![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 months ago
Closed 7 months ago
#17512 closed defect (duplicate)
Crash moving window between screens
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| 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-15.4.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
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{
"uptime" : 600000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,9",
"coalitionID" : 4061,
"osVersion" : {
"train" : "macOS 15.4.1",
"build" : "24E263",
"releaseType" : "User"
},
"captureTime" : "2025-04-29 10:30:44.6992 -0400",
"codeSigningMonitor" : 1,
"incident" : "C10C303A-9BC3-4810-909F-6866EC92FDC8",
"pid" : 509,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-04-28 18:07:10.2339 -0400",
"procStartAbsTime" : 13895661400974,
"procExitAbsTime" : 14437046674850,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "925A907F-B9A8-BBC0-1189-890C7FE9DEDF",
"appleIntelligenceStatus" : {"state":"available"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
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"sleepWakeUUID" : "92A6E127-D181-4330-8B8E-F5F087050AB6",
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"exception" : {"codes":"0x0000000000000001, 0x0000000000000169","rawCodes":[1,361],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000169"},
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"size" : 16384,
"uuid" : "de871a78-14f2-3e72-9bde-e4f2c7493f1b",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/graphics\/_graphics.cpython-311-darwin.so",
"name" : "_graphics.cpython-311-darwin.so"
},
{
"source" : "P",
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"size" : 475136,
"uuid" : "0c6e9a11-e483-3d7d-a88f-8ad0507af167",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/mmcif.cpython-311-darwin.so",
"name" : "mmcif.cpython-311-darwin.so"
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{
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/_mmcif.cpython-311-darwin.so",
"name" : "_mmcif.cpython-311-darwin.so"
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{
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/psutil\/_psutil_osx.abi3.so",
"name" : "_psutil_osx.abi3.so"
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{
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"uuid" : "a516c5bc-1157-318a-a306-5c9b350e0c09",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/psutil\/_psutil_posix.abi3.so",
"name" : "_psutil_posix.abi3.so"
},
{
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"arch" : "arm64",
"base" : 13017677824,
"size" : 81920,
"uuid" : "d7bd530c-3353-37a6-b81f-ee3179d65811",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lz4\/_version.cpython-311-darwin.so",
"name" : "_version.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 13019103232,
"size" : 180224,
"uuid" : "87eed069-25fc-30f6-aa30-1e54859d92e2",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lz4\/frame\/_frame.cpython-311-darwin.so",
"name" : "_frame.cpython-311-darwin.so"
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{
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"uuid" : "c1a3c2d3-b21b-3231-839d-fcbc83ca2028",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/core\/_serialize.cpython-311-darwin.so",
"name" : "_serialize.cpython-311-darwin.so"
},
{
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"base" : 13030309888,
"size" : 131072,
"uuid" : "650aead6-ce16-39bb-9ba1-4bf9986b96d6",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/msgpack\/_cmsgpack.cpython-311-darwin.so",
"name" : "_cmsgpack.cpython-311-darwin.so"
},
{
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"uuid" : "8abbdcef-1901-3d4b-9e6b-a38214b79214",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/_imagingmath.cpython-311-darwin.so",
"name" : "_imagingmath.cpython-311-darwin.so"
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"uuid" : "8d27ec9a-d919-31a4-8df8-31a2fd2e593c",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
},
{
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"size" : 529520,
"uuid" : "20ebe22e-66e2-3556-b70b-54a04e8363a8",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
},
{
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"arch" : "arm64e",
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"size" : 31568,
"uuid" : "27ed40c8-6b18-3266-93a7-387fb33ca186",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
},
{
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"CFBundleShortVersionString" : "6.9",
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"size" : 21564928,
"uuid" : "1d6df541-4a74-3a0e-8a8f-15aee6f93da9",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
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"CFBundleVersion" : "2575.50.27"
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{
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"size" : 633476,
"uuid" : "aca43a8d-6369-3a2c-af92-3d4c458523d6",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"size" : 0,
"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
