id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 10039 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 0x00007ff858962700 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 892 in init File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 1043 in File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code File ""/Applications/ChimeraX-1.6.1.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"":""2023-10-21 21:01:54.00 +0200"",""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"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 13.6 (22G120)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""D22DEF93-8E23-4B1F-B2BF-BB2DF0059522""} { ""uptime"" : 24000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 502, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro14,1"", ""coalitionID"" : 1346, ""osVersion"" : { ""train"" : ""macOS 13.6"", ""build"" : ""22G120"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2023-10-21 21:01:34.4621 +0200"", ""incident"" : ""D22DEF93-8E23-4B1F-B2BF-BB2DF0059522"", ""pid"" : 2445, ""cpuType"" : ""X86-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2023-10-21 14:04:12.7753 +0200"", ""procStartAbsTime"" : 2259648454170, ""procExitAbsTime"" : 24408481382761, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.6.1"",""CFBundleVersion"":""1.6.1.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""8A3E5B6F-CB07-58CB-B464-8BF5066EF728"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""E42A0C0F-3F75-6953-8AA3-C5AE878B565C"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 0, ""wakeTime"" : 17424, ""sleepWakeUUID"" : ""7BE25886-BEE4-485A-A564-374A747B7B8D"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x18 is not in any region. 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31 \n=========== ======= ======= \nTOTAL 3.5G 4124 \nTOTAL, minus reserved VM space 3.3G 4124 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""1f8df15f76495ddc69b3389a5a0a6e0c71b9b2d3"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""62fe74515312cd4599bd3c80"", ""factorPackIds"" : { ""MYRIAD_BOOSTS"" : ""62fe74805312cd4599bd3c81"" }, ""deploymentId"" : 240000006 }, { ""rolloutId"" : ""645c2d2f9e69a025b0a37e29"", ""factorPackIds"" : { }, ""deploymentId"" : 240000003 } ], ""experiments"" : [ { ""treatmentId"" : ""6dd670af-0633-45e4-ae5f-122ae4df02be"", ""experimentId"" : ""64406ba83deb637ac8a04419"", ""deploymentId"" : 900000017 } ] } } ===== 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/max.graf/Downloads/pdbfiles/PDB/TREX2-UAP56_on_P203-J138-coot-9.pdb Summary of feedback from opening /Users/max.graf/Downloads/pdbfiles/PDB/TREX2-UAP56_on_P203-J138-coot-9.pdb --- warnings | Start residue of secondary structure not found: SHEET 1 AA1 7 VAL A 107 PHE A 110 0 Start residue of secondary structure not found: SHEET 2 AA1 7 ILE A 130 GLY A 133 1 Start residue of secondary structure not found: SHEET 3 AA1 7 VAL A 78 MET A 81 1 Start residue of secondary structure not found: SHEET 4 AA1 7 HIS A 154 ASP A 158 1 Start residue of secondary structure not found: SHEET 5 AA1 7 GLN A 185 SER A 190 1 9 messages similar to the above omitted End residue of secondary structure not found: SHEET 1 AA3 7 VAL B 107 PHE B 110 0 Start residue of secondary structure not found: SHEET 2 AA3 7 ILE B 130 GLY B 133 1 Start residue of secondary structure not found: SHEET 3 AA3 7 VAL B 78 MET B 81 1 Start residue of secondary structure not found: SHEET 4 AA3 7 HIS B 154 ASP B 158 1 Start residue of secondary structure not found: SHEET 5 AA3 7 GLN B 185 SER B 190 1 Start residue of secondary structure not found: SHEET 6 AA3 7 VAL B 47 GLN B 50 1 8 messages similar to the above omitted Chain information for TREX2-UAP56_on_P203-J138-coot-9.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available H | No description available > open /Users/max.graf/Downloads/pdbfiles/PDB/TREX2_P203_J189-coot-3.pdb Summary of feedback from opening /Users/max.graf/Downloads/pdbfiles/PDB/TREX2_P203_J189-coot-3.pdb --- warnings | Start residue of secondary structure not found: HELIX 59 59 PHE H 47 PHE H 50 1 4 Start residue of secondary structure not found: HELIX 60 60 PRO H 54 ASP H 62 1 9 Start residue of secondary structure not found: HELIX 61 61 GLU H 70 GLN H 78 1 9 Start residue of secondary structure not found: HELIX 62 62 ALA H 79 LEU H 81 1 3 Start residue of secondary structure not found: HELIX 63 63 LYS H 95 GLN H 106 1 12 15 messages similar to the above omitted Cannot find LINK/SSBOND residue GLY (92 ) Cannot find LINK/SSBOND residue LYS (95 ) Cannot find LINK/SSBOND residue THR (96 ) Chain information for TREX2_P203_J189-coot-3.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available > open /Users/max.graf/Downloads/pdbfiles/PDB/HsUAP56_5suq_conf.pdb Summary of feedback from opening /Users/max.graf/Downloads/pdbfiles/PDB/HsUAP56_5suq_conf.pdb --- warning | Ignored bad PDB record found on line 1 Chain information for HsUAP56_5suq_conf.pdb #3 --- Chain | Description H | No description available Y | No description available > open > /Users/max.graf/Downloads/pdbfiles/PDB/maps/cryosparc_P203_J138_004_volume_map_sharp.mrc Opened cryosparc_P203_J138_004_volume_map_sharp.mrc as #4, grid size 256,256,256, pixel 0.878, shown at level 0.0592, step 1, values float32 > open > /Users/max.graf/Downloads/pdbfiles/PDB/maps/cryosparc_P203_J189_map_sharp_onGrid_J138.mrc Opened cryosparc_P203_J189_map_sharp_onGrid_J138.mrc as #5, grid size 256,256,256, pixel 0.878, shown at level 0.0513, step 1, values float32 > open > /Users/max.graf/Downloads/pdbfiles/PDB/maps/cryosparc_P203_J138_004_volume_map.mrc Opened cryosparc_P203_J138_004_volume_map.mrc as #6, grid size 256,256,256, pixel 0.878, shown at level 0.0429, step 1, values float32 > open > /Users/max.graf/Downloads/pdbfiles/PDB/maps/cryosparc_P203_J183_001_volume_map.mrc Opened cryosparc_P203_J183_001_volume_map.mrc as #7, grid size 256,256,256, pixel 0.878, shown at level 0.0513, step 1, values float32 > open > /Users/max.graf/Downloads/pdbfiles/PDB/maps/cryosparc_P203_J192_map_J183_lowpass_10.mrc Opened cryosparc_P203_J192_map_J183_lowpass_10.mrc as #8, grid size 256,256,256, pixel 0.878, shown at level 0.0528, step 1, values float32 > open > /Users/max.graf/Downloads/pdbfiles/PDB/maps/cryosparc_P203_J192_map_J183_lowpass_10_RecA2-only.mrc Opened cryosparc_P203_J192_map_J183_lowpass_10_RecA2-only.mrc as #9, grid size 256,256,256, pixel 0.878, shown at level 9.62e-06, step 1, values float32 > hide > show nucleic > hide protein|solvent|H > surface hidePatches > style (protein|nucleic|solvent) & @@draw_mode=0 stick Changed 0 atom styles > cartoon > cartoon style modeHelix default arrows true arrowsHelix false arrowScale 2 > width 2 thickness 0.4 sides 12 divisions 20 > cartoon style ~(nucleic|strand) xsection round > cartoon style (nucleic|strand) xsection rectangle > cartoon style protein modeHelix tube radius 2.2 sides 24 thickness 1.2 > cartoon style nucleic xsection round width 1.6 thickness 1.6 > nucleotides stubs > lighting shadows false > lighting soft intensity 0.4 fillIntensity 0.5 ambientIntensity 1 > camera ortho > graphics silhouettes true > windowsize 800 800 > size #1-10 pseudobondRadius 0.5 Changed 10 pseudobond radii > select #1-10 minimumLength 1 10 pseudobonds, 2 models selected > hide sel > set bgColor white > color #1/H plum target abcspf > color #1,2/B #334195 target abcspf > color #1,2/A #92D2FD target abcspf > color #1,2/C dodger blue target abcspf > view matrix camera > 0.041991,-0.17428,-0.9838,-48.918,0.4868,0.86346,-0.13218,93.226,0.8725,-0.47336,0.1211,130.91 > windowsize 600 600 > hide #!4 models > hide #!5 models > hide #!6 models > hide #!7 models > hide #3 models > show #3 models > hide #!8 models > hide #!9 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > hide > cartoon style modeHelix default arrows true arrowsHelix false arrowScale 2 > width 2 thickness 0.8 sides 12 divisions 20 > select add #3 3052 atoms, 3106 bonds, 10 pseudobonds, 377 residues, 3 models selected > show #!2 models > hide #!1 models > view matrix camera > 0.041991,-0.17428,-0.9838,-48.918,0.4868,0.86346,-0.13218,93.226,0.8725,-0.47336,0.1211,130.91 > view matrix view matrix camera 0.041991,-0.17428,-0.9838,-48.051,0.4868,0.86346,-0.13218,90.538,0.8725,-0.47336,0.1211,135.02 view matrix models #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#8,1,0,0,0,0,1,0,0,0,0,1,0,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#9,1,0,0,0,0,1,0,0,0,0,1,0,#9.1,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix camera > 0.041991,-0.17428,-0.9838,-48.051,0.4868,0.86346,-0.13218,90.538,0.8725,-0.47336,0.1211,135.02 > show #!1 models > hide #!1 models > zoom 0.9 > show #!1 models > hide #!2 models > zoom 1.05 > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > hide #!1 models > show #!2 models > view matrix camera > 0.041991,-0.17428,-0.9838,-48.051,0.4868,0.86346,-0.13218,90.538,0.8725,-0.47336,0.1211,135.02 > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > view matrix view matrix camera 0.041991,-0.17428,-0.9838,-48.807,0.4868,0.86346,-0.13218,94.019,0.8725,-0.47336,0.1211,132.68 view matrix models #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#8,1,0,0,0,0,1,0,0,0,0,1,0,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#9,1,0,0,0,0,1,0,0,0,0,1,0,#9.1,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix camera > 0.041991,-0.17428,-0.9838,-48.807,0.4868,0.86346,-0.13218,94.019,0.8725,-0.47336,0.1211,132.68 > hide #3 models > save /Volumes/Plaschka/max.graf/Master_thesis/png/fig6D_trex2.png pixelSize > 0.1 supersample 4 transparentBackground true > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!1 models > show #!2 models > hide #!1 models > select subtract #3 10 pseudobonds, 2 models selected > show #!1 models > hide #!2 models > save /Volumes/Plaschka/max.graf/Master_thesis/png/fig6D_trex2-uap56reca2.png > pixelSize 0.1 supersample 4 transparentBackground true > show #1/B,C target s > show #1/A target s > open > /Volumes/groups/plaschka/max.graf/Bioinfo/sequence_alignments/clustalo_alignment_9971470_PCID2.clustal Summary of feedback from opening /Volumes/groups/plaschka/max.graf/Bioinfo/sequence_alignments/clustalo_alignment_9971470_PCID2.clustal --- notes | Alignment identifier is clustalo_alignment_9971470_PCID2.clustal Associated TREX2-UAP56_on_P203-J138-coot-9.pdb chain B to sp|Q5JVF3|PCID2_HUMAN with 0 mismatches Associated TREX2_P203_J189-coot-3.pdb chain B to sp|Q5JVF3|PCID2_HUMAN with 0 mismatches Showing conservation header (""seq_conservation"" residue attribute) for alignment clustalo_alignment_9971470_PCID2.clustal Opened 8 sequences from clustalo_alignment_9971470_PCID2.clustal > color byattribute seq_conservation palette blue:red:yellow 17493 atoms, 2156 residues, 3 surfaces, atom seq_conservation range -1.79 to 2.59 > color byattribute seq_conservation 17493 atoms, 2156 residues, 3 surfaces, atom seq_conservation range -1.79 to 2.59 > hide #1/C target acs > view matrix camera > 0.041991,-0.17428,-0.9838,-48.807,0.4868,0.86346,-0.13218,94.019,0.8725,-0.47336,0.1211,132.68 > turn y 15 > undo > view matrix camera > 0.041991,-0.17428,-0.9838,-48.807,0.4868,0.86346,-0.13218,94.019,0.8725,-0.47336,0.1211,132.68 > open /Users/max.graf/Downloads/clustalo_alignment_4391299_GANP.clustal Summary of feedback from opening /Users/max.graf/Downloads/clustalo_alignment_4391299_GANP.clustal --- notes | Alignment identifier is clustalo_alignment_4391299_GANP.clustal Associated TREX2-UAP56_on_P203-J138-coot-9.pdb chain A to H.sapiens with 0 mismatches Associated TREX2_P203_J189-coot-3.pdb chain A to H.sapiens with 0 mismatches Showing conservation header (""seq_conservation"" residue attribute) for alignment clustalo_alignment_4391299_GANP.clustal Opened 8 sequences from clustalo_alignment_4391299_GANP.clustal > select up 10 pseudobonds, 2 models selected > color byattribute seq_conservation 17493 atoms, 2156 residues, 3 surfaces, atom seq_conservation range -1.79 to 2.85 > select clear > view matrix camera > 0.041991,-0.17428,-0.9838,-48.807,0.4868,0.86346,-0.13218,94.019,0.8725,-0.47336,0.1211,132.68 > turn y 30 > show #1/H:10-15 target a y 30 Expected a keyword > show #1/H:10-15 target a > color byhetero > undo > color #1/H byhetero > size stickRadius 0.3 Changed 17856 bond radii > size stickRadius 0.4 Changed 17856 bond radii > size stickRadius 0.3 Changed 17856 bond radii > turn y -30 > transparency #1/A 80 target s > transparency #1/A 80 target cs > transparency #1/A 80 target acs > transparency #1/A 90 target acs > transparency #1/A 0 target acs > hide #1/A,B target s > view matrix camera > 0.041991,-0.17428,-0.9838,-48.807,0.4868,0.86346,-0.13218,94.019,0.8725,-0.47336,0.1211,132.68 > color #1,2/B #334195 target abcspf > color #1,2/A #92D2FD target abcspf > color #1,2/C dodger blue target abcspf > view matrix camera > 0.041991,-0.17428,-0.9838,-48.807,0.4868,0.86346,-0.13218,94.019,0.8725,-0.47336,0.1211,132.68 > zoom 1.25 > turn y 30 > show #1/B:374,376,388 target a > color byhetero > turn y -30 > turn y 25 > show #1/A:891 target a > show #1/A:895 target a > hide #1/A:891 target a > zoom 1.25 > turn y5 Expected an axis vector or a keyword > turn y 5 > turn y -5 > undo > view matrix view matrix camera -0.21504,-0.20983,-0.9538,-39.646,0.44046,0.85084,-0.28648,44.383,0.87163,-0.48171,-0.09054,114.94 view matrix models #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#1.4,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#8,1,0,0,0,0,1,0,0,0,0,1,0,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#9,1,0,0,0,0,1,0,0,0,0,1,0,#9.1,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix camera > -0.21504,-0.20983,-0.9538,-39.646,0.44046,0.85084,-0.28648,44.383,0.87163,-0.48171,-0.09054,114.94 > ui tool show ""Side View"" > save /Volumes/Plaschka/max.graf/Master_thesis/png/fig6D_trex2-uap56reca2.png > pixelSize 0.1 supersample 4 transparentBackground true > save /Volumes/Plaschka/max.graf/Master_thesis/png/fig6D_trex2-uap56ntd.png > pixelSize 0.1 supersample 4 transparentBackground true > view matrix camera > 0.75602,0.035073,-0.6536,-20.296,-0.14069,-0.96651,-0.2146,29.646,-0.63925,0.2542,-0.72577,-47.817 > view matrix camera > 0.929,-0.040789,-0.36783,-1.2168,-0.094083,-0.98728,-0.12815,35.885,-0.35793,0.15366,-0.92102,-62.294 > view matrix camera > -0.21504,-0.20983,-0.9538,-39.646,0.44046,0.85084,-0.28648,44.383,0.87163,-0.48171,-0.09054,114.94 > save /Volumes/Plaschka/max.graf/Master_thesis/png/fig6D_trex2-uap56ntd.png > pixelSize 0.1 supersample 4 transparentBackground true > save /Volumes/Plaschka/max.graf/Master_thesis/png/fig8a_trex2-uap56ntd.png > pixelSize 0.1 supersample 4 transparentBackground true > show #1/A,B target s > open /Users/max.graf/Downloads/clustalo_alignment_4391299_GANP.clustal Summary of feedback from opening /Users/max.graf/Downloads/clustalo_alignment_4391299_GANP.clustal --- notes | Alignment identifier is clustalo_alignment_4391299_GANP.clustal Associated TREX2-UAP56_on_P203-J138-coot-9.pdb chain A to H.sapiens with 0 mismatches Associated TREX2_P203_J189-coot-3.pdb chain A to H.sapiens with 0 mismatches Showing conservation header (""seq_conservation"" residue attribute) for alignment clustalo_alignment_4391299_GANP.clustal Opened 8 sequences from clustalo_alignment_4391299_GANP.clustal > open > /Volumes/groups/plaschka/max.graf/Bioinfo/sequence_alignments/clustalo_alignment_9971470_PCID2.clustal Summary of feedback from opening /Volumes/groups/plaschka/max.graf/Bioinfo/sequence_alignments/clustalo_alignment_9971470_PCID2.clustal --- notes | Alignment identifier is clustalo_alignment_9971470_PCID2.clustal Associated TREX2-UAP56_on_P203-J138-coot-9.pdb chain B to sp|Q5JVF3|PCID2_HUMAN with 0 mismatches Associated TREX2_P203_J189-coot-3.pdb chain B to sp|Q5JVF3|PCID2_HUMAN with 0 mismatches Showing conservation header (""seq_conservation"" residue attribute) for alignment clustalo_alignment_9971470_PCID2.clustal Opened 8 sequences from clustalo_alignment_9971470_PCID2.clustal > color byattribute seq_conservation 17493 atoms, 2156 residues, 3 surfaces, atom seq_conservation range -1.79 to 2.85 > save > /Volumes/Plaschka/max.graf/Master_thesis/png/fig8a_trex2-uap56ntd_conservation.png > pixelSize 0.1 supersample 4 transparentBackground true > hide #1/A target c > transparency #1/A 90 > hide #1/A target ac > transparency #1/A 95 > save > /Volumes/Plaschka/max.graf/Master_thesis/png/fig8a_trex2-uap56ntd_conservation.png > pixelSize 0.1 supersample 4 transparentBackground true 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-20.6.4 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640 OpenGL vendor: Intel Inc. Python: 3.9.11 Locale: 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: MacBookPro14,1 Processor Name: Dual-Core Intel Core i5 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 4 MB Hyper-Threading Technology: Enabled Memory: 8 GB System Firmware Version: 515.0.0.0.0 OS Loader Version: 577.140.2~15 SMC Version (system): 2.43f11 Software: System Software Overview: System Version: macOS 13.6 (22G120) Kernel Version: Darwin 22.6.0 Time since boot: 20 hours, 51 minutes Graphics/Displays: Intel Iris Plus Graphics 640: Chipset Model: Intel Iris Plus Graphics 640 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x5926 Revision ID: 0x0006 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL U2723QE: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 30.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: 6C0HGH3 Main Display: Yes Mirror: Off Online: Yes Rotation: Supported 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: 2022.9.26 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