The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 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 0x000000010fced600 (most recent call first):
File "/opt/sbgrid/i386-mac/chimerax/1.5/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 283 in event_loop
File "/opt/sbgrid/i386-mac/chimerax/1.5/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 884 in init
File "/opt/sbgrid/i386-mac/chimerax/1.5/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1035 in
File "/opt/sbgrid/i386-mac/chimerax/1.5/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/opt/sbgrid/i386-mac/chimerax/1.5/ChimeraX.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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{
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"procLaunch" : "2023-08-02 10:18:56.3404 +0200",
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,1",
"procStartAbsTime" : 42625746645554,
"coalitionID" : 3258,
"osVersion" : {
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"build" : "21G320",
"releaseType" : "User"
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"captureTime" : "2023-08-02 12:29:50.6262 +0200",
"incident" : "6C2C1964-9324-4F9C-A630-5D72B1B2E5A5",
"bug_type" : "309",
"pid" : 19725,
"procExitAbsTime" : 50479962837121,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/opt\/sbgrid\/*\/ChimeraX.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.5.0","CFBundleVersion":"1.5.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "19CCC37A-33D6-4584-2DD0-78BED36A390F",
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"bridgeVersion" : {"build":"20P2059","train":"7.1"},
"sleepWakeUUID" : "D0CDDF4B-B2AF-4062-9C7C-A7D9E7BA3B1E",
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"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4475539456\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10ac35000-10ac36000 [ 4K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"isCorpse" : 1,
"exception" : {"codes":"0x000000000000000d, 0x0000000000000000","rawCodes":[13,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"UNKNOWN_0xD at 0x0000000000000000"},
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4475539456\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10ac35000-10ac36000 [ 4K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
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"path" : "\/opt\/sbgrid\/*\/ChimeraX.app\/Contents\/MacOS\/ChimeraX",
"name" : "ChimeraX",
"CFBundleVersion" : "1.5.0.0"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4559654912,
"size" : 442368,
"uuid" : "b53641ea-6cd4-39c9-9b14-59c92cfd9584",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4627251200,
"size" : 64028672,
"uuid" : "24c9d5c5-4854-3af4-9550-cb0204044dfa",
"path" : "\/opt\/sbgrid\/*\/ChimeraX.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" : 5093224448,
"size" : 165052416,
"uuid" : "4aa1de3e-464c-340c-ab61-bcd39bfc7658",
"path" : "\/opt\/sbgrid\/*\/ChimeraX.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" : 5512650752,
"size" : 147456,
"uuid" : "9a744198-7fb3-3c4f-b935-3646fa131615",
"path" : "\/opt\/sbgrid\/*\/ChimeraX.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numexpr\/interpreter.cpython-39-darwin.so",
"name" : "interpreter.cpython-39-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5822758912,
"size" : 63373312,
"uuid" : "ccf8b470-9ccf-3558-9748-04374e88d1ea",
"path" : "\/opt\/sbgrid\/*\/ChimeraX.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/scipy\/.dylibs\/libopenblas.0.dylib",
"name" : "libopenblas.0.dylib"
}
],
"sharedCache" : {
"base" : 140703557423104,
"size" : 19331678208,
