Opened 13 months ago

Closed 12 months ago

#16123 closed defect (can't reproduce)

Crash in Qt redraw after screen disconnect

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Window Toolkit Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

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 0x0000000200b5d2c0 (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/save_command/dialog.py", line 39 in display
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/save_command/dialog.py", line 127 in show_save_file_dialog
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/save_command/dialog.py", line 116 in 
  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


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{
  "uptime" : 280000,
  "procRole" : "Background",
  "version" : 2,
  "userID" : 379343813,
  "deployVersion" : 210,
  "modelCode" : "Mac14,9",
  "coalitionID" : 55424,
  "osVersion" : {
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    "build" : "22D68",
    "releaseType" : "User"
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  "captureTime" : "2024-10-11 15:22:50.1374 -0700",
  "incident" : "13C00820-787A-428A-99E6-DBEAB6E80419",
  "pid" : 44219,
  "translated" : true,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2024-10-10 18:31:25.3037 -0700",
  "procStartAbsTime" : 6381774426100,
  "procExitAbsTime" : 6786744790867,
  "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":"4FC7D034-2ACA-5BED-8456-AEF1ED111E4F","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "49A7EAB0-B44A-F787-66C8-922581B31ABB",
  "throttleTimeout" : 2147483647,
  "wakeTime" : 3846,
  "sleepWakeUUID" : "6F25391E-09F7-4EE4-9499-03499A6EA9A1",
  "sip" : "enabled",
  "vmRegionInfo" : "0x24 is not in any region.  Bytes before following region: 140722769100764\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      mapped file              7ffc92aa0000-7ffc9d56c000 [170.8M] r-x\/r-x SM=COW  ...t_id=1d6702c5",
  "exception" : {"codes":"0x0000000000000001, 0x0000000000000024","rawCodes":[1,36],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000024"},
  "vmregioninfo" : "0x24 is not in any region.  Bytes before following region: 140722769100764\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      mapped file              7ffc92aa0000-7ffc9d56c000 [170.8M] r-x\/r-x SM=COW  ...t_id=1d6702c5",
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  "faultingThread" : 0,
  "threads" : 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    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703429365760,
    "CFBundleShortVersionString" : "2.1.1",
    "CFBundleIdentifier" : "com.apple.HIToolbox",
    "size" : 3112958,
    "uuid" : "7bf47984-29cb-319e-a6da-0884d158f96a",
    "path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
    "name" : "HIToolbox"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703313932288,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.AppKit",
    "size" : 16814067,
    "uuid" : "540cedfd-5a35-3f35-8953-dcb7c4834eb5",
    "path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
    "name" : "AppKit",
    "CFBundleVersion" : "2299.40.118"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4447399936,
    "CFBundleShortVersionString" : "3.9.11, (c) 2001-2021 Python Software Foundation.",
    "CFBundleIdentifier" : "org.python.python",
    "size" : 2527232,
    "uuid" : "ef9cc1f4-5991-3213-9a9e-e68c578b6c1b",
    "path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/Python",
    "name" : "Python",
    "CFBundleVersion" : "3.9.11"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4532838400,
    "size" : 1605632,
    "uuid" : "5590e5eb-1a53-3bf0-9ffc-71d23992c730",
    "path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/QtCore.abi3.so",
    "name" : "QtCore.abi3.so"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 5052956672,
    "size" : 1490944,
    "uuid" : "9c3eb0df-69a3-3b03-ab77-80606e4891d2",
    "path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/QtGui.abi3.so",
    "name" : "QtGui.abi3.so"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4303298560,
    "CFBundleShortVersionString" : "1.6.1",
    "CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
    "size" : 4096,
    "uuid" : "5df621ee-554e-36a8-b448-93b2334e5480",
    "path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
    "name" : "ChimeraX",
    "CFBundleVersion" : "1.6.1.0"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 8601178112,
    "size" : 622592,
    "uuid" : "bba77709-6cad-3592-ab03-09d0f7b8610e",
    "path" : "\/usr\/lib\/dyld",
    "name" : "dyld"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 140703126978560,
    "size" : 196608,
    "uuid" : "f066db2c-ed38-3f37-8d21-81d15fa908fe",
    "path" : "\/usr\/libexec\/rosetta\/runtime",
    "name" : "runtime"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 5244915712,
    "size" : 174571520,
    "uuid" : "473ca65c-6149-3bfa-a88b-95ac735bcd3b",
    "path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
    "name" : "QtWebEngineCore"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4542709760,
    "size" : 64028672,
    "uuid" : "24c9d5c5-4854-3af4-9550-cb0204044dfa",
    "path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
    "name" : "libopenblas64_.0.dylib"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703313543168,
    "size" : 61440,
    "uuid" : "94cc87c8-6b63-3219-9354-ff94c63b7f9f",
    "path" : "\/usr\/lib\/system\/libsystem_notify.dylib",
    "name" : "libsystem_notify.dylib"
  }
],
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "6112e3d2fc54bc3389840661",
      "factorPackIds" : {
        "SIRI_TEXT_TO_SPEECH" : "648b9b0febdf9e3e398fa6b5"
      },
      "deploymentId" : 240000478
    },
    {
      "rolloutId" : "60da5e84ab0ca017dace9abf",
      "factorPackIds" : {

