id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15180 Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-13.4-arm64-arm-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 0x00000001e3ab5e00 (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"":""2024-05-13 11:29:11.00 +0200"",""app_version"":""1.6.1"",""slice_uuid"":""a5992708-d5b4-36ec-ac0a-e525f6105b56"",""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 13.4 (22F66)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""210BD774-2EF6-42ED-8FAC-1A69A67DF78C""} { ""uptime"" : 69000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 503, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro18,1"", ""coalitionID"" : 571, ""osVersion"" : { ""train"" : ""macOS 13.4"", ""build"" : ""22F66"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2024-05-13 11:29:04.5979 +0200"", ""incident"" : ""210BD774-2EF6-42ED-8FAC-1A69A67DF78C"", ""pid"" : 92798, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2024-05-12 23:01:13.5305 +0200"", ""procStartAbsTime"" : 1202179468074, ""procExitAbsTime"" : 1679074774062, ""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"":""DC29D6E6-BD88-583F-A7B5-0ACAB477B8B2"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""D4ADD245-BCE5-8352-501B-75B83AD8CBFC"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 0, ""wakeTime"" : 3, ""sleepWakeUUID"" : ""14CBFECF-1EBC-4AE1-956F-E0A7D7A5D1EF"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x18 is not in any region. Bytes before following region: 105555129532392\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO (reserved) 600078000000-600080000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)"", ""exception"" : {""codes"":""0x0000000000000001, 0x0000000000000018"",""rawCodes"":[1,24],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x0000000000000018""}, ""vmregioninfo"" : ""0x18 is not in any region. 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\nTOTAL 22.4G 5999 \nTOTAL, minus reserved VM space 21.2G 5999 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""76093b707ed197260bed99be5b00e67c97445f03"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""62fe74515312cd4599bd3c80"", ""factorPackIds"" : { ""MYRIAD_BOOSTS"" : ""62fe74805312cd4599bd3c81"" }, ""deploymentId"" : 240000006 }, { ""rolloutId"" : ""63582c5f8a53461413999550"", ""factorPackIds"" : { }, ""deploymentId"" : 240000002 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle 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/barrass/Documents/Projects/HIV/Revitrified_and > _Pristine_0.6:1.0/Experiment1_October2023/3DVariabilityRangeMaps/Section0_PristineOnly/Model/Section0_Model9.pdb"" Chain information for Section0_Model9.pdb #1 --- Chain | Description A I | No description available B | No description available D | No description available E | No description available F | No description available > show cartoons > hide atoms > color #1 #07b5d8ff > set bgColor white > open ""/Users/barrass/Documents/Projects/HIV/Revitrified_and > _Pristine_0.6:1.0/Experiment1_October2023/3DVariabilityRangeMaps/Section6_RevandPristine/Model/Model3.pdb"" Chain information for Model3.pdb #2 --- Chain | Description A E I | No description available B | No description available D | No description available F | No description available > show cartoons > hide atoms > color #2 #d80053ff > style stick Changed 55694 atom styles > show atoms > open ""/Users/barrass/Documents/Projects/HIV/Revitrified_and > _Pristine_0.6:1.0/Experiment1_October2023/3DVariabilityRangeMaps/Section6_RevandPristine/Flipped/cryosparc_P7_J1764_map_flipped.mrc"" Opened cryosparc_P7_J1764_map_flipped.mrc as #3, grid size 480,480,480, pixel 0.83, shown at level 0.0289, step 2, values float32 > volume #3 step 1 > volume #3 style mesh > volume #3 level 0.09081 > volume #3 level 0.1797 > transparency 50 > volume #3 level 0.08497 > volume #3 style surface > open ""/Users/barrass/Documents/Projects/HIV/Revitrified_and > _Pristine_0.6:1.0/Experiment1_October2023/3DVariabilityRangeMaps/Section0_PristineOnly/Flipped/J1762_map_flipped.mrc"" Opened J1762_map_flipped.mrc as #4, grid size 480,480,480, pixel 0.83, shown at level 0.0293, step 2, values float32 > volume #4 step 1 > volume #4 style mesh > volume #4 level 0.06768 > volume #4 level 0.1532 > volume #4 style surface > volume #4 level 0.1203 > volume #4 level 0.1028 > volume #4 level 0.07974 > volume #4 style image > volume #4 style mesh > volume #4 style surface > volume #4 change image level -0.00998,0 level 0.02925,0.8 level 0.414,1 > volume #4 level 0.1017 > hide #!4 models > hide #!3 models > hide cartoons > show cartoons > hide atoms > volume #3 level 0.1072 > volume #4 style mesh > volume #4 style surface > transparency 0 > transparency 50 > volume #3 level 0.09666 > volume #4 style mesh > volume #4 color #0010ff80 > volume #4 level 0.08193 > hide #!2 models > hide #!3 models > show #!3 models > hide #!1 models > volume #3 > volume #4 style surface > volume #3 level 0.0819 > volume #4 color #a732f580 > volume #3 color #006cbf80 > lighting soft > transparency 0 > volume #3 color #42a3ff > volume #4 color #9e00ef > volume #4 color #a800ff > volume #3 color #9ad2f9 > volume #4 color #00a7f6 > volume #3 color #f100f7 > volume morph #4 #3 constantVolume true Opened morph as #5, grid size 480,480,480, pixel 0.83, shown at step 1, values float32 > close #5 > volume #3 color #c556f1 > volume morph #4 #3 constantVolume true Opened morph as #5, grid size 480,480,480, pixel 0.83, shown at step 1, values float32 > surface dust #5 size 8.3 > volume #3 level 0.0819 > volume #5 level 0.1068 > volume #5 level 0.08308 > volume #5 level 0.1028 > surface undust #3 > close #5 > volume morph #4 #3 constantVolume true Opened morph as #5, grid size 480,480,480, pixel 0.83, shown at step 1, values float32 > volume #5 level 0.1134 > volume morph #4 #3 Opened morph as #6, grid size 480,480,480, pixel 0.83, shown at step 1, values float32 > close #5 Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic models, 1 maps. > surface dust #6 size 8.3 > volume #6 level 0.1079 > volume #6 level 0.05711 > volume #6 level 0.1101 > volume #6 level 0.07636 > volume #6 level 0.1181 > volume #6 level 0.1531 > volume #6 level 0.09772 > surface undust #3 > surface undust #6 > volume #6 level 0.1587 > volume #6 level 0.1142 > show #!1 models > volume #6 style mesh > hide #!1 models > show #!2 models > volume #6 level 0.1467 > show #!1 models > 6UDA Unknown command: 6UDA > open PDB 6UDA 'PDB' has no suffix > open pdb6UDA 'pdb6UDA' has no suffix > open pdb:6UDA 6uda title: Cryo-EM structure of CH235UCA bound to Man5-enriched CH505.N279K.G458Y.SOSIP.664 [more info...] Chain information for 6uda #5 --- Chain | Description | UniProt A E I | CH505.N279K.G458Y.SOSIP.664 gp120 | M4M0W3_9HIV1 35-504 C G K | CH235 UCA heavy chain Fab | D H L | CH235 UCA light chain Fab | F J Z | CH505.N279K.G458Y.SOSIP.664 gp41 | Q2N0S5_9HIV1 511-664 Non-standard residues in 6uda #5 --- BMA — beta-D-mannopyranose MAN — alpha-D-mannopyranose NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose > open pdb:6UDA 6uda title: Cryo-EM structure of CH235UCA bound to Man5-enriched CH505.N279K.G458Y.SOSIP.664 [more info...] Chain information for 6uda #7 --- Chain | Description | UniProt A E I | CH505.N279K.G458Y.SOSIP.664 gp120 | M4M0W3_9HIV1 35-504 C G K | CH235 UCA heavy chain Fab | D H L | CH235 UCA light chain Fab | F J Z | CH505.N279K.G458Y.SOSIP.664 gp41 | Q2N0S5_9HIV1 511-664 Non-standard residues in 6uda #7 --- BMA — beta-D-mannopyranose MAN — alpha-D-mannopyranose NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose > ui tool show Matchmaker > close #5 > matchmaker #!7 to #1 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 Section0_Model9.pdb, chain I (#1) with 6uda, chain A (#7), sequence alignment score = 2181.2 RMSD between 379 pruned atom pairs is 0.870 angstroms; (across all 452 pairs: 2.179) > hide #!2 models > show #!1,7 cartoons > hide #!1,7 atoms > color #7 #d03700ff > select #7/C#7/G#7/K 4935 atoms, 5055 bonds, 3 pseudobonds, 660 residues, 2 models selected > delete atoms (#!7 & sel) > delete bonds (#!7 & sel) > select #7/D#7/H#7/L 4860 atoms, 4974 bonds, 630 residues, 1 model selected > delete atoms sel > delete bonds sel > close #7 > open pdb:6UDA 6uda title: Cryo-EM structure of CH235UCA bound to Man5-enriched CH505.N279K.G458Y.SOSIP.664 [more info...] Chain information for 6uda #5 --- Chain | Description | UniProt A E I | CH505.N279K.G458Y.SOSIP.664 gp120 | M4M0W3_9HIV1 35-504 C G K | CH235 UCA heavy chain Fab | D H L | CH235 UCA light chain Fab | F J Z | CH505.N279K.G458Y.SOSIP.664 gp41 | Q2N0S5_9HIV1 511-664 Non-standard residues in 6uda #5 --- BMA — beta-D-mannopyranose MAN — alpha-D-mannopyranose NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose > ui tool show Matchmaker > matchmaker #!5 to #1 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 Section0_Model9.pdb, chain I (#1) with 6uda, chain A (#5), sequence alignment score = 2181.2 RMSD between 379 pruned atom pairs is 0.870 angstroms; (across all 452 pairs: 2.179) > color #5 #d04580ff > hide #!1,5 atoms > show #!1,5 cartoons > select #5/C#5/G#5/K 4935 atoms, 5055 bonds, 3 pseudobonds, 660 residues, 2 models selected > color (#!5 & sel) forest green > select #5/D#5/H#5/L 4860 atoms, 4974 bonds, 630 residues, 1 model selected > color sel light sea green > select clear > show #!1,5 atoms > style #!1,5 stick Changed 51541 atom styles > show #!1,5 atoms > hide #!1,5 atoms > show #!1,5 atoms > show #!1,5 cartoons > hide #!1,5 atoms > select #5/E:160 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #1/A:154 22 atoms, 20 bonds, 2 residues, 2 models selected > select add #5/I:171 31 atoms, 28 bonds, 3 residues, 2 models selected > select add #1/E:153 51 atoms, 48 bonds, 4 residues, 2 models selected > select up 298 atoms, 297 bonds, 25 residues, 2 models selected > select up 21498 atoms, 21825 bonds, 1822 residues, 2 models selected > hide sel target a > cartoon hide sel > select #5/G:48 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #5/H:123 17 atoms, 15 bonds, 2 residues, 1 model selected > select add #5/C:199 24 atoms, 22 bonds, 3 residues, 1 model selected > select add #5/D:180 31 atoms, 28 bonds, 4 residues, 1 model selected > select up 210 atoms, 209 bonds, 28 residues, 1 model selected > select up 4885 atoms, 5001 bonds, 640 residues, 1 model selected > cartoon hide sel > select #5/C:21 6 atoms, 5 bonds, 1 residue, 1 model selected > select add #5/G:206 15 atoms, 13 bonds, 2 residues, 1 model selected > select #5/C:20 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 55 atoms, 54 bonds, 8 residues, 1 model selected > select up 1036 atoms, 1061 bonds, 137 residues, 1 model selected > select add #5/G:200 1042 atoms, 1066 bonds, 138 residues, 1 model selected > select up 1080 atoms, 1104 bonds, 144 residues, 1 model selected > select up 2254 atoms, 2309 bonds, 303 residues, 1 model selected > hide sel target a > hide sel cartoons > show sel cartoons > select #5/G:198 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 30 atoms, 30 bonds, 4 residues, 1 model selected > select up 609 atoms, 624 bonds, 83 residues, 1 model selected > hide sel cartoons > show sel atoms > select add #1 28417 atoms, 28740 bonds, 4 pseudobonds, 1855 residues, 3 models selected > select add #5 51541 atoms, 52395 bonds, 13 pseudobonds, 4814 residues, 4 models selected > show sel atoms > select clear > show #!6 models > hide #!6 models > show #!2 models > hide #!2 models > show #!3 models > hide #!5 models > show #!5 models > show #!6 models > hide #!6 models > hide #!3 models > hide #!1,5 atoms > OPEN PDB 8T4K Unknown command: OPEN PDB 8T4K > OPEN PDB:8T4K Unknown command: OPEN PDB:8T4K > OPEN PDB:8T4K Unknown command: OPEN PDB:8T4K > open pdb:8T4K Summary of feedback from opening 8T4K fetched from pdb --- note | Fetching compressed mmCIF 8t4k from http://files.rcsb.org/download/8t4k.cif 8t4k title: MD64 N332-GT5 sosip [more info...] Chain information for 8t4k #7 --- Chain | Description | UniProt A C D | MD64 N332-GT5 SOSIP gp120 | B E F | MD64 N332-GT5 SOSIP gp41 | Q2N0S8_9HIV1 512-664 Non-standard residues in 8t4k #7 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > ui tool show Matchmaker > matchmaker #!7 to #1 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 Section0_Model9.pdb, chain A (#1) with 8t4k, chain A (#7), sequence alignment score = 1859 RMSD between 371 pruned atom pairs is 0.993 angstroms; (across all 421 pairs: 1.862) > hide #!5 models > show #!1,7 cartoons > hide #!1,7 atoms > show #!5 models > hide #!7 models > hide #!5 models > hide #!1 models > open > /Users/barrass/Downloads/J2074_viewing_direction_distribution_iteration_012.bild.bild Opened BILD data containing 3072 objects > open /Users/barrass/Downloads/cryosparc_P7_J2074_012_volume_map.mrc Opened cryosparc_P7_J2074_012_volume_map.mrc as #9, grid size 480,480,480, pixel 0.83, shown at level 0.0102, step 2, values float32 > volume #9 step 1 > volume #9 level 0.05467 > show #!1 models > hide #!1 models > hide #8 models > show #!1 models > hide #!9 models > hide #!1 models > show #!9 models > close #8 > open > /Users/barrass/Downloads/J2074_viewing_direction_distribution_iteration_012.bild.bild Opened BILD data containing 3072 objects > open > /Users/barrass/Downloads/J2074_viewing_direction_distribution_iteration_012.bild.bild Opened BILD data containing 3072 objects > close #8 > close #10 > open > /Users/barrass/Downloads/J2074_viewing_direction_distribution_iteration_012.bild.bild Opened BILD data containing 3072 objects > volume flip #8 > close #8 > close #9 > open /Users/barrass/Downloads/cryosparc_P7_J1653_011_volume_map.mrc Opened cryosparc_P7_J1653_011_volume_map.mrc as #8, grid size 480,480,480, pixel 0.83, shown at level 0.00897, step 2, values float32 > volume #8 level 0.04616 > show #!5 models > hide #!5 models > show #!7 models > hide #!7 models > hide #!8 models > show #!1 models > hide #!1 models > show #!8 models > open > /Users/barrass/Downloads/J1653_viewing_direction_distribution_iteration_011.bild.bild Summary of feedback from opening /Users/barrass/Downloads/J1653_viewing_direction_distribution_iteration_011.bild.bild --- warning | text is not implemented on line 1 Opened BILD data containing 3072 objects > select add #8 2 models selected > color #8.1 cornflower blue > surface dust #8 size 8.3 > select clear > open /Users/barrass/Downloads/cryosparc_P7_J2075_volume_map.mrc Opened cryosparc_P7_J2075_volume_map.mrc as #10, grid size 480,480,480, pixel 0.83, shown at level 0.0171, step 2, values float32 > hide #9 models > volume #10 step 1 > volume #10 level 0.08417 > open /Users/barrass/Downloads/J2075_viewing_direction_distribution.bild.bild Opened BILD data containing 3072 objects > select add #10 2 models selected > select add #11 3 models selected > select add #11 3 models selected > select add #11 3 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #10,-0.97111,0.21034,0.11268,328.85,0.2158,0.97568,0.038511,-45.474,-0.10184,0.061714,-0.99289,389.32,#11,-0.97111,0.21034,0.11268,328.85,0.2158,0.97568,0.038511,-45.474,-0.10184,0.061714,-0.99289,389.32 > ui mousemode right ""move picked models"" > ui mousemode right ""translate selected models"" > view matrix models > #10,-0.97111,0.21034,0.11268,329.44,0.2158,0.97568,0.038511,-46.031,-0.10184,0.061714,-0.99289,403.48,#11,-0.97111,0.21034,0.11268,329.44,0.2158,0.97568,0.038511,-46.031,-0.10184,0.061714,-0.99289,403.48 > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models > #10,-0.97111,0.21034,0.11268,327.4,0.2158,0.97568,0.038511,-47.258,-0.10184,0.061714,-0.99289,405.62,#11,-0.97111,0.21034,0.11268,327.4,0.2158,0.97568,0.038511,-47.258,-0.10184,0.061714,-0.99289,405.62 > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models > #10,-0.97111,0.21034,0.11268,325.08,0.2158,0.97568,0.038511,-45.422,-0.10184,0.061714,-0.99289,405.26,#11,-0.97111,0.21034,0.11268,325.08,0.2158,0.97568,0.038511,-45.422,-0.10184,0.061714,-0.99289,405.26 > ui mousemode right translate > select clear > select add #10 2 models selected > select add #11 3 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #10,-0.9777,0.17391,0.11772,332.69,0.18186,0.98146,0.060463,-44.021,-0.10502,0.080523,-0.9912,401.82,#11,-0.9777,0.17391,0.11772,332.69,0.18186,0.98146,0.060463,-44.021,-0.10502,0.080523,-0.9912,401.82 > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > view matrix models > #10,-0.9777,0.17391,0.11772,333.46,0.18186,0.98146,0.060463,-44.856,-0.10502,0.080523,-0.9912,402.18,#11,-0.9777,0.17391,0.11772,333.46,0.18186,0.98146,0.060463,-44.856,-0.10502,0.080523,-0.9912,402.18 > view matrix models > #10,-0.9777,0.17391,0.11772,334.33,0.18186,0.98146,0.060463,-44.867,-0.10502,0.080523,-0.9912,402.11,#11,-0.9777,0.17391,0.11772,334.33,0.18186,0.98146,0.060463,-44.867,-0.10502,0.080523,-0.9912,402.11 > ui mousemode right ""translate selected models"" > ui mousemode right translate > volume flip #8 Opened cryosparc_P7_J1653_011_volume_map.mrc z flip as #12, grid size 480,480,480, pixel 0.83, shown at step 1, values float32 > redo > close #11#10 > hide #!12 models > show #!12 models > show #9 models > hide #9 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > close #12 > show #!8 models > show #9 models > open /Users/barrass/Downloads/cryosparc_P7_J2075_volume_map.mrc Opened cryosparc_P7_J2075_volume_map.mrc as #10, grid size 480,480,480, pixel 0.83, shown at level 0.0171, step 2, values float32 > open /Users/barrass/Downloads/J2075_viewing_direction_distribution.bild.bild Opened BILD data containing 3072 objects > volume flip #11 > volume #10 step 1 > volume #10 level 0.05697 > select add #10 2 models selected > select add #11 3 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #10,0.73586,0.67622,0.035138,-89.053,0.63112,-0.70374,0.32625,151.84,0.24535,-0.2179,-0.94463,366.76,#11,0.73586,0.67622,0.035138,-89.053,0.63112,-0.70374,0.32625,151.84,0.24535,-0.2179,-0.94463,366.76 > ui mousemode right translate > volume #10 level 0.08999 > ui mousemode right ""translate selected models"" > view matrix models > #10,0.73586,0.67622,0.035138,-85.936,0.63112,-0.70374,0.32625,152.35,0.24535,-0.2179,-0.94463,386.19,#11,0.73586,0.67622,0.035138,-85.936,0.63112,-0.70374,0.32625,152.35,0.24535,-0.2179,-0.94463,386.19 > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models > #10,0.73586,0.67622,0.035138,-87.37,0.63112,-0.70374,0.32625,146.08,0.24535,-0.2179,-0.94463,384.57,#11,0.73586,0.67622,0.035138,-87.37,0.63112,-0.70374,0.32625,146.08,0.24535,-0.2179,-0.94463,384.57 > ui mousemode right ""rotate selected models"" > view matrix models > #10,0.61509,0.78313,0.091505,-95.444,0.7459,-0.61557,0.25436,119.4,0.25553,-0.088203,-0.96277,360.14,#11,0.61509,0.78313,0.091505,-95.444,0.7459,-0.61557,0.25436,119.4,0.25553,-0.088203,-0.96277,360.14 > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models > #10,0.61509,0.78313,0.091505,-96.73,0.7459,-0.61557,0.25436,121.01,0.25553,-0.088203,-0.96277,360.44,#11,0.61509,0.78313,0.091505,-96.73,0.7459,-0.61557,0.25436,121.01,0.25553,-0.088203,-0.96277,360.44 > ui mousemode right translate > select clear > select add #10 2 models selected > color #10.1 hot pink > select subtract #10 Nothing selected > view orient > hide #!10 models > hide #11 models > show #11 models > hide #11 models > save ""/Users/barrass/Documents/Projects/HIV/Figures/Revtrified build image > 130624.tif"" width 4713 height 3000 supersample 3 transparentBackground true > hide #!8 models > hide #9 models > show #!10 models > show #11 models > surface dust #10 size 8.3 > save ""/Users/barrass/Documents/Projects/HIV/Figures/Revitrified build image > 130624.tif"" width 4713 height 3000 supersample 3 transparentBackground true > hide #!10 models > hide #11 models > show #!7 models > show #!1 models > hide #!1 models > hide #!7 models > show #!1 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > show #!5 models > select add #5 23733 atoms, 24279 bonds, 9 pseudobonds, 3042 residues, 2 models selected > show sel cartoons > select clear > hide #!5 models > hide #!1 models > show #!1 models > hide #!1 models > show #!3 models > show #!4 models > hide #!3 models > select add #4 3 models selected > ui tool show ""Color Actions"" > color sel turquoise > show #!3 models > select clear > surface dust #3 size 8.3 > surface dust #4 size 8.3 > volume #3 level 0.09 > volume #4 level 0.09 > volume #3 level 0.085 > volume #4 level 0.085 > volume #4 level 0.0839 > volume #4 level 0.085 > volume #3 level 0.1 > volume #4 level 0.1 > save ""/Users/barrass/Documents/Projects/HIV/Figures/Overlay of section= and > section6.tif"" width 4713 height 3000 supersample 3 transparentBackground > true QPainter::begin: Paint device returned engine == 0, type: 3 ===== Log before crash end ===== Log: Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle 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 Metal - 83.1 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple 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: MacBookPro18,1 Model Number: MK193SM/A Chip: Apple M1 Pro Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 8422.121.1 OS Loader Version: 8422.121.1 Software: System Software Overview: System Version: macOS 13.4 (22F66) Kernel Version: Darwin 22.5.0 Time since boot: 1 day, 13 hours, 43 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: DELL U2717D: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal 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-Clipper: 0.21.0 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-ISOLDE: 1.6.0 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 all ChimeraX