"uuid" : "3172f8f5-c412-3210-95e0-1cfd89e01f8a"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=6.1G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=6.1G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG backing stores 3648K 8 \nCG image 196K 36 \nColorSync 236K 28 \nCoreAnimation 120K 19 \nCoreGraphics 16K 3 \nCoreUI image data 3144K 40 \nFoundation 52K 2 \nKernel Alloc Once 8K 1 \nMALLOC 3.8G 464 \nMALLOC guard page 48K 10 \nMALLOC_MEDIUM (reserved) 1.2G 13 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated)\nMach message 16K 2 \nObjC additional data 15K 1 \nOpenGL GLSL 384K 4 \nSTACK GUARD 168K 42 \nStack 149.3M 43 \nStack Guard 56.0M 1 \nVM_ALLOCATE 329.4M 256 \nVM_ALLOCATE (reserved) 384.0M 4 reserved VM address space (unallocated)\n__CTF 756 1 \n__DATA 62.8M 836 \n__DATA_CONST 32.7M 347 \n__DATA_DIRTY 1644K 214 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 696.9M 282 \n__TEXT 930.6M 815 \n__UNICODE 592K 1 \ndyld private memory 1280K 3 \nmapped file 190.3M 55 \nshared memory 2996K 30 \n=========== ======= ======= \nTOTAL 8.1G 3568 \nTOTAL, minus reserved VM space 6.2G 3568 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "5f72dc58705eff005a46b3a9",
"factorPackIds" : {
},
"deploymentId" : 240000015
},
{
"rolloutId" : "6112e14f37f5d11121dcd519",
"factorPackIds" : {
"SIRI_TEXT_TO_SPEECH" : "634710168e8be655c1316aaa"
},
"deploymentId" : 240000231
}
],
"experiments" : [
]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/laura/Documents/RSC/Cartes
> cryo/Cartes1/cryosparc_P197_J770_map_sharp.mrc"
Opened cryosparc_P197_J770_map_sharp.mrc as #1, grid size 300,300,300, pixel
0.84, shown at level 0.00718, step 2, values float32
> open "/Users/laura/Documents/RSC/Cartes
> cryo/Cartes2/cryosparc_P197_J776_005_volume_map_sharp.mrc"
Opened cryosparc_P197_J776_005_volume_map_sharp.mrc as #2, grid size
450,450,450, pixel 0.84, shown at level 0.134, step 2, values float32
> open "/Users/laura/Documents/RSC/Cartes
> cryo/Cartes2/cryosparc_P197_J781_006_volume_map_sharp.mrc"
Opened cryosparc_P197_J781_006_volume_map_sharp.mrc as #3, grid size
450,450,450, pixel 0.84, shown at level 0.098, step 2, values float32
> surface dust #1 size 8.4
> surface dust #2 size 8.4
> surface dust #3 size 8.4
> select add #1
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,73.35,0,1,0,48.727,0,0,1,21.941
> view matrix models #1,1,0,0,67.432,0,1,0,61.636,0,0,1,65.522
> hide #!3 models
> fitmap #1 inMap #2
Fit map cryosparc_P197_J770_map_sharp.mrc in map
cryosparc_P197_J776_005_volume_map_sharp.mrc using 33713 points
correlation = 0.6277, correlation about mean = 0.1895, overlap = 128.2
steps = 224, shift = 5.36, angle = 0.0797 degrees
Position of cryosparc_P197_J770_map_sharp.mrc (#1) relative to
cryosparc_P197_J776_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99999932 -0.00116308 -0.00001622 63.12179987
0.00116307 0.99999903 -0.00076285 62.85346570
0.00001710 0.00076283 0.99999971 62.73337612
Axis 0.54840367 -0.01197720 0.83612796
Axis point -54918.73081233 13604.09595806 0.00000000
Rotation angle (degrees) 0.07969975
Shift along axis 86.31654756
> open "/Users/laura/Documents/RSC/Cartes
> cryo/Cartes3/cryosparc_P197_J792_007_volume_map_sharp.mrc"
Opened cryosparc_P197_J792_007_volume_map_sharp.mrc as #4, grid size
450,450,450, pixel 0.84, shown at level 0.0932, step 2, values float32
> view matrix models
> #1,1,-0.0011631,-1.6217e-05,62.5,0.0011631,1,-0.00076285,53.468,1.7104e-05,0.00076283,1,58.168
> undo
> save "/Users/laura/Documents/RSC/Cartes
> cryo/Cartes1/cryosparc_P197_J746_map_sharp.mrc" models #1
> close #1
> open "/Users/laura/Documents/RSC/Cartes
> cryo/Cartes1/cryosparc_P197_J746_map_sharp.mrc"
Opened cryosparc_P197_J746_map_sharp.mrc as #1, grid size 300,300,300, pixel
0.84, shown at level 0.00718, step 2, values float32
> open "/Users/laura/Documents/RSC/Cartes
> cryo/Cartes1/cryosparc_P197_J770_map_sharp.mrc"
Opened cryosparc_P197_J770_map_sharp.mrc as #5, grid size 300,300,300, pixel
0.84, shown at level 0.00718, step 2, values float32
> close #1
> hide #!2 models
> select add #5
2 models selected
> view matrix models #5,1,0,0,51.186,0,1,0,56.553,0,0,1,79.865