      },
      "deploymentId" : 240000008
    }
  ],
  "experiments" : [
    {
      "treatmentId" : "c47ab4cc-c9c3-4b5d-a87c-e2433ce02597",
      "experimentId" : "6639bc6ba73d460582162323",
      "deploymentId" : 400000006
    }
  ]
},
  "reportNotes" : [
  "dyld_process_snapshot_create_for_process failed with 5"
]
}
===== 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 5W1K

Summary of feedback from opening 5W1K fetched from pdb  
---  
note | Fetching compressed mmCIF 5w1k from
http://files.rcsb.org/download/5w1k.cif  
  
5w1k title:  
JUNV GP1 CR1-10 Fab CR1-28 Fab complex [more info...]  
  
Chain information for 5w1k #1  
---  
Chain | Description | UniProt  
A F K S | CR1-28 Fab light chain | IGK_HUMAN 104-207  
B G L T | CR1-28 Fab heavy chain | S6C4R2_HUMAN 127-226  
C H M N | CR1-10 Fab light chain | Q6PIL8_HUMAN 107-214  
D I O Q | CR1-10 Fab heavy chain | S6B2B6_HUMAN 127-226  
E J P R | Pre-glycoprotein polyprotein GP complex | GLYC_JUNIN 87-228  
  
Non-standard residues in 5w1k #1  
---  
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)  
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)  
  
5w1k mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
3| author_defined_assembly  
4| author_defined_assembly  
  

> delete /D/I/O

> delete /C/H/M

> close

> open 5W1K format mmcif fromDatabase pdb

5w1k title:  
JUNV GP1 CR1-10 Fab CR1-28 Fab complex [more info...]  
  
Chain information for 5w1k #1  
---  
Chain | Description | UniProt  
A F K S | CR1-28 Fab light chain | IGK_HUMAN 104-207  
B G L T | CR1-28 Fab heavy chain | S6C4R2_HUMAN 127-226  
C H M N | CR1-10 Fab light chain | Q6PIL8_HUMAN 107-214  
D I O Q | CR1-10 Fab heavy chain | S6B2B6_HUMAN 127-226  
E J P R | Pre-glycoprotein polyprotein GP complex | GLYC_JUNIN 87-228  
  
Non-standard residues in 5w1k #1  
---  
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)  
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)  
  
5w1k mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
3| author_defined_assembly  
4| author_defined_assembly  
  

> delete /A/B/P/O/N

> ui mousemode right select

Drag select of 1769 atoms  

> delete sel

Drag select of 13786 atoms, 72 bonds, 33 pseudobonds  

> delete sel

> delete /W

Drag select of 45 atoms  

> select add #1

7787 atoms, 7995 bonds, 1015 residues, 1 model selected  

> select subtract #1

Nothing selected  

> ui mousemode right "translate selected models"

> set bgColor white

> lighting soft

> show cartoons

> hide atoms

> cartoon style thickness 1.2

> open 8P4T

8p4t title:  
The spike complex of the Lujo Virus [more info...]  
  
