![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
#9414 closed defect (fixed)
Crash emitting color_pause signal
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | UI | Version: | |
| Keywords: | Cc: | pett | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.4.1-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
Thread 0x00000002ed05f000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1297 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x00000001eb7dde00 (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/widgets/color_button.py", line 147 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" : 140000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,2",
"coalitionID" : 602,
"osVersion" : {
"train" : "macOS 13.4.1",
"build" : "22F770820d",
"releaseType" : "User"
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"captureTime" : "2023-07-20 11:19:51.5345 -0400",
"incident" : "BE93C56E-9089-4F2C-B766-07136306954B",
"pid" : 24915,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-07-20 07:56:40.2969 -0400",
"procStartAbsTime" : 3291303570121,
"procExitAbsTime" : 3532848225163,
"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":"32B13DDB-F408-570B-BF11-58BEA8459E37","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "9E68BBFB-41E2-9468-5E03-195041F4BA66",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 2781,
"sleepWakeUUID" : "5A246FC4-F638-4B01-BFFB-445A7D156D43",
"sip" : "enabled",
"vmRegionInfo" : "0xa2 is not in any region. Bytes before following region: 105554055790430\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO (reserved) 600038000000-600040000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)",
"exception" : {"codes":"0x0000000000000001, 0x00000000000000a2","rawCodes":[1,162],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a2"},
"vmregioninfo" : "0xa2 is not in any region. Bytes before following region: 105554055790430\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO (reserved) 600038000000-600040000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)",
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"faultingThread" : 0,
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===== 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/edk4001/Desktop/phenix_HCN1_20oct19/isolde8.pdb
Chain information for isolde8.pdb #1
---
Chain | Description
A B C D | No description available
> open /Users/edk4001/Desktop/phenix_HCN1_20oct19/20oct19_5U6Oaligned.pdb
20oct19_5U6Oaligned.pdb title:
Structure of the human HCN1 hyperpolarization-activated cyclic nucleotide-
gated ion channel [more info...]
Chain information for 20oct19_5U6Oaligned.pdb #2
---
Chain | Description | UniProt
A B C D | potassium/sodium hyperpolarization-activated cyclic nucleotide-gated
channel 1 | HCN1_HUMAN 1-635 636-660
> ui tool show Matchmaker
> matchmaker #!1 to #2
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 20oct19_5U6Oaligned.pdb, chain A (#2) with isolde8.pdb, chain A
(#1), sequence alignment score = 2445.1
RMSD between 437 pruned atom pairs is 1.053 angstroms; (across all 482 pairs:
1.408)
> matchmaker #!1 to #2
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 20oct19_5U6Oaligned.pdb, chain A (#2) with isolde8.pdb, chain A
(#1), sequence alignment score = 2445.1
RMSD between 437 pruned atom pairs is 1.053 angstroms; (across all 482 pairs:
1.408)
> select add #1
27884 atoms, 28248 bonds, 4 pseudobonds, 1936 residues, 2 models selected
> select add #2
42364 atoms, 43088 bonds, 12 pseudobonds, 3864 residues, 4 models selected
> show sel atoms
> style (#!1-2 & sel) stick
Changed 42364 atom styles
> select subtract #1
14480 atoms, 14840 bonds, 8 pseudobonds, 1928 residues, 2 models selected
> select subtract #2