> view matrix models #5,1,0,0,58.952,0,1,0,66.296,0,0,1,71.87
> fitmap #5 inMap #4
Fit map cryosparc_P197_J770_map_sharp.mrc in map
cryosparc_P197_J792_007_volume_map_sharp.mrc using 33713 points
correlation = 0.7575, correlation about mean = 0.3654, overlap = 104
steps = 180, shift = 10, angle = 0.425 degrees
Position of cryosparc_P197_J770_map_sharp.mrc (#5) relative to
cryosparc_P197_J792_007_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.99998711 -0.00096386 0.00498545 62.24168851
0.00099083 0.99998488 -0.00540888 63.66915768
-0.00498016 0.00541375 0.99997294 63.13195481
Axis 0.72922522 0.67147898 0.13170631
Axis point 0.00000000 -9315.71233593 -177.09722883
Rotation angle (degrees) 0.42517502
Shift along axis 96.45558723
> surface dust #5 size 8.4
> show #!3 models
> show #!2 models
> select subtract #5
Nothing selected
> surface dust #2 size 8.4
> surface dust #3 size 8.4
> surface dust #4 size 8.4
> surface dust #5 size 8.4
> select add #5
2 models selected
> hide #!4 models
> hide #!3 models
> hide #!2 models
> save "/Users/laura/Documents/RSC/Cartes cryo/Cartes1/J770.ccp4" models #5
> open "/Users/laura/Documents/RSC/Cartes cryo/Cartes1/J770.ccp4"
Opened J770.ccp4 as #1, grid size 300,300,300, pixel 0.84, shown at level
0.00718, step 2, values float32
> hide #!1 models
> show #!4 models
> hide #!4 models
> ui tool show "Map Coordinates"
> toolshed show
> save "/Users/laura/Documents/RSC/Cartes
> cryo/Cartes1/cryosparc_P197_J770_map_sharp.mrc" models #5
> close #5
> open "/Users/laura/Documents/RSC/Cartes
> cryo/Cartes1/cryosparc_P197_J770_map_sharp.mrc"
Opened cryosparc_P197_J770_map_sharp.mrc as #5, grid size 300,300,300, pixel
0.84, shown at level 0.00718, step 2, values float32
> show #!2 models
> open /Users/laura/Documents/RSC/compil_RSC_2(2).pdb
Chain information for compil_RSC_2(2).pdb #6
---
Chain | Description
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
K | No description available
M | No description available
N | No description available
> select add #2
2 models selected
> select subtract #2
Nothing selected
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> show #!3 models
> show #!4 models
> hide #!5 models
> hide #!6 models
> open /Users/laura/Documents/RSC/CombineFocusedMaps_29/composite_map.ccp4
Opened composite_map.ccp4 as #7, grid size 300,300,300, pixel 0.84, shown at
level 4.53, step 2, values float32
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> surface dust #7 size 8.4
> volume #7 step 1
> open /Volumes/ibs-equipe-
> petosa/CaRSC_Structure/cryosparc_P197_J610_006_volume_map_sharp.mrc
Opened cryosparc_P197_J610_006_volume_map_sharp.mrc as #8, grid size
450,450,450, pixel 0.84, shown at level 0.0871, step 2, values float32
> volume #8 step 1
> surface dust #7 size 8.4
> surface dust #8 size 8.4
> volume #8 level 0.2037
> volume #8 level 0.2391
> surface dust #7 size 8.4
> surface dust #8 size 8.4
> open /Users/laura/Documents/RSC/CombineFocusedMaps_30/composite_map.ccp4
Opened composite_map.ccp4 as #9, grid size 300,300,300, pixel 0.84, shown at
level 4.02, step 2, values float32
> volume #9 step 1
> hide #!8 models
> select add #7
2 models selected
> fitmap #7 inMap #9
Fit map composite_map.ccp4 in map composite_map.ccp4 using 269205 points
correlation = 1, correlation about mean = 0.9999, overlap = 1.968e+07
steps = 40, shift = 0.00529, angle = 0.00411 degrees
Position of composite_map.ccp4 (#7) relative to composite_map.ccp4 (#9)
coordinates:
Matrix rotation and translation
1.00000000 -0.00004964 0.00002951 0.00748722
0.00004965 1.00000000 -0.00004258 -0.00301688
-0.00002951 0.00004258 1.00000000 -0.00128371
Axis 0.59343575 0.41122406 0.69190230
Axis point 79.94345503 123.14827405 0.00000000
Rotation angle (degrees) 0.00411108
Shift along axis 0.00231437
> hide #!7 models
> select subtract #7
Nothing selected
> surface dust #9 size 8.4
> open /Users/laura/Downloads/6v8o.pdb
6v8o.pdb title:
RSC core [more info...]
