id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14826 Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x00007ff84a3ae7c0 (most recent call first): File ""/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 892 in init File ""/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 1043 in File ""/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code File ""/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 197 in _run_module_as_main {""app_name"":""ChimeraX"",""timestamp"":""2024-03-26 12:34:18.00 -0400"",""app_version"":""1.6.1"",""slice_uuid"":""5df621ee-554e-36a8-b448-93b2334e5480"",""build_version"":""1.6.1.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":1,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 14.3.1 (23D60)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""A5CA75D3-E854-482B-AB1B-093989A7842A""} { ""uptime"" : 290000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro15,2"", ""coalitionID"" : 594, ""osVersion"" : { ""train"" : ""macOS 14.3.1"", ""build"" : ""23D60"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2024-03-26 12:34:06.6434 -0400"", ""codeSigningMonitor"" : 0, ""incident"" : ""A5CA75D3-E854-482B-AB1B-093989A7842A"", ""pid"" : 70941, ""cpuType"" : ""X86-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2024-03-21 15:13:10.3956 -0400"", ""procStartAbsTime"" : 213915793684297, ""procExitAbsTime"" : 293830416714734, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/programs\/*\/ChimeraX.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.6.1"",""CFBundleVersion"":""1.6.1.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""AC853681-4A58-5B5D-82C4-63AC68D7F50B"",""thirdParty"":true}, ""parentProc"" : ""Exited process"", ""parentPid"" : 70940, ""coalitionName"" : ""com.apple.Terminal"", ""crashReporterKey"" : ""230C5750-009B-40BA-F65F-DA55A59EC0A2"", ""lowPowerMode"" : 1, ""responsiblePid"" : 18353, ""responsibleProc"" : ""Terminal"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""wakeTime"" : 35, ""bridgeVersion"" : {""build"":""21P3049"",""train"":""8.3""}, ""sleepWakeUUID"" : ""6B26C274-B1F8-4C83-9F1D-3CED0470F8A3"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x18 is not in any region. 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""path"" : ""\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox"", ""name"" : ""HIToolbox"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 140703241715712, ""size"" : 290814, ""uuid"" : ""c964889c-7792-333d-93f6-8f3e51a9f4c2"", ""path"" : ""\/usr\/lib\/system\/libdispatch.dylib"", ""name"" : ""libdispatch.dylib"" } ], ""sharedCache"" : { ""base"" : 140703239028736, ""size"" : 25769803776, ""uuid"" : ""812473cc-f3ee-3c27-a996-84e3ebdc0dc8"" }, ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""d3c69a5ac30a68aab167356e1e06b37f43ceb514"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""6112d17137f5d11121dcd4e2"", ""factorPackIds"" : { }, ""deploymentId"" : 240000522 }, { ""rolloutId"" : ""652eff3d1bce5442b8d753c9"", ""factorPackIds"" : { }, ""deploymentId"" : 240000009 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/J117_component_000_frame_000.mrc > /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/J117_component_000_frame_001.mrc > /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/J117_component_000_frame_002.mrc > /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/J117_component_000_frame_003.mrc > /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/J117_component_000_frame_004.mrc > /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/J117_component_000_frame_005.mrc > /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/J117_component_000_frame_006.mrc > /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/J117_component_000_frame_007.mrc > /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/J117_component_000_frame_008.mrc > /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/J117_component_000_frame_009.mrc > /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/J117_component_000_frame_010.mrc > /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/J117_component_000_frame_011.mrc > /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/J117_component_000_frame_012.mrc > /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/J117_component_000_frame_013.mrc > /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/J117_component_000_frame_014.mrc > /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/J117_component_000_frame_015.mrc > /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/J117_component_000_frame_016.mrc > /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/J117_component_000_frame_017.mrc > /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/J117_component_000_frame_018.mrc > /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/J117_component_000_frame_019.mrc Opened J117_component_000_frame_000.mrc as #1.1, grid size 320,320,320, pixel 0.861, shown at level 0.0226, step 2, values float32 Opened J117_component_000_frame_001.mrc as #1.2, grid size 320,320,320, pixel 0.861, shown at level 0.0226, step 2, values float32 Opened J117_component_000_frame_002.mrc as #1.3, grid size 320,320,320, pixel 0.861, shown at level 0.0227, step 2, values float32 Opened J117_component_000_frame_003.mrc as #1.4, grid size 320,320,320, pixel 0.861, shown at level 0.0228, step 2, values float32 Opened J117_component_000_frame_004.mrc as #1.5, grid size 320,320,320, pixel 0.861, shown at level 0.023, step 2, values float32 Opened J117_component_000_frame_005.mrc as #1.6, grid size 320,320,320, pixel 0.861, shown at level 0.0232, step 2, values float32 Opened J117_component_000_frame_006.mrc as #1.7, grid size 320,320,320, pixel 0.861, shown at level 0.0234, step 2, values float32 Opened J117_component_000_frame_007.mrc as #1.8, grid size 320,320,320, pixel 0.861, shown at level 0.0237, step 2, values float32 Opened J117_component_000_frame_008.mrc as #1.9, grid size 320,320,320, pixel 0.861, shown at level 0.024, step 2, values float32 Opened J117_component_000_frame_009.mrc as #1.10, grid size 320,320,320, pixel 0.861, shown at level 0.0243, step 2, values float32 Opened J117_component_000_frame_010.mrc as #1.11, grid size 320,320,320, pixel 0.861, shown at level 0.0246, step 2, values float32 Opened J117_component_000_frame_011.mrc as #1.12, grid size 320,320,320, pixel 0.861, shown at level 0.0249, step 2, values float32 Opened J117_component_000_frame_012.mrc as #1.13, grid size 320,320,320, pixel 0.861, shown at level 0.0253, step 2, values float32 Opened J117_component_000_frame_013.mrc as #1.14, grid size 320,320,320, pixel 0.861, shown at level 0.0257, step 2, values float32 Opened J117_component_000_frame_014.mrc as #1.15, grid size 320,320,320, pixel 0.861, shown at level 0.0261, step 2, values float32 Opened J117_component_000_frame_015.mrc as #1.16, grid size 320,320,320, pixel 0.861, shown at level 0.0267, step 2, values float32 Opened J117_component_000_frame_016.mrc as #1.17, grid size 320,320,320, pixel 0.861, shown at level 0.0272, step 2, values float32 Opened J117_component_000_frame_017.mrc as #1.18, grid size 320,320,320, pixel 0.861, shown at level 0.0278, step 2, values float32 Opened J117_component_000_frame_018.mrc as #1.19, grid size 320,320,320, pixel 0.861, shown at level 0.0284, step 2, values float32 Opened J117_component_000_frame_019.mrc as #1.20, grid size 320,320,320, pixel 0.861, shown at level 0.029, step 2, values float32 > vseries play #1 loop true No volume series specified > open > /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_000/*.mrc > vseries true Opened map series J117_component_000_frame_000.mrc as #2, 20 images, grid size 320,320,320, pixel 0.861, shown at level 0.0226, step 2, values float32 > close #1 > vseries play #2 loop true > stop > vseries stop Missing or invalid ""series"" argument: empty atom specifier > vseries stop #2 > volume #2.7 step 1 > volume #2.7 level 0.06643 > volume #2.7 level 0.07131 > volume #2.7 level 0.07023 > vseries play #2 loop true > movie record > movie encode /Users/bravine/Desktop/movie.mp4 framerate 25.0 Movie saved to /Users/bravine/Desktop/movie.mp4 > movie record > movie encode /Users/bravine/Desktop/movie.mp4 framerate 25.0 Movie saved to /Users/bravine/Desktop/movie.mp4 > movie record > movie encode /Users/bravine/Desktop/movie.mp4 framerate 25.0 Error processing trigger ""new frame"": Movie encoding failed because no images were recorded. > vseries stop #2 loop true Expected fewer arguments > vseries stop #2 > open > /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_001/*.mrc > vseries true Opened map series J117_component_001_frame_000.mrc as #1, 20 images, grid size 320,320,320, pixel 0.861, shown at level 0.0251, step 2, values float32 > open > /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_002/*.mrc > vseries true Opened map series J117_component_002_frame_000.mrc as #3, 20 images, grid size 320,320,320, pixel 0.861, shown at level 0.0247, step 2, values float32 > open > /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_003/*.mrc > vseries true Opened map series J117_component_003_frame_000.mrc as #4, 20 images, grid size 320,320,320, pixel 0.861, shown at level 0.0279, step 2, values float32 > open > /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J117_component_004/*.mrc > vseries true Opened map series J117_component_004_frame_000.mrc as #5, 20 images, grid size 320,320,320, pixel 0.861, shown at level 0.0243, step 2, values float32 > volume #1.20 color #ff4e54 > volume #1.20 color #ff6d6c > volume #1.20 color #85ffa1 > volume #1.20 color #99ff9a > volume #1.20 level 0.07 > volume #4.20 level 0.07 > volume #5.20 level 0.07 > volume #1.20 step 1 > volume #3.20 step 1 > volume #4.20 step 1 > volume #5.20 step 1 > volume #3.20 level 0.07 > hide #!2 models > show #!2 models > hide #!2 models > hide #!1 models > show #!1 models > hide #!3 models > hide #!4 models > hide #!5 models > select down Nothing selected > vseries play #1 loop true > vseries stop # Missing or invalid ""series"" argument: invalid map series specifier > vseries stop #1 > vseries play #1 loop false > vseries play #2 loop false > show #!2 models > hide #!1 models > vseries play #2 loop false > hide #!2 models > show #!3 models > vseries play #3 loop false > show #!1 models > hide #!3 models > vseries play #1 loop false > show #!2 models > hide #!1 models > vseries play #2 loop false > show #!4 models > hide #!2 models > vseries play #4 loop false > hide #!4 models > show #!5 models > vseries play #5 loop false > show #!1 models > show #!2 models > hide #!1 models > hide #!5 models > vseries play #5 loop false > vseries play #2 loop false > close #1-5 > open > /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/ChimeraX/cryosparc_P339_J103_NMIDPIWImask.mrc > /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/ChimeraX/cryosparc_P339_J108_PAZmask.mrc Opened cryosparc_P339_J103_NMIDPIWImask.mrc as #1.1, grid size 320,320,320, pixel 0.861, shown at level 1, step 2, values float32 Opened cryosparc_P339_J108_PAZmask.mrc as #1.2, grid size 320,320,320, pixel 0.861, shown at level 0.798, step 2, values float32 > volume #1.1 step 1 > volume #1.2 step 1 > volume #1.2 level 0.9749 > close #1 > open > /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/ChimeraX/cryosparc_P339_J103_NMIDPIWImask.mrc Opened cryosparc_P339_J103_NMIDPIWImask.mrc as #1, grid size 320,320,320, pixel 0.861, shown at level 1, step 2, values float32 > volume #1 level 0.9749 > open > /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/ChimeraX/cryosparc_P339_J108_PAZmask.mrc Opened cryosparc_P339_J108_PAZmask.mrc as #2, grid size 320,320,320, pixel 0.861, shown at level 0.798, step 2, values float32 > volume #2 step 1 > volume #1 step 1 > volume #2 level 0.9809 > ui mousemode right ""mark plane"" > volume #1 color #b2b2b24c > volume #1 color #b2b2b24d > volume #2 color #ffffb271 > volume #2 color #ffffb270 > volume #2 color #ffffb25e > ui mousemode right ""mark plane"" > ui mousemode right ""mark point"" > marker #3 position 136.6,142.6,139.3 color yellow radius 1 > marker #3 position 123.9,140.2,124.7 color yellow radius 1 > ui mousemode right ""delete markers"" > marker delete #3:2 > ui mousemode right ""move markers"" > marker change #3:1 position 133.6,142.1,136.1 > marker change #3:1 position 118.6,152.2,123.5 > marker change Missing or invalid ""someMarkers"" argument: empty atom specifier > marker change coordinateSystem #1 Missing or invalid ""someMarkers"" argument: invalid atoms specifier > marker change #3 coordinateSystem #1 > getcrd #3 Atom /M:1@M 118.582 152.189 123.484 > marker change #3 coordinateSystem #2 > getcrd #3 Atom /M:1@M 118.582 152.189 123.484 > close #1 > close #3 > close #2 > open > /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J118_component_000/*.mrc > vseries true Opened map series J118_component_000_frame_000.mrc as #1, 20 images, grid size 320,320,320, pixel 0.861, shown at level 0.0278, step 2, values float32 > open > /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J118_component_001/*.mrc > vseries true Opened map series J118_component_001_frame_000.mrc as #2, 20 images, grid size 320,320,320, pixel 0.861, shown at level 0.0252, step 2, values float32 > open > /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J118_component_002/*.mrc > vseries true Opened map series J118_component_002_frame_000.mrc as #3, 20 images, grid size 320,320,320, pixel 0.861, shown at level 0.026, step 2, values float32 > open > /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J118_component_003/*.mrc > vseries true Opened map series J118_component_003_frame_000.mrc as #4, 20 images, grid size 320,320,320, pixel 0.861, shown at level 0.0255, step 2, values float32 > open > /Users/bravine/Documents/JTLab/WAGOs/CryoEM/101023_17218-SST-T09PPP/P339/cryosparc_P339_J118_component_004/*.mrc > vseries true Opened map series J118_component_004_frame_000.mrc as #5, 20 images, grid size 320,320,320, pixel 0.861, shown at level 0.0254, step 2, values float32 > color #2 #76bf80ff models > volume #1.1 step 1 > volume #2.1 step 1 > volume #3.1 step 1 > volume #4.1 step 1 > volume #5.1 step 1 > volume #1.1 level 0.03509 > volume #2.1 level 0.035 > volume #3.1 level 0.035 > volume #5.1 level 0.035 > vseries play #1 loop false > vseries play #2 loop false > hide #!1 models > vseries play #2 loop false > vseries play #3 loop false > hide #!2 models > vseries play #3 loop false > hide #!3 models > vseries play #4 loop false > hide #!4 models > vseries play #5 loop false > hide #!5 models > show #!1 models > vseries play #1 loop false > ui tool show Rotamers Window position QRect(2415,251 600x300) outside any known screen, using primary screen No residues selected > close #1-5 > open /Users/bravine/Documents/JTLab/WAGOs/structural-overlays/AGO- > clade/4f3t-hAgo2.cif /Users/bravine/Documents/JTLab/WAGOs/structural- > overlays/AGO-clade/4kre-hAgo1.cif > /Users/bravine/Documents/JTLab/WAGOs/structural-overlays/AGO-clade/4krf- > hAgo1.cif /Users/bravine/Documents/JTLab/WAGOs/structural-overlays/AGO- > clade/5js2-hAgo2.cif /Users/bravine/Documents/JTLab/WAGOs/structural- > overlays/AGO-clade/5vm9-hAgo3.cif > /Users/bravine/Documents/JTLab/WAGOs/structural-overlays/AGO- > clade/5w6v-hAgo1.cif /Users/bravine/Documents/JTLab/WAGOs/structural- > overlays/AGO-clade/6oon-hAgo4.cif 4f3t-hAgo2.cif title: Human Argonaute-2 - miR-20a complex [more info...] Chain information for 4f3t-hAgo2.cif #1 --- Chain | Description | UniProt A | Protein argonaute-2 | AGO2_HUMAN 1-859 R | RNA (5'-R(P*UP*AP*AP*AP*GP*UP*GP*CP*UP*UP*AP*UP*AP*GP*UP*G*CP*AP*GP*G)-3') | Non-standard residues in 4f3t-hAgo2.cif #1 --- IPH — phenol 4kre-hAgo1.cif title: Structure of Human Argonaute-1 bound to endogenous Sf9 RNA [more info...] Chain information for 4kre-hAgo1.cif #2 --- Chain | Description | UniProt A | Protein argonaute-1 | AGO1_HUMAN 1-857 R | RNA (5'-R(P*AP*AP*UP*AP*UP*UP*AP*AP*A*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3') | 4krf-hAgo1.cif title: Structure of Human Argonaute-1 let-7 complex [more info...] Chain information for 4krf-hAgo1.cif #3 --- Chain | Description | UniProt A | Protein argonaute-1 | AGO1_HUMAN 1-857 R | RNA (5'-R(P*UP*GP*AP*GP*GP*UP*AP*GP*UP*AP*GP*GP*UP*UP*GP*UP*AP*UP*AP*GP*UP*U)-3') | 5js2-hAgo2.cif title: Human Argonaute-2 Bound to a Modified siRNA [more info...] Chain information for 5js2-hAgo2.cif #4 --- Chain | Description | UniProt A | Protein argonaute-2 | AGO2_HUMAN 1-859 B | modified siRNA | Non-standard residues in 5js2-hAgo2.cif #4 --- 6NW — 2'-O-methyl-5'-O-thiophosphonoadenosine 6OO — 2'-O-methyl-5'-O-thiophosphonocytidine 6OP — 1-[(5E)-5,6-dideoxy-2-O-(2-methoxyethyl)-6-phosphono-beta-D-ribo- hex-5-enofuranosyl]-5-methylpyrimidine-2,4(1H,3H)-dione F2T — 2'-deoxy-2'-fluoro-5'-O-thiophosphonouridine IPH — phenol MG — magnesium ion PO4 — phosphate ion UFT — 2'-deoxy-2'-fluorouridine 5'-(dihydrogen phosphate) 5vm9-hAgo3.cif title: Human Argonaute3 bound to guide RNA [more info...] Chain information for 5vm9-hAgo3.cif #5 --- Chain | Description | UniProt A C | Protein argonaute-3 | AGO3_HUMAN 1-860 B | RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*UP*U)-3') | D | RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*UP*U)-3') | 5vm9-hAgo3.cif mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 5w6v-hAgo1.cif title: The Structure of human Argonaute-1 in complex with the hook motif of human GW182 [more info...] Chain information for 5w6v-hAgo1.cif #6 --- Chain | Description | UniProt A | Protein argonaute-1 | AGO1_HUMAN 1-857 B | Trinucleotide repeat-containing gene 6A protein | TNR6A_HUMAN 820-841 R | RNA (5'-R(P*AP*AP*UP*AP*UP*UP*AP*AP*AP*A)-3') | 6oon-hAgo4.cif title: Human Argonaute4 bound to guide RNA [more info...] Chain information for 6oon-hAgo4.cif #7 --- Chain | Description | UniProt A | Protein argonaute-4 | AGO4_HUMAN 1-861 B | RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*UP*U)-3') | Unsupported scale factor (0.000000) detected on Display0 QPainter::begin: Paint device returned engine == 0, type: 3 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-22.1.29 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655 OpenGL vendor: Intel Inc. Python: 3.9.11 Locale: en_US.UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro15,2 Processor Name: Quad-Core Intel Core i5 Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 2020.80.5.0.1 (iBridge: 21.16.3049.0.0,0) OS Loader Version: 580~1337 Software: System Software Overview: System Version: macOS 14.3.1 (23D60) Kernel Version: Darwin 23.3.0 Time since boot: 13 days, 15 hours, 42 minutes Graphics/Displays: Intel Iris Plus Graphics 655: Chipset Model: Intel Iris Plus Graphics 655 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3ea5 Revision ID: 0x0001 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Thunderbolt Display: Display Type: LCD Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: C02PX25NF2GC Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: Yes Connection Type: Thunderbolt/DisplayPort Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 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: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 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: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.2.22 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect closed normal Window Toolkit duplicate Tom Goddard all ChimeraX