Nothing selected
> select add #1
27884 atoms, 28248 bonds, 4 pseudobonds, 1936 residues, 2 models selected
> select H
13336 atoms, 1936 residues, 1 model selected
> delete sel
> hide #!2 models
> show #!2 models
> open /Users/edk4001/Desktop/phenix_HCN1_20oct19/20oct19_isolde1-coot-0.pdb
Summary of feedback from opening
/Users/edk4001/Desktop/phenix_HCN1_20oct19/20oct19_isolde1-coot-0.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
10855 messages similar to the above omitted
Chain information for 20oct19_isolde1-coot-0.pdb #3
---
Chain | Description
A B C D | No description available
> hide #!1 models
> select add #3
14480 atoms, 14840 bonds, 8 pseudobonds, 1928 residues, 2 models selected
> show sel atoms
> show #!1 models
> hide #!1 models
> hide #!2 models
> open
> /Users/edk4001/Desktop/HCN1_20oct19_j252_run_ct17_class001_highRes_mask.mrc
Opened HCN1_20oct19_j252_run_ct17_class001_highRes_mask.mrc as #4, grid size
256,256,256, pixel 1.1, shown at level 0.0596, step 1, values float32
> volume #4 level 0.1394
> surface dust #4 size 11
> volume #4 level 0.1698
> ui tool show "Hide Dust"
> surface dust #4 size 1.1
> surface dust #4 size 9.58
> hide #!3 models
> show #!2 models
> surface dust #4 size 10.08
> surface dust #4 size 17.25
> surface dust #4 size 16.69
> surface dust #4 size 70.8
> surface dust #4 size 8.1
> open "/Users/edk4001/Desktop/Macbook Pro
> Desktop/Desktop/ekim_HCN1/HCN1_21mar08/HCN1_21mar08_j201_run_ct13_class001_invert.mrc"
Opened HCN1_21mar08_j201_run_ct13_class001_invert.mrc as #5, grid size
256,256,256, pixel 1.08, shown at level 0.0147, step 1, values float32
> hide #!2 models
> volume #5 level 0.0199
> hide #!4 models
> volume #5 level 0.0166
> volume #5 level 0.0177
> close #5
> open "/Users/edk4001/Desktop/Macbook Pro
> Desktop/Desktop/21mar08/HCN1_21mar08_j160_mask.mrc"
Opened HCN1_21mar08_j160_mask.mrc as #5, grid size 256,256,256, pixel 1.08,
shown at level 1, step 1, values float32
> volume #5 level 1
> close #5
> open
> /Users/edk4001/Desktop/HCN1_21mar08_j159_run_ct19_class001_highRes_mask.mrc
Opened HCN1_21mar08_j159_run_ct19_class001_highRes_mask.mrc as #5, grid size
256,256,256, pixel 1.08, shown at level 0.059, step 1, values float32
> volume #5 level 0.255
> surface dust #5 size 10.8
> volume #5 level 0.2091
> surface dust #5 size 11.07
> surface dust #5 size 11.83
> hide #!5 models
> show #!4 models
> set bgColor white
> lighting soft
> surface dust #4 size 7.57
> surface dust #4 size 10.42
> volume #4 level 0.2269
> surface dust #4 size 10.6
> surface dust #4 size 7.57
> close #5
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> close #1
> close #2
> close #3
> open
> /Users/edk4001/Desktop/HCN1_20oct19_j252_run_ct17_class001_highRes_mask.mrc
Opened HCN1_20oct19_j252_run_ct17_class001_highRes_mask.mrc as #1, grid size
256,256,256, pixel 1.1, shown at level 0.0596, step 1, values float32
> close #4
> color #1 #d6d6d6ff models
> surface dust #1 size 6.58
> volume #1 level 0.2079
> lighting soft
> color #1 darkgrey models
> surface dust #1 size 6.85
> surface dust #1 size 9.58
> surface dust #1 size 9.42
> surface dust #1 size 7.96
> open /Users/edk4001/Desktop/phenix_HCN1_20oct19/isolde8.pdb
Chain information for isolde8.pdb #2
---
Chain | Description
A B C D | No description available
> color #1 #a9a9a958 models
> select add #2
27884 atoms, 28248 bonds, 4 pseudobonds, 1936 residues, 2 models selected
> color #1 #a9a9a959 models
> show sel atoms
> select H
13336 atoms, 1936 residues, 1 model selected
> delete sel
> open /Users/edk4001/Desktop/phenix_HCN1_20oct19/20oct19_5U6Oaligned.pdb
20oct19_5U6Oaligned.pdb title:
Structure of the human HCN1 hyperpolarization-activated cyclic nucleotide-
gated ion channel [more info...]