Chain information for 6v8o.pdb #10
---
Chain | Description | UniProt
2 | unknown protein |
3 4 | unknown protein |
5 | unknown protein |
6 | unknown protein |
7 | unknown protein |
C | chromatin structure-remodeling complex protein HTL1 | HTL1_YEAST
D | chromatin structure-remodeling complex protein RSC14 | LDB7_YEAST
E | chromatin structure-remodeling complex subunit RSC7 | RSC7_YEAST
F | chromatin structure-remodeling complex subunit RSC2 | RSC2_YEAST
G | remodel THE structure OF chromatin complex subunit 3 | RSC3_YEAST
H | chromatin structure-remodeling complex subunit RSC4 | RSC4_YEAST
I J K L | chromatin structure-remodeling complex protein RSC8 | RSC8_YEAST
M | remodel THE structure OF chromatin complex subunit 6 | RSC6_YEAST
N | chromatin structure-remodeling complex subunit RSC9 | RSC9_YEAST
O | remodel THE structure OF chromatin complex subunit 58 | RSC58_YEAST
Q | chromatin structure-remodeling complex subunit SFH1 | SFH1_YEAST
R | nuclear protein STH1/NPS1 | STH1_YEAST
S | remodel THE structure OF chromatin complex subunit 30 | RSC30_YEAST
Non-standard residues in 6v8o.pdb #10
---
ZN — zinc ion
> close #10
> open /Users/laura/Downloads/emd_21102.map
Opened emd_21102.map as #10, grid size 288,288,288, pixel 1.44, shown at level
0.0146, step 2, values float32
> surface dust #9 size 8.4
> surface dust #10 size 14.4
> volume #10 step 1
> volume #10 level 0.03015
> save /Users/laura/Documents/RSC/CombineFocusedMaps_30/composite.mrc models
> #9
> open
> /Users/laura/Documents/RSC/LocalAnisoSharpen_34/cryosparc_P197_J768_flex_map_sharpened.ccp4
Opened cryosparc_P197_J768_flex_map_sharpened.ccp4 as #11, grid size
300,300,300, pixel 0.84, shown at level 0.00783, step 2, values float32
> hide #!9 models
> surface dust #11 size 8.4
> volume #11 step 1
> open /Users/laura/Documents/RSC/CombineFocusedMaps_31/composite_map.ccp4
Opened composite_map.ccp4 as #12, grid size 300,300,300, pixel 0.84, shown at
level 4.51, step 2, values float32
> hide #!11 models
> volume #12 step 1
> surface dust #12 size 8.4
> volume #12 level 4.845
> open /Users/laura/Documents/RSC/CombineFocusedMaps_31/composite_map.ccp4
Opened composite_map.ccp4 as #13, grid size 300,300,300, pixel 0.84, shown at
level 4.51, step 2, values float32
> hide #!12 models
> show #!12 models
> close #12
> show #!9 models
> volume #13 step 1
> volume #13 level 4.02
> surface dust #9 size 8.4
> surface dust #13 size 8.4
> open /Users/laura/Documents/RSC/CombineFocusedMaps_31/composite_map.pdb
Summary of feedback from opening
/Users/laura/Documents/RSC/CombineFocusedMaps_31/composite_map.pdb
---
warning | Ignored bad PDB record found on line 20334
Chain information for composite_map.pdb #12
---
Chain | Description
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
K | No description available
M | No description available
N | No description available
> hide #!12 surfaces
> hide #!12 cartoons
> show #!12 atoms
> style #!12 stick
Changed 20180 atom styles
> hide #!12 models
> hide #!13 models
> hide #!9 models
> show #!12 models
> ui tool show XMAS
Peptide pair mapping of Xi evidence file:
/Users/laura/Documents/RSC/Xlink_Mass_SpecFDR_rpfdr5.0/RSC_Rep1_Xi1.7.6.7_PeptidePairs_xiFDR2.1.5.5.csv
Unique peptide pairs: 938 out of 1003
Unique peptide pairs with pseudobonds: 105
Pseudobonds are stored in
/Users/laura/Documents/RSC/Xlink_Mass_SpecFDR_rpfdr5.0/RSC_Rep1_Xi1.7.6.7_PeptidePairs_xiFDR2.1.5.5_12.pb
Mapping information is stored in
/Users/laura/Documents/RSC/Xlink_Mass_SpecFDR_rpfdr5.0/RSC_Rep1_Xi1.7.6.7_PeptidePairs_xiFDR2.1.5.5_12.tsv
Peptide pair mapping of Xi evidence file:
/Users/laura/Documents/RSC/Xlink_Mass_SpecFDR_rpfdr5.0/RSC_Rep2_Xi1.7.6.7_PeptidePairs_xiFDR2.1.5.5.csv
Unique peptide pairs: 850 out of 910