Chain information for 8p4t #2  
---  
Chain | Description | UniProt  
A B C | Glycoprotein | C5ILC1_9VIRU 59-221  
SA SB SC | Glycoprotein | C5ILC1_9VIRU -2-55  
a b c | Glycoprotein | C5ILC1_9VIRU 222-454  
  
Non-standard residues in 8p4t #2  
---  
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)  
FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose;
L-fucose; fucose)  
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)  
NA — sodium ion  
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)  
  

> mmaker #2 to #1/E

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 5w1k, chain E (#1) with 8p4t, chain A (#2), sequence alignment
score = 98.7  
RMSD between 50 pruned atom pairs is 1.263 angstroms; (across all 119 pairs:
4.347)  
  

> hide atoms

> show atoms

> show cartoons

> hide atoms

> cartoon style thickness 1.2

> color #2 grey

> color #1 purple

> ui tool show "Side View"

> graphics silhouettes true

> mmaker #2 to #1/B

No 'to' model specified  

> mmaker #1/E to #2/B

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 8p4t, chain B (#2) with 5w1k, chain E (#1), sequence alignment
score = 98.7  
RMSD between 50 pruned atom pairs is 1.263 angstroms; (across all 119 pairs:
4.347)  
  

> mmaker #1/E to #2/C

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 8p4t, chain C (#2) with 5w1k, chain E (#1), sequence alignment
score = 98.7  
RMSD between 50 pruned atom pairs is 1.263 angstroms; (across all 119 pairs:
4.347)  
  

> open
> /Users/tgewering/Downloads/cryosparc_P64_J902_class_00_00040_volume_sharp.mrc

Opened cryosparc_P64_J902_class_00_00040_volume_sharp.mrc as #3, grid size
64,64,64, pixel 5.28, shown at level 0.109, step 1, values float32  

> ui tool show "Side View"

> select add #3

4 models selected  

> view matrix models #3,1,0,0,-126.37,0,1,0,-121.29,0,0,1,-55.903

> view matrix models #3,1,0,0,-198.23,0,1,0,-233.28,0,0,1,-120.28

> volume #3 level 0.4641

> hide #!2 models

> view matrix models #3,1,0,0,-214.77,0,1,0,-249.4,0,0,1,-127.75

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.26183,-0.39834,-0.87907,214.19,0.63753,-0.75522,0.15233,-73.699,-0.72457,-0.52054,0.4517,177.1

> fitmap #1 inMap #3

Fit molecule 5w1k (#1) to map
cryosparc_P64_J902_class_00_00040_volume_sharp.mrc (#3) using 7787 atoms  
average map value = 0.008733, steps = 140  
shifted from previous position = 28.8  
rotated from previous position = 50.2 degrees  
atoms outside contour = 7787, contour level = 0.4641  
  
Position of 5w1k (#1) relative to
cryosparc_P64_J902_class_00_00040_volume_sharp.mrc (#3) coordinates:  
Matrix rotation and translation  
0.66803839 0.13089917 -0.73252312 287.15892146  
-0.00306040 -0.98391467 -0.17861290 133.48619549  
-0.74412052 0.12156208 -0.65689217 103.92663988  
Axis 0.91262340 0.03525963 -0.40727790  
Axis point 0.00000000 52.33535540 121.73464757  
Rotation angle (degrees) 170.53429629  
Shift along axis 224.44760017  
  

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.26183,-0.39834,-0.87907,177.93,0.63753,-0.75522,0.15233,-35.858,-0.72457,-0.52054,0.4517,152.54

> view matrix models
> #3,-0.26183,-0.39834,-0.87907,168.97,0.63753,-0.75522,0.15233,-14.813,-0.72457,-0.52054,0.4517,137.84

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.49697,-0.48153,-0.72191,30.122,-0.025404,-0.83963,0.54256,45.333,-0.8674,-0.2513,-0.4295,262.71

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.49697,-0.48153,-0.72191,24.763,-0.025404,-0.83963,0.54256,54.057,-0.8674,-0.2513,-0.4295,257.24

> view matrix models
> #3,0.49697,-0.48153,-0.72191,31.71,-0.025404,-0.83963,0.54256,53.043,-0.8674,-0.2513,-0.4295,261.12