Chain information for 20oct19_5U6Oaligned.pdb #3
---
Chain | Description | UniProt
A B C D | potassium/sodium hyperpolarization-activated cyclic nucleotide-gated
channel 1 | HCN1_HUMAN 1-635 636-660
> select add #3
14480 atoms, 14840 bonds, 8 pseudobonds, 1928 residues, 2 models selected
> show sel atoms
> select subtract #3
Nothing selected
> hide #!3 models
> select #2/C,D
7274 atoms, 7456 bonds, 2 pseudobonds, 968 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> ui mousemode right "map eraser"
> volume erase #1 center 109,149.2,108.15 radius 19.426
Opened HCN1_20oct19_j252_run_ct17_class001_highRes_mask.mrc copy as #5, grid
size 256,256,256, pixel 1.1, shown at step 1, values float32
> volume erase #5 center 119.42,150.45,105.46 radius 19.36
> volume erase #5 center 125.93,117.36,109.54 radius 19.36
> volume erase #5 center 134.66,104.04,117.67 radius 19.36
> volume erase #5 center 121.59,97.523,113.09 radius 19.36
> color #5 darkgrey models
> volume erase #5 center 102.94,150.39,139.66 radius 19.36
> volume erase #5 center 96.712,144.03,143.58 radius 19.36
Window position QRect(1860,1281 414x26) outside any known screen, using
primary screen
> surface dust #5 size 6.58
> ui mousemode right "map eraser"
> volume erase #5 center 133.2,134.95,114.18 radius 8.6597
> volume erase #5 center 131.9,132.23,105 radius 8.6597
> volume erase #5 center 135.21,133.28,117.2 radius 8.6597
> volume erase #5 center 132.22,144.39,112.84 radius 8.6597
> volume erase #5 center 133.47,144.18,113.69 radius 8.6597
> volume erase #5 center 135.06,138.15,112.18 radius 8.6597
> ui mousemode right "map eraser"
> volume erase #5 center 142.97,141.01,113.34 radius 3.4827
> volume erase #5 center 142.89,139.25,118.45 radius 3.4827
> ui mousemode right "map eraser"
> volume erase #5 center 152.3,152.71,125.87 radius 2.7297
> volume erase #5 center 149.39,153.98,128.81 radius 2.7297
> volume erase #5 center 147.69,154.62,131.84 radius 2.7297
> volume erase #5 center 149.89,156.08,139.18 radius 2.7297
> volume erase #5 center 153.93,149.33,133.84 radius 2.7297
> volume erase #5 center 154.22,151.54,138.67 radius 2.7297
> volume erase #5 center 160.46,148.53,138.41 radius 2.7297
> volume erase #5 center 152.18,156.92,125.37 radius 2.7297
> volume erase #5 center 153.39,157.29,131.06 radius 2.7297
> volume erase #5 center 149.79,156.96,130.84 radius 2.7297
> volume erase #5 center 153.43,161.39,133.38 radius 2.7297
> volume erase #5 center 153.77,161.35,125.42 radius 2.7297
> volume erase #5 center 154.23,162.12,121.07 radius 2.7297
> volume erase #5 center 165.42,146.25,110.98 radius 2.7297
> volume erase #5 center 166.61,146.97,105.21 radius 2.7297
> volume erase #5 center 162.97,150.55,111.39 radius 2.7297
> volume erase #5 center 162.64,146.29,116.04 radius 2.7297
> volume erase #5 center 168.58,152.39,111.76 radius 2.7297
> volume erase #5 center 166.9,152.07,110.66 radius 2.7297
> volume erase #5 center 160.3,162.1,136.14 radius 2.7297
> volume erase #5 center 159.79,162.51,132.3 radius 2.7297
> volume erase #5 center 163.09,164.17,127.07 radius 2.7297
> volume erase #5 center 144.76,161.51,129.87 radius 2.7297
> volume erase #5 center 140.27,163.26,124.57 radius 2.7297
> show #!1 models
> color #1 darkgrey models
> ui mousemode right "map eraser"
Can only have one displayed volume when erasing
> hide #!5 models
> hide #!2 models
> select add #2
14548 atoms, 14912 bonds, 4 pseudobonds, 1936 residues, 2 models selected
> select add #1
14548 atoms, 14912 bonds, 4 pseudobonds, 1936 residues, 4 models selected
> select subtract #2
2 models selected
> volume erase #1 center 164.04,148.52,125.19 radius 12.065 outside true
Opened HCN1_20oct19_j252_run_ct17_class001_highRes_mask.mrc copy as #6, grid
size 256,256,256, pixel 1.1, shown at step 1, values float32
> show #!1 models
> hide #!1 models
> select subtract #1
Nothing selected
> show #!5 models
> show #!2 models
> hide #!5 models
> ui mousemode right "map eraser"
> surface dust #6 size 11
> volume #6 level 0.1512
> surface dust #6 size 10.36
> surface dust #6 size 4.45
> volume erase #6 center 158.08,143.34,134.14 radius 5.9475
> volume erase #6 center 160.31,139.19,124.7 radius 5.9475
> volume erase #6 center 158.41,140.16,127.94 radius 5.9475
> volume erase #6 center 166.51,137.9,125.33 radius 5.9475
> volume erase #6 center 164.91,142.45,118.16 radius 5.9475
> volume erase #6 center 158.67,147.6,114.17 radius 5.9475
> volume erase #6 center 152.44,151.74,119.16 radius 5.9475
> color #6 #fffc79ff models
> show #!5 models
> volume #6 level 0.1307
> ui tool show "Side View"
> hide #!5 models
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> ui mousemode right "map eraser"
> volume erase #5 center 153.18,145.93,124.94 radius 2.0708
> show #!6 models
> volume #6 color #fffc7940
> volume #6 color #fffc7927
> volume #6 color #fffc7926
> color #5 #a9a9a92a models
> color #5 #a9a9a928 models
> color #5 #a9a9a924 models
> color #5 #a9a9a929 models
> color #5 #a9a9a91b models
> color #5 #a9a9a926 models
> color #5 #a9a9a927 models
> color #5 #a9a9a926 models
> hide #!5 models
> hide #!6 models
> select #2/A
3637 atoms, 3728 bonds, 1 pseudobond, 484 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light slate gray
> select #2/B
3637 atoms, 3728 bonds, 1 pseudobond, 484 residues, 2 models selected
> ui tool show "Color Actions"
> color sel pale goldenrod
> hide sel atoms
> select #2/A
3637 atoms, 3728 bonds, 1 pseudobond, 484 residues, 2 models selected
> hide sel atoms
> select #2/A:386
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #2/A:389
23 atoms, 23 bonds, 2 residues, 1 model selected
> select add #2/A:302
31 atoms, 30 bonds, 3 residues, 1 model selected
> select add #2/A:305
39 atoms, 37 bonds, 4 residues, 1 model selected
> select add #2/A:306
47 atoms, 44 bonds, 5 residues, 1 model selected
> select add #2/A:309
53 atoms, 49 bonds, 6 residues, 1 model selected
> show sel atoms
> select add #2/B:384
60 atoms, 55 bonds, 7 residues, 1 model selected
> select add #2/B:383
65 atoms, 59 bonds, 8 residues, 1 model selected
> show sel atoms
> select add #2/B:380
73 atoms, 66 bonds, 9 residues, 1 model selected
> show sel atoms
> select add #2/A:357
81 atoms, 73 bonds, 10 residues, 1 model selected
> show sel atoms
> select add #2/A:353
89 atoms, 80 bonds, 11 residues, 1 model selected
> show sel atoms
> ui tool show "Color Actions"
> color sel dark slate blue
> size sel stickRadius 0.27
Changed 82 bond radii
> show #!6 models
> color #6 #fffc795a models
> color #6 #fffc7949 models
> color #6 #fffc794e models
===== 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 Metal - 83.1
OpenGL renderer: Apple M1 Max
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: MacBookPro18,2
Model Number: Z14X000HSLL/A
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 64 GB
System Firmware Version: 8422.121.1
OS Loader Version: 8422.121.1
Software:
System Software Overview:
System Version: macOS 13.4.1 (c) (22F770820d)
Kernel Version: Darwin 22.5.0
Time since boot: 6 days, 5 hours, 53 minutes
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 32
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
G236HL:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
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
Change History (7)
comment:1 by , 2 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → UI |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash emitting color_pause signal |
comment:2 by , 2 years ago
Tom, it looks like the ColorButton is getting destroyed between the time the color_pause timer starts and when the timer goes off and tries to emit the color_pause signal. Is it possible to add a test to QTimer lambda to check that the Qt PushButton is still alive?
comment:3 by , 2 years ago
This is the same as previous #9409 report from the same person. Here's what I commented on that bug. Yes I think there is a PyQt reference count bug here and we could probably work around it if we can reproduce it. I will try.
The crash was calling the color_pause signal for the color chooser 1 second after the color was last changed. Then it crashes trying to emit the signal apparently calling into Python. This might mean that a reference is not being held and Python garbage collects and then tries to call deleted Python objects. I know Qt Timer has this problem that it will get deleted if you don't hold a reference to it.