Unique peptide pairs with pseudobonds: 86
Pseudobonds are stored in
/Users/laura/Documents/RSC/Xlink_Mass_SpecFDR_rpfdr5.0/RSC_Rep2_Xi1.7.6.7_PeptidePairs_xiFDR2.1.5.5_12.pb
Mapping information is stored in
/Users/laura/Documents/RSC/Xlink_Mass_SpecFDR_rpfdr5.0/RSC_Rep2_Xi1.7.6.7_PeptidePairs_xiFDR2.1.5.5_12.tsv
Peptide pair mapping of Xi evidence file:
/Users/laura/Documents/RSC/Xlink_Mass_SpecFDR_rpfdr5.0/RSC_Rep3_Xi1.7.6.7_PeptidePairs_xiFDR2.1.5.5.csv
Unique peptide pairs: 930 out of 1003
Unique peptide pairs with pseudobonds: 96
Pseudobonds are stored in
/Users/laura/Documents/RSC/Xlink_Mass_SpecFDR_rpfdr5.0/RSC_Rep3_Xi1.7.6.7_PeptidePairs_xiFDR2.1.5.5_12.pb
Mapping information is stored in
/Users/laura/Documents/RSC/Xlink_Mass_SpecFDR_rpfdr5.0/RSC_Rep3_Xi1.7.6.7_PeptidePairs_xiFDR2.1.5.5_12.tsv
> select subtract #16
218 pseudobonds, 2 models selected
> select subtract #15
120 pseudobonds, 1 model selected
> select subtract #14
Nothing selected
> hide #15 models
> hide #16 models
> hide #14 models
> show #15 models
> hide #15 models
> show #16 models
Traceback (most recent call last):
File "/Users/laura/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 1810, in
line_edit.textChanged.connect(lambda text: function(text,
File "/Users/laura/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 1917, in change_pseudobonds_style
value = convert_function(value)
ValueError: could not convert string to float: '0,'
ValueError: could not convert string to float: '0,'
File "/Users/laura/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/xmas/tool.py", line 1917, in change_pseudobonds_style
value = convert_function(value)
See log for complete Python traceback.
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-4.8.101
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 8-Core Intel Core i9
Processor Speed: 2,3 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 32 GB
System Firmware Version: 1916.60.2.0.0 (iBridge: 20.16.2059.0.0,0)
OS Loader Version: 540.120.3~22
Software:
System Software Overview:
System Version: macOS 12.6.2 (21G320)
Kernel Version: Darwin 21.6.0
Time since boot: 8 days 20:59
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0002
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Family: Supported, Metal GPUFamily macOS 2
AMD Radeon Pro 5500M:
Chipset Model: AMD Radeon Pro 5500M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0040
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32206U1-019
Option ROM Version: 113-D32206U1-019
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
PHL 258B6QU:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 59.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: UHB1949004141
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: Thunderbolt/DisplayPort
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
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: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
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-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
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
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
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
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-XMAS: 1.1.2
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
et-xmlfile: 1.1.0
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openpyxl: 3.1.0
openvr: 1.23.701
packaging: 21.3
pandas: 1.5.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
QtRangeSlider: 0.1.5
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
seaborn: 0.12.2
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Fixed with newest release of XMAS (1.1.3)