3 nearAtoms sel distance 2.46 > show all atoms > hide all atoms > show sel atoms > color sel #f395ab > surface zone #3 nearAtoms sel distance 2.57 > surface zone #3 nearAtoms sel distance 2.03 > volume #3 level 0.06035 > color #3 #F8DD9A > select clear > volume #3 level 0.06965 > volume #3 level 0.0603 > volume #3 level 0.062 > transparency 70 > select #1/d:65-90 198 atoms, 200 bonds, 26 residues, 1 model selected > select #1/D:89 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/D:65-89 193 atoms, 195 bonds, 25 residues, 1 model selected > select #1/D:90 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/D:90 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/D:89 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/D:89 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/D:90 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/D:90 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/D:65 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/D:65 9 atoms, 8 bonds, 1 residue, 1 model selected > select clear > view name H2B > save /users/gaurideak/desktop/Model/H2B_chain_D_aa_65-90.tiff > select #1/C 836 atoms, 845 bonds, 108 residues, 1 model selected Alignment identifier is 1/C > select #1/C:64 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/C:64 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/C:97 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/C:97-124 194 atoms, 195 bonds, 28 residues, 1 model selected > select #1/C:95-120 180 atoms, 181 bonds, 26 residues, 1 model selected > select #1/C:100-125 187 atoms, 188 bonds, 26 residues, 1 model selected > show sel atoms > color sel #ee9b00 > hide #1/d atoms > surface zone #3 nearAtoms sel distance 2.03 > view name H2A > save /users/gaurideak/desktop/Model/H2A_chainC_aa_100-125.tiff > select clear > save /users/gaurideak/desktop/Model/H2A_chainC_aa_100-125.tiff > select #1/A 764 atoms, 774 bonds, 96 residues, 1 model selected Alignment identifier is 1/A > select #1/A:64 11 atoms, 11 bonds, 1 residue, 1 model selected > select #1/A:64 11 atoms, 11 bonds, 1 residue, 1 model selected > select #1/A:83 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/A:83-110 205 atoms, 206 bonds, 28 residues, 1 model selected > select #1/A:85-110 193 atoms, 194 bonds, 26 residues, 1 model selected Destroying pre-existing alignment with identifier 1/A Alignment identifier is 1/A > hide #1 atoms > show sel atoms > surface zone #3 nearAtoms sel distance 2.03 > view list Named views: H2A, H2B > view H2A > color sel #5772C5 > select clear No atoms selected for zoning > select #1/A:85-110 193 atoms, 194 bonds, 26 residues, 1 model selected > surface zone #3 nearAtoms sel distance 2.24 > surface zone #3 nearAtoms sel distance 2.06 > surface zone #3 nearAtoms sel distance 2.12 > surface zone #3 nearAtoms sel distance 1.98 > surface zone #3 nearAtoms sel distance 2.09 > select clear > view name H3 > save /users/gaurideak/desktop/Model/H3_chainA_aa_85-110.tiff > select #1/B 600 atoms, 605 bonds, 76 residues, 1 model selected Alignment identifier is 1/B > select #1/B:24 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/B:24 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/B:48-49 20 atoms, 20 bonds, 2 residues, 1 model selected > select #1/B:48-73 210 atoms, 213 bonds, 26 residues, 1 model selected > select #1/B:45-70 199 atoms, 201 bonds, 26 residues, 1 model selected > hide all atoms > show sel atoms > surface zone #3 nearAtoms sel distance 2.09 > color sel green > select clear > view name H4 > save /users/gaurideak/desktop/Model/H4_chainB_aa_45-70.tiff > hide all atoms > show #1 atoms > select #1/i,j 5863 atoms, 6576 bonds, 286 residues, 1 model selected Alignment identifier is 1/I Alignment identifier is 1/J > select clear > select #1/I:68-69 39 atoms, 42 bonds, 2 residues, 1 model selected > select #1/I:39-69 634 atoms, 710 bonds, 31 residues, 1 model selected > select #1/i:45-70 535 atoms, 