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/color_button.py", line 147
Crash is calling the lambda in this code in 1.6
def _set_pause_timer(self):
delay = self._pause_delay
if delay is None:
return
t = self._pause_timer
if t is not None:
t.stop()
from Qt.QtCore import QTimer
self._pause_timer = t = QTimer()
t.setSingleShot(True)
t.timeout.connect(lambda *, p=self.color_pause, c=self._color: p.emit(c))
t.start(int(1000*self._pause_delay))
comment:4 by , 2 years ago
Hi Eric and Tom, Sorry for the double submission. It is possible that this happens when I am modifying colors - I do not remember exactly what happened just before the crash. I tend to have multiple maps and pdbs open to overlay views for generating figures. I am working to rebuild my session again and will try to pay closer attention to what exactly causes the crash. Thanks for looking into this, Elizabeth
comment:5 by , 2 years ago
No trouble. The problem is a bug in ChimeraX and we may have enough information to reproduce it and fix it thanks to your bug report. Thanks for reporting it. My guess is that the bug happens when the color chooser or the panel with the color button is closed within 1 second of changing the color. The crash happens when one second after the color changed it tries to log an equivalent command that does that color change. My guess is that one second later the color button was already deleted and somehow that leads to a crash. You'll get another email if we manage to fix it in the daily builds.
comment:6 by , 2 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Fixed a few months ago in daily builds.
This crash was fixed in ChimeraX daily builds right after the ChimeraX 1.6.1 release.
I was able to reproduce this crash by clicking the color button in the Volume Viewer pane, then change the color in the color chooser dialog, and then close the Volume Viewer panel with its titlebar close button less than one second later.
It is a bit tricky to close the Volume Viewer that fast after changing the color. But by changing the R,G,or B value text entry, then hovering the mouse over the VolumeViewer close button then pressing return to change the color and immediately mouse clicking to close the panel, crashed ChimeraX 1.6.1 every time with the same stack trace.
The fix changed the lambda in t.timeout.connect(lambda ...) to t.timeout.connect(self._emit_pause). So it looks like the lambda gets deleted if the ColorButton is deleted and then the timer calls it. So I suspect that the connect() call is failing to add a reference count to the function. But I am a bit confused by that explanation because there would not be any other reference to that lambda so it should get deleted immediately. Another possibility is that the connect() does hold a reference, but when the timer fires it drops that reference before it actually calls the function. Another theory is that the Signal object did not hold a reference to the Volume Viewer instance and it was deleted and it is the emit(color) that causes the crash. I don't think that is the problem because the fixed code would have the same crash if that was the problem.
comment:7 by , 2 years ago
I did some more debugging to understand what PyQt problem caused this crash. Here's the explanation. The ColorButton code looks like
class ColorButton(QPushButton):
color_pause = Signal(ndarray)
...
Here color_pause is some weird object type pyqtSignal that is not implemented in Python and that seems to be an unbound method
ColorButton.color_pause
-> <unbound PYQT_SIGNAL color_pause(PyQt_PyObject)>
and creating a ColorButton makes it a bound method
ColorButton().color_pause
-> <bound PYQT_SIGNAL color_pause of ColorButton object at 0x170ac4f70>
When the timer goes off a second after the color was changed with the color chooser if the ColorButton instance has been deleted then this bound method type implemented by PyQt is going to have a self value which is a deleted ColorButton. I guess a bound method is supposed to hold a reference to its self instance so that self cannot be deleted before the bound method. But I guess a bound pyqtSignal is not holding a reference to self then if its emit() method is called it crashes because of the deleted self. If the ColorButton timer uses a callback method (self._emit_pause in the daily build), then the timer holds a references to bound method self._emit_pause and that keeps self alive.
So in summary this crash appears to be a bug in PyQt in that a pyqtSignal bound method does not hold a reference to the instance it is bound to.
In most cases this will not cause a crash because the pyqtSignal emit() method in most cases will be called from a method of the instance and so the instance will be guaranteed to be alive. But in this crash it was called from a lambda after a timer.
The fix for this crash was made in response to an earlier report of the same crash #8783 but I did not find a test case to reproduce it and but fortuitously guessed the solution.
We get a fair number of crashes from the Qt event loop and missing PyQt reference counts in other scenarios (not involving Signal) may be behind these. Some day we might switch from PyQt to PySide to allow distribution without a commercial license and without GPL restrictions.
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Reported by Elizabeth Kim