},
{
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"arch" : "arm64e",
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"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 5500928,
"uuid" : "39e0f63a-3ab8-39e9-97f8-333cde9a7ba4",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "3423"
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{
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"arch" : "arm64e",
"base" : 6475669504,
"CFBundleShortVersionString" : "6.9",
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"size" : 14676544,
"uuid" : "5ab66e9b-19c0-3fe8-9793-d5156d1c7050",
"path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=6.0G written=67.8M(1%) resident=3020K(0%) swapped_out=64.8M(1%) unallocated=5.9G(99%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nCG image 1376K 62 \nColorSync 704K 38 \nCoreAnimation 3280K 177 \nCoreGraphics 48K 3 \nCoreServices 624K 2 \nCoreUI image data 6832K 59 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 5.2G 135 \nMALLOC guard page 288K 18 \nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 56.7M 42 \nStack 194.4M 42 \nVM_ALLOCATE 348.6M 257 \nVM_ALLOCATE (reserved) 256.0M 3 reserved VM address space (unallocated)\n__AUTH 5486K 695 \n__AUTH_CONST 77.2M 942 \n__CTF 824 1 \n__DATA 34.0M 1081 \n__DATA_CONST 36.8M 1100 \n__DATA_DIRTY 2775K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 651.3M 153 \n__OBJC_RO 61.3M 1 \n__OBJC_RW 2391K 1 \n__TEXT 1.3G 1117 \n__TEXT (graphics) 688K 3 \n__TPRO_CONST 128K 2 \ndyld private memory 2976K 26 \nmapped file 656.6M 125 \npage table in kernel 3020K 1 \nshared memory 3168K 26 \n=========== ======= ======= \nTOTAL 8.8G 6469 \nTOTAL, minus reserved VM space 8.6G 6469 \n",
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Log:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/minggu/Library/CloudStorage/GoogleDrive-
> mgumoon@gmail.com/.shortcut-targets-by-
> id/1sftYzLId9yIBBjmdGpeH1geeI-5Gldvc/QCR_Caa3/figure/Fig.S6_representative_dendity_map/chimerax/20250428_CtaF.cxs
Opened 20250417_qcr_caa3_composite.mrc as #2, grid size 360,360,360, pixel
0.825, shown at level 0.0799, step 1, values float32
Log from Tue Apr 29 10:13:06 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/minggu/Library/CloudStorage/GoogleDrive-
> mgumoon@gmail.com/.shortcut-targets-by-
> id/1sftYzLId9yIBBjmdGpeH1geeI-5Gldvc/QCR_Caa3/Qcr_deposite/Qcr_Caa3_Composite/250424_qcrABC_Caa3_composite.pdb
Chain information for 250424_qcrABC_Caa3_composite.pdb #1
---
Chain | Description
A | No description available
B b | No description available
C c | No description available
D d | No description available
E e | No description available
F f | No description available
G g | No description available
H h | No description available
I i | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
a | No description available
> open /Users/minggu/Library/CloudStorage/GoogleDrive-
> mgumoon@gmail.com/.shortcut-targets-by-
> id/1sftYzLId9yIBBjmdGpeH1geeI-5Gldvc/QCR_Caa3/Qcr_deposite/Qcr_Caa3_Composite/20250417_qcr_caa3_composite.mrc
Opened 20250417_qcr_caa3_composite.mrc as #2, grid size 360,360,360, pixel
0.825, shown at level 0.0799, step 2, values float32
> volume #2 step 1
> set bgColor white
> open /Users/minggu/Library/CloudStorage/GoogleDrive-
> mgumoon@gmail.com/.shortcut-targets-by-
> id/1sftYzLId9yIBBjmdGpeH1geeI-5Gldvc/QCR_Caa3/Qcr_deposite/Qcr_Caa3_Global/250424_qcrABC_Caa3_J190_G02.pdb
Chain information for 250424_qcrABC_Caa3_J190_G02.pdb #3
---
Chain | Description
A | No description available
B b | No description available
C | No description available
D d | No description available
E e | No description available
F f | No description available
G g | No description available
H h | No description available
I i | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
a | No description available
c | No description available
> open "/Users/minggu/Library/CloudStorage/GoogleDrive-
> mgumoon@gmail.com/.shortcut-targets-by-
> id/1sftYzLId9yIBBjmdGpeH1geeI-5Gldvc/QCR_Caa3/Qcr_deposite/Qcr_Caa3_Global/G02_P39_J190_BC1_Caa3_R
> (1).mrc"
Opened G02_P39_J190_BC1_Caa3_R (1).mrc as #4, grid size 360,360,360, pixel
0.825, shown at level 0.0576, step 2, values float32
> volume #4 step 1
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> select #1/A,a
2593 atoms, 2665 bonds, 11 pseudobonds, 324 residues, 2 models selected
> show #!1 models
> hide sel atoms
> show sel atoms
> select add #1
27762 atoms, 28527 bonds, 76 pseudobonds, 3381 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> hide sel cartoons
> show #!3 models
> select add #3
55151 atoms, 56680 bonds, 153 pseudobonds, 6715 residues, 4 models selected
> hide #!1 models
> select subtract #1
27389 atoms, 28153 bonds, 77 pseudobonds, 3334 residues, 2 models selected
> hide sel atoms
> show #!1 models
> hide #!3 models
> select subtract #3
Nothing selected
> select add #1
27762 atoms, 28527 bonds, 76 pseudobonds, 3381 residues, 2 models selected
> select #1/A,a
2593 atoms, 2665 bonds, 11 pseudobonds, 324 residues, 2 models selected
> show sel cartoons
> volume #2 style mesh