> view matrix models
> #3,0.49697,-0.48153,-0.72191,26.69,-0.025404,-0.83963,0.54256,65.752,-0.8674,-0.2513,-0.4295,258.11

> fitmap #1 inMap #3

Fit molecule 5w1k (#1) to map
cryosparc_P64_J902_class_00_00040_volume_sharp.mrc (#3) using 7787 atoms  
average map value = 0.6428, steps = 100  
shifted from previous position = 11.9  
rotated from previous position = 28.9 degrees  
atoms outside contour = 2840, contour level = 0.4641  
  
Position of 5w1k (#1) relative to
cryosparc_P64_J902_class_00_00040_volume_sharp.mrc (#3) coordinates:  
Matrix rotation and translation  
0.96106099 0.10672836 0.25489377 269.82197391  
0.18113642 -0.93991137 -0.28940665 165.21166593  
0.20868965 0.32430799 -0.92264454 152.70036082  
Axis 0.98996915 0.07453081 0.12002596  
Axis point 0.00000000 63.06237054 71.47106152  
Rotation angle (degrees) 161.94278546  
Shift along axis 297.75679800  
  

> view matrix models
> #3,0.49697,-0.48153,-0.72191,18.686,-0.025404,-0.83963,0.54256,61.279,-0.8674,-0.2513,-0.4295,253.67

> fitmap #1 inMap #3

Fit molecule 5w1k (#1) to map
cryosparc_P64_J902_class_00_00040_volume_sharp.mrc (#3) using 7787 atoms  
average map value = 0.6429, steps = 104  
shifted from previous position = 10.2  
rotated from previous position = 0.463 degrees  
atoms outside contour = 2838, contour level = 0.4641  
  
Position of 5w1k (#1) relative to
cryosparc_P64_J902_class_00_00040_volume_sharp.mrc (#3) coordinates:  
Matrix rotation and translation  
0.95943424 0.11406066 0.25782959 269.79914230  
0.18897732 -0.93883155 -0.28789388 166.03775511  
0.20922119 0.32493919 -0.92230202 152.75094570  
Axis 0.98954844 0.07848854 0.12096877  
Axis point 0.00000000 62.96399151 71.32204480  
Rotation angle (degrees) 161.96168679  
Shift along axis 298.48947304  
  

> select subtract #3

Nothing selected  

> open /Users/tgewering/Downloads/cryosparc_P64_J908_004_volume_map.mrc

Opened cryosparc_P64_J908_004_volume_map.mrc as #4, grid size 226,226,226,
pixel 1.32, shown at level 0.00845, step 1, values float32  

> hide #!1 models

> hide #!3 models

> ui mousemode right zoom

> view orient

> volume #4 level 0.06252

> ui mousemode right "map eraser"

> volume erase #4 center 151.49,157.23,152.55 radius 52.232 outside true

Opened cryosparc_P64_J908_004_volume_map.mrc copy as #6, grid size
226,226,226, pixel 1.32, shown at step 1, values float32  

> volume erase #6 center 169.23,124.16,65.982 radius 52.206

> volume erase #6 center 142.19,137.45,90.639 radius 26.252

> volume erase #6 center 152.94,158.68,82.337 radius 26.252

> volume erase #6 center 157.68,138.85,216.37 radius 26.252

> volume erase #6 center 173.26,129.89,211.01 radius 26.252

> volume erase #6 center 138.64,148.9,217.66 radius 26.252


===== 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
OpenGL renderer: Apple M2 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: Mac
      Model Identifier: Mac14,9
      Model Number: MPHE3LL/A
      Chip: Unknown
      Total Number of Cores: 10 (6 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 8419.80.7
      OS Loader Version: 8419.80.7

Software:

    System Software Overview:

      System Version: macOS 13.2.1 (22D68)
      Kernel Version: Darwin 22.3.0
      Time since boot: 1 minute

Graphics/Displays:

    Apple M2 Pro:

      Chipset Model: Apple M2 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: 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: 2022.9.26
    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

Change History (2)

comment:1 by Eric Pettersen, 12 months ago

Component: Unassigned → Window Toolkit
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash in Qt redraw after screen disconnect

comment:2 by Eric Pettersen, 12 months ago

Resolution: → can't reproduce
Status: accepted → closed
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