599 bonds, 26 residues, 1 model selected > select #1/i:50-70 431 atoms, 482 bonds, 21 residues, 1 model selected > select #1/i:50-60 224 atoms, 250 bonds, 11 residues, 1 model selected > select #1/i:45-60 328 atoms, 367 bonds, 16 residues, 1 model selected > select #1/i:50-60 224 atoms, 250 bonds, 11 residues, 1 model selected > select #1/J:-50@P 1 atom, 1 residue, 1 model selected > select #1/J:-50@P 1 atom, 1 residue, 1 model selected > select #1/j:50-60 227 atoms, 254 bonds, 11 residues, 1 model selected > select #1/j:-50- -60 Expected an objects specifier or a keyword > select #1/j:-50 19 atoms, 20 bonds, 1 residue, 1 model selected > select #1/J:-50 19 atoms, 20 bonds, 1 residue, 1 model selected > select #1/J:-50--28 471 atoms, 527 bonds, 23 residues, 1 model selected > select #1/J:-50 19 atoms, 20 bonds, 1 residue, 1 model selected > select #1/J:-64--50 306 atoms, 342 bonds, 15 residues, 1 model selected > select #1/J:-60--50 227 atoms, 254 bonds, 11 residues, 1 model selected > select #1/I:50-60 /J:-60--50 451 atoms, 504 bonds, 22 residues, 1 model selected > surface zone #3 nearAtoms sel distance 2.09 > hide all atoms > show sel atoms > surface zone #3 nearAtoms sel distance 2.06 > surface zone #3 nearAtoms sel distance 3.29 > volume #3 level 0.04223 > surface zone #3 nearAtoms sel distance 3.07 > surface zone #3 nearAtoms sel distance 4.52 > volume #3 level 0.04921 > select clear > volume #!3 style mesh > transparency #3.1 0 > volume #!3 style surface > transparency #3.1 50 > surface unzone #3 > hide all atoms > show #1 cartoons > color #3 #F8DD9A > ui tool show ""Side View"" > volume #3 level 0.062 > volume #2 level 0.04107 > hide #!2 models > volume #3 level 0.05502 > volume #3 level 0.05037 > volume #3 level 0.04456 > show #!2 models > hide #!3 models > volume #2 level 0.04508 > hide #!2 models > show #!2 models > ui tool show ""Color Zone"" > ui tool show ""Surface Zone"" > surface unzone #2 > ui tool show ""Surface Color"" > ui tool show ""Color Zone"" > color #1/A,E blue > color #1/B,F green > color #1/C,G #ee9b00 > color #9/D,H #f395ab > color #9/I,J light grey > color #1/A,E #5772C5 #1/B,F green Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color #1/C,G #ee9b00 > color #1/D,H #f395ab > color #1/I,J light grey > color #1/a,e #5772C5 > select clear > color zone #2 near #1 distance 4.97 > volume #2 level 0.0319 > volume #2 level 0.0323 > hide #!2 models > show #!2 models > volume #2 level 0.0279 > volume #2 level 0.03549 > volume #2 level 0.0279 > color #2 light grey > color zone #2 near #1 distance 4.97 > hide #1 models > turn y -60 > turn y -30 > transparency #2.1 50 > show #1 models > hide #1 models > transparency #2.1 0 > save /users/gaurideak/desktop/map_coloured_by_histone.tiff > transparency #2.1 50 > show #1 models > save /users/gaurideak/desktop/map_with_model.tiff > turn y -90 > save /users/gaurideak/desktop/map_with_model_90.tiff > turn y 90 > turn y -90 > view name front > hide #1 models > show #1 models > hide #!2 models > save /users/gaurideak/desktop/model_alone.tiff > show #!2 models > hide #!2 models > show #!3 models > volume #3 level 0.03717 > hide #!3 models > select #1/J:-46 19 atoms, 20 bonds, 1 residue, 1 model selected > select add #1/J:-33 40 atoms, 43 bonds, 2 residues, 1 model selected Alignment identifier is 1/J > select #1/J:-45 21 atoms, 23 bonds, 1 residue, 1 model selected > select #1/J:-45--29 352 atoms, 395 bonds, 17 residues, 1 model selected > select #1/J:-45--30 333 atoms, 374 bonds, 16 residues, 1 model selected > hide sel cartoons > show sel atoms > select #1/I:45 20 atoms, 21 bonds, 1 residue, 1 model selected > select #1/J:-45--30 /I:30-45 656 atoms, 734 bonds, 32 residues, 1 model selected > hide sel cartoons > show sel atoms > ui tool show ""Surface Zone"" > surface zone #3 nearAtoms #1 distance 4.97 > show #!3 models > surface zone #3 nearAtoms #1 distance 4.97 > surface zone #3 nearAtoms sel distance 4.97 > hide all cartoons > surface zone #3 nearAtoms sel distance 4.65 > surface zone #3 nearAtoms sel distance 2.93 > select clear No atoms selected for zoning > select #1/J:-45--30 /I:30-45 656 atoms, 734 bonds, 32 residues, 1 model selected > surface zone #3 nearAtoms sel distance 2.67 > surface zone #3 nearAtoms sel distance 2.52 > surface zone #3 nearAtoms sel distance 2.7 > surface zone #3 nearAtoms sel distance 2.49 > surface zone #3 nearAtoms sel distance 2.55 > hide #!3 models > show #!3 models > volume #3 level 0.04944 > select clear > save /users/gaurideak/desktop/DNA_bases_30-45.tiff > transparency 70 > transparency 60 > transparency 70 > save /users/gaurideak/desktop/DNA.tiff > hide #!3 models > hide all atoms > show #1 cartoons > open 8com 8com title: Structure of the Nucleosome Core Particle from Trypanosoma brucei [more info...] Chain information for 8com #6 --- Chain | Description | UniProt A E | Histone H3, putative | Q4GYX7_TRYB2 1-132 B F | Histone H4 | Q57Z31_TRYB2 1-99 C G | Histone H2A | Q57YA3_TRYB2 1-133 D H | Histone H2B | Q389T1_TRYB2 1-111 I | Widom 601 145 bp DNA (127-mer ordered and built) | J | Widom 601 145 bp DNA (127-mer ordered and built) | > mmaker #6 to #1 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 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 TbH2AZ-H2BV_v29.2.pdb, chain J (#1) with 8com, chain J (#6), sequence alignment score = 789.4 RMSD between 90 pruned atom pairs is 1.164 angstroms; (across all 127 pairs: 1.881) > hide all atoms > show #8 cartoons > show #6 cartoons > color #6 light pink > color #6 grey > ui tool show Clashes > select #1/c 836 atoms, 845 bonds, 108 residues, 1 model selected > select #1/g 833 atoms, 842 bonds, 108 residues, 1 model selected > select #1/c 836 atoms, 845 bonds, 108 residues, 1 model selected > select clear > select #6/J:55 20 atoms, 21 bonds, 1 residue, 1 model selected > select #1/J:55 20 atoms, 21 bonds, 1 residue, 1 model selected > select #6/J:55 20 atoms, 21 bonds, 1 residue, 1 model selected > select #6/J:56 19 atoms, 20 bonds, 1 residue, 1 model selected > select #1/J:56 19 atoms, 20 bonds, 1 residue, 1 model selected > select clear > select #1/c 836 atoms, 845 bonds, 108 residues, 1 model selected > select #1/c #8/d 836 atoms, 845 bonds, 108 residues, 1 model selected > select #1/c #8/d 836 atoms, 845 bonds, 108 residues, 1 model selected > select #1/c #8/d 836 atoms, 845 bonds, 108 residues, 1 model selected > select #1/c #6/d 1567 atoms, 1583 bonds, 201 residues, 2 models selected > clashes sel restrict both ignoreHiddenModels true reveal true 83 clashes > clashes sel saveFile /Users/gaurideak/Desktop/H2AZ-H2B_clashes restrict both > ignoreHiddenModels true reveal true 83 clashes > select #1/c:75 #6/d:92 13 atoms, 11 bonds, 2 residues, 2 models selected > select #1/c:92 #6/d:75 20 atoms, 18 bonds, 19 pseudobonds, 2 residues, 3 models selected > style sel stick Changed 20 atom styles > hide #7 models > select add #7 20 atoms, 18 bonds, 83 pseudobonds, 2 residues, 3 models selected > select clear > hide all atoms > hide #!6 models > show #!6 models > hide #!6 models > select #1/C:156 4 atoms, 3 bonds, 1 residue, 1 model selected Alignment identifier is 1/C > select #1/C:156 4 atoms, 3 bonds, 1 residue, 1 model selected > select #1/C:156-170 116 atoms, 118 bonds, 15 residues, 1 model selected > show sel atoms > color sel byhetero > select clear > select #1/E:53 11 atoms, 10 bonds, 1 residue, 1 model selected Alignment identifier is 1/E > select #1/E:53 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/E:35-53 173 atoms, 176 bonds, 19 residues, 1 model selected > show sel atoms > style sel stick Changed 173 atom styles > style sel stick Changed 173 atom styles > color sel byhetero > select clear > select #1/J:70 22 atoms, 24 bonds, 1 residue, 1 model selected > select add #1/I:-67 42 atoms, 45 bonds, 2 residues, 1 model selected > show sel atoms > select #1/J:69 19 atoms, 20 bonds, 1 residue, 1 model selected > show sel atoms > select #1/I:-67 20 atoms, 21 bonds, 1 residue, 1 model selected > select clear > select #1/I:-68 21 atoms, 23 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select #1/E:42 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/E:35-36 20 atoms, 19 bonds, 2 residues, 1 model selected > select #1/E:35-42 74 atoms, 76 bonds, 8 residues, 1 model selected > hide sel atoms > select #1/E:46 11 atoms, 10 bonds, 1 residue, 1 model selected > select add #1/E:43 18 atoms, 16 bonds, 2 residues, 1 model selected > select add #1/E:50 27 atoms, 24 bonds, 3 residues, 1 model selected > select add #1/E:53 38 atoms, 34 bonds, 4 residues, 1 model selected > hide sel atoms > select clear > select #1/C:158 7 atoms, 6 bonds, 1 residue, 1 model selected > select add #1/C:159 14 atoms, 12 bonds, 2 residues, 1 model selected > hide sel atoms > select clear > hide #1/i,j atoms > select clear > open 9B3P Summary of feedback from opening 9B3P fetched from pdb --- note | Fetching compressed mmCIF 9b3p from http://files.rcsb.org/download/9b3p.cif 9b3p title: The cryo-EM structure of the H2A.Z-H3.3 double-variant nucleosome [more info...] Chain information for 9b3p #8 --- Chain | Description | UniProt A E | Histone H3.3 | H33_HUMAN 0-135 B F | Histone H4 | H4_XENLA 0-102 C G | Histone H2A.Z | H2AZ_MOUSE 0-127 D H | Histone H2B 1.1 | H2B11_XENLA 0-125 I | DNA (128-MER) | J | DNA (128-MER) | > mmaker #8 to #1 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 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 TbH2AZ-H2BV_v29.2.pdb, chain J (#1) with 9b3p, chain J (#8), sequence alignment score = 761.6 RMSD between 111 pruned atom pairs is 1.256 angstroms; (across all 128 pairs: 1.552) > mmaker #8/c to #1/xc No 'to' model specified > mmaker #8/c to #1/c Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 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 TbH2AZ-H2BV_v29.2.pdb, chain C (#1) with 9b3p, chain C (#8), sequence alignment score = 373.4 RMSD between 93 pruned atom pairs is 0.894 angstroms; (across all 98 pairs: 1.056) > hide #8 atoms > show #8 cartoons > ui tool show ""Side View"" > color #8/A,E cornflower blue > color #8/B,F medium sea green > color #8/C,G khaki > color #8/D,H light pink > color #8/I,J light grey > show #!6 models > mmaker #8 to #6 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 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 8com, chain J (#6) with 9b3p, chain J (#8), sequence alignment score = 752 RMSD between 65 pruned atom pairs is 1.285 angstroms; (across all 120 pairs: 2.074) > hide #!8 models > show #!8 models > hide #!6 models > color #8/c,g wheat > open 7xd1 Summary of feedback from opening 7xd1 fetched from pdb --- note | Fetching compressed mmCIF 7xd1 from http://files.rcsb.org/download/7xd1.cif 7xd1 title: cryo-EM structure of unmodified nucleosome [more info...] Chain information for 7xd1 #9 --- Chain | Description | UniProt A E | Histone H3 | A0A6I9KHI6_CHRAS 37-134 B F | Histone H4 | A0A0P9AXL3_DROAN 22-101 C G | Histone H2A type 1-B/E | H2A1B_HUMAN 10-118 D H | Histone H2B type 1-K | H2B1K_HUMAN 31-124 I | DNA (147-MER) | J | DNA (147-MER) | > mmaker #3 to #1 No molecules/chains to match specified > mmaker #9 to #1 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 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 TbH2AZ-H2BV_v29.2.pdb, chain J (#1) with 7xd1, chain J (#9), sequence alignment score = 778.5 RMSD between 111 pruned atom pairs is 1.120 angstroms; (across all 143 pairs: 1.646) > mmaker #9/c to #1/c Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 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 TbH2AZ-H2BV_v29.2.pdb, chain C (#1) with 7xd1, chain C (#9), sequence alignment score = 321.7 RMSD between 97 pruned atom pairs is 0.729 angstroms; (across all 106 pairs: 1.536) > hide all atoms > show #9 cartoons > hide #1,8,9/d,h,b,f cartoons > hide #1,8,9/d,h,b,f,g,a cartoons > mmaker #8/c to #1/c Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 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 TbH2AZ-H2BV_v29.2.pdb, chain C (#1) with 9b3p, chain C (#8), sequence alignment score = 373.4 RMSD between 93 pruned atom pairs is 0.894 angstroms; (across all 98 pairs: 1.056) > color #9/i,j light grey > color #9/c,g khaki > hide #1,8,9/c,g cartoons > hide #1,8,9/c,a cartoons > hide #1,8,9/c,e cartoons > show #1,8,9/g,a cartoons > color #9/a,e cornflower blue > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #1 models > show #1 models > hide #!9 models > close #5 > close #7 > show #!9 models > hide #!9 models > open 1f66 Summary of feedback from opening 1f66 fetched from pdb --- notes | Fetching compressed mmCIF 1f66 from http://files.rcsb.org/download/1f66.cif Fetching CCD MN from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/MN/MN.cif 1f66 title: 2.6 A crystal structure of A nucleosome core particle containing the variant histone H2A.Z [more info...] Chain information for 1f66 #5 --- Chain | Description | UniProt A E | HISTONE H3 | Q7ZT64_9ZZZZ 400-535 600-635 B F | HISTONE H4 | H4_MOUSE 0-102 200-302 C G | HISTONE H2A.Z | H2AZ_HUMAN 801-927 1001-1127 D H | HISTONE H2B | H2B1_XENLA 1198-1322 1398-1522 I J | PALINDROMIC 146 BASE PAIR DNA FRAGMENT | Non-standard residues in 1f66 #5 --- MN — manganese (II) ion > show #!6 models > hide #!5 models > hide #!6 models > hide #!8 models > show #!5 models > mmaker #5 to #9 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 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 7xd1, chain A (#9) with 1f66, chain A (#5), sequence alignment score = 477.5 RMSD between 97 pruned atom pairs is 0.377 angstroms; (across all 98 pairs: 0.553) > hide all atoms > show all cartoons > hide #!5 models > show #!5 models > hide #!5 models > open 9k43 Summary of feedback from opening 9k43 fetched from pdb --- note | Fetching compressed mmCIF 9k43 from http://files.rcsb.org/download/9k43.cif 9k43 title: Cryo-EM structure of Arabidopsis thaliana H2A.Z-nucleosome with 147bp Widom 601 DNA (C2 symmetry) [more info...] Chain information for 9k43 #7 --- Chain | Description | UniProt A E | Histone H3.1 | H31_ARATH 0-135 B F | Histone H4 | H4_ARATH 0-102 C G | Probable histone H2A variant 3 | H2AV3_ARATH 0-133 D H | Histone H2B.1 | H2B1_ARATH 0-147 I | Widom 601 DNA (147-MER) | J | Widom 601 DNA (147-MER) | > mmaker #7 to #8 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 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 9b3p, chain J (#8) with 9k43, chain I (#7), sequence alignment score = 803.2 RMSD between 120 pruned atom pairs is 1.046 angstroms; (across all 128 pairs: 1.179) > hide #1#!7 atoms > show #1#!7 cartoons > select clear > open 7m1x Summary of feedback from opening 7m1x fetched from pdb --- note | Fetching compressed mmCIF 7m1x from http://files.rcsb.org/download/7m1x.cif 7m1x title: Cryo-EM Structure of Nucleosome containing mouse histone variant H2A.Z [more info...] Chain information for 7m1x #10 --- Chain | Description | UniProt A E | Histone H3 | A0A310TTQ1_XENLA 400-535 600-735 B F | Histone H4 | H4_XENLA 0-102 200-302 C G | Histone H2A.Z | H2AZ_MOUSE 800-927 1000-1127 D H | Histone H2B 1.1 | H2B11_XENLA 1197-1322 1397-1522 I | DNA (136-MER) | J | DNA (136-MER) | > mmaker #10 to #1 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 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 TbH2AZ-H2BV_v29.2.pdb, chain J (#1) with 7m1x, chain J (#10), sequence alignment score = 768.5 RMSD between 121 pruned atom pairs is 1.070 angstroms; (across all 134 pairs: 1.440) > hide #1#!7,10 atoms > show #1#!7,10 cartoons > mmaker #10/c to #1/c Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 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 TbH2AZ-H2BV_v29.2.pdb, chain C (#1) with 7m1x, chain C (#10), sequence alignment score = 380 RMSD between 98 pruned atom pairs is 0.689 angstroms; (across all 103 pairs: 1.088) > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > open ""/Users/gaurideak/Desktop/EM maps > inventory/H2AZ_structures/emd_44148_9B3P_Hs.map"" Opened emd_44148_9B3P_Hs.map as #11, grid size 256,256,256, pixel 1.08, shown at level 0.00622, step 1, values float32 > open ""/Users/gaurideak/Desktop/EM maps > inventory/H2AZ_structures/emd_62042_9K43_Arabidopsis.map"" Opened emd_62042_9K43_Arabidopsis.map as #12, grid size 256,256,256, pixel 1.07, shown at level 0.182, step 1, values float32 > open ""/Users/gaurideak/Desktop/EM maps > inventory/HsCanonical_structures/emd_33132_7XD1.map"" Opened emd_33132_7XD1.map as #13, grid size 256,256,256, pixel 1.07, shown at level 0.00466, step 1, values float32 > open ""/Users/gaurideak/Desktop/EM maps inventory/emd_16777_8COM.map"" Opened emd_16777_8COM.map as #14, grid size 316,316,316, pixel 0.829, shown at level 0.197, step 2, values float32 > open ""/Users/gaurideak/Desktop/EM maps > inventory/H2AZ_structures/emd_23626_7M1X_mouse.map"" Opened emd_23626_7M1X_mouse.map as #15, grid size 200,200,200, pixel 1.1, shown at level 0.026, step 1, values float32 > hide #!15 models > hide #!14 models > hide #!13 models > hide #!12 models > hide #!11 models > hide #!10 models > hide #!7 models > show #!11 models > volume #11 level 0.0368 > volume #11 level 0.03841 > select add #11 2 models selected > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #11,-0.86367,-0.11873,0.48987,194.5,-0.1366,-0.88036,-0.4542,351.78,0.48519,-0.4592,0.74413,37.746 > view matrix models > #11,-0.75563,-0.090423,0.64873,154.04,-0.27764,-0.85283,-0.44226,364.75,0.59325,-0.5143,0.61932,48.826 > ui mousemode right ""translate selected models"" > view matrix models > #11,-0.75563,-0.090423,0.64873,155.53,-0.27764,-0.85283,-0.44226,344.47,0.59325,-0.5143,0.61932,27.703 > ui mousemode right ""rotate selected models"" > view matrix models > #11,-0.75565,-0.35676,0.54928,207.71,-0.024752,-0.82248,-0.56826,324.33,0.65451,-0.443,0.61267,10.298 > ui mousemode right ""translate selected models"" > view matrix models > #11,-0.75565,-0.35676,0.54928,196.42,-0.024752,-0.82248,-0.56826,321.37,0.65451,-0.443,0.61267,12.291 > ui mousemode right ""rotate selected models"" > view matrix models > #11,-0.88619,-0.30487,0.34888,234.11,0.034286,-0.79409,-0.60683,314.88,0.46204,-0.52581,0.71417,35.425 > view matrix models > #11,-0.87856,-0.30998,0.36338,231.82,0.068426,-0.83463,-0.54655,307.8,0.4727,-0.45531,0.75448,18.261 > view matrix models > #11,-0.87561,-0.3116,0.36908,230.86,0.08182,-0.84874,-0.52244,304.71,0.47605,-0.42725,0.76866,11.808 > ui mousemode right ""translate selected models"" > view matrix models > #11,-0.87561,-0.3116,0.36908,237.93,0.08182,-0.84874,-0.52244,303.87,0.47605,-0.42725,0.76866,11.859 > show #!2 models ===== 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 M1 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: MacBookPro17,1 Model Number: MYD92B/A Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 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: 10 days, 53 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal PHL24E1N1300A: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 100.00Hz 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: 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-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-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 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-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 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-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 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-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 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 closed normal Window Toolkit duplicate all ChimeraX