> ui tool show "Surface Zone"
> show sel atoms
> style sel stick
Changed 2593 atom styles
> color (#!1 & sel) byhetero
> surface zone #2 nearAtoms sel distance 2
> show #!2 models
> select add #1
27762 atoms, 28527 bonds, 76 pseudobonds, 3381 residues, 2 models selected
> hide sel atoms
> show cartoons
> color /A/a orange
> color /B/b forest green
> color /C/c orange red
> color /D/d blue
> color /E/e yellow
> color /G/g dark goldenrod
> color /H/h medium slate blue
> color /I/i olive
> color /J teal
> color /F/f dim gray
> color /K cornflower blue
> color /L light pink
> color /M spring green
> color /N salmon
> select #1/A,a
2593 atoms, 2665 bonds, 11 pseudobonds, 324 residues, 2 models selected
> select #1 & ~sel
25169 atoms, 25862 bonds, 65 pseudobonds, 3057 residues, 2 models selected
> hide sel cartoons
> ui mousemode right select
Drag select of 321 residues, 2 20250417_qcr_caa3_composite.mrc
> hide sel cartoons
> undo
> hide sel cartoons
> select clear
> select #1/A:9-37
227 atoms, 231 bonds, 29 residues, 1 model selected
> show sel
> show sel cartoons
> surface zone #2 nearAtoms sel distance 2
> color sel byhetero
> lighting soft
[Repeated 1 time(s)]
> lighting full
> label sel text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> label height 1.5
> label height 1
> hide #1.2 models
> select clear
> save "/Users/minggu/Google Drive/My
> Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/chimerax/20250428_QcrA.cxs"
> includeMaps true
> save "/Users/minggu/Google Drive/My
> Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/Rawpng/20250428_QcrA.png"
> width 936 height 739 supersample 4
> volume subdivideSurface true
> volume surfaceSmoothing true
> color #2 #d6d6d6ff models
> save "/Users/minggu/Google Drive/My
> Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/Rawpng/20250428_QcrA.png"
> width 936 height 739 supersample 4
> save "/Users/minggu/Google Drive/My
> Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/chimerax/20250428_QcrA.cxs"
> includeMaps true
> color #2 silver models
> save "/Users/minggu/Google Drive/My
> Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/chimerax/20250428_QcrA.cxs"
> includeMaps true
> save "/Users/minggu/Google Drive/My
> Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/Rawpng/20250428_QcrA.png"
> width 936 height 739 supersample 4
> lighting soft
> lighting full
> save "/Users/minggu/Google Drive/My
> Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/Rawpng/20250428_QcrA-2.png"
> width 936 height 739 supersample 4
> color #2 #d6d6d6ff models
> save "/Users/minggu/Google Drive/My
> Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/Rawpng/20250428_QcrA.png"
> width 936 height 739 supersample 4
> lighting soft
> color #2 darkgrey models
> save "/Users/minggu/Google Drive/My
> Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/Rawpng/20250428_QcrA_soft.png"
> width 936 height 739 supersample 4
> subdivideSurface true subdivisionLevels 2
Unknown command: subdivideSurface true subdivisionLevels 2
> volume subdivideSurface true subdivisionLevels 2
> volume subdivideSurface true subdivisionLevels 1
> volume subdivideSurface true subdivisionLevels 1.5
Invalid "subdivisionLevels" argument: Expected an integer
> volume subdivideSurface true subdivisionLevels 0
> volume subdivideSurface true subdivisionLevels 1
> volume subdivideSurface true subdivisionLevels 2
> volume subdivideSurface true subdivisionLevels 1
[Repeated 1 time(s)]
> save "/Users/minggu/Google Drive/My
> Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/Rawpng/20250428_QcrA_soft-2.png"
> width 936 height 739 supersample 4
> show #1.2 models
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting soft
Drag select of 138 atoms, 29 residues, 117 bonds, 2
20250417_qcr_caa3_composite.mrc
> hide sel cartoons
> hide sel atoms
> select clear
> close #3
> close #4
> select #1/B,b
4058 atoms, 4200 bonds, 28 pseudobonds, 458 residues, 2 models selected
> show sel
> hide sel atoms
> show sel cartoons
> surface zone #2 nearAtoms sel distance 2
> surface zone #2 nearAtoms sel distance 1.84
> surface zone #2 nearAtoms sel distance 1.49
[Repeated 1 time(s)]
> surface zone #2 nearAtoms sel distance 1.39
> surface zone #2 nearAtoms sel distance 1.49
> surface zone #2 nearAtoms sel distance 1.59
> surface zone #2 nearAtoms sel distance 1.69
> show sel atoms
> style sel stick
Changed 4058 atom styles
> color (#!1 & sel) byhetero
> select clear
> select #1/B,b
4058 atoms, 4200 bonds, 28 pseudobonds, 458 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> undo
> hide sel atoms
> select #1/B:23-64
331 atoms, 343 bonds, 42 residues, 1 model selected
> show sel cartoons
> show sel atoms
> select #1/B:23
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #1/B:24-64
326 atoms, 338 bonds, 41 residues, 1 model selected
> surface zone #2 nearAtoms sel distance 1.69
> surface zone #2 nearAtoms sel distance 1.79
> surface zone #2 nearAtoms sel distance 1.89
> surface zone #2 nearAtoms sel distance 1.99
> surface zone #2 nearAtoms sel distance 2.09
> surface zone #2 nearAtoms sel distance 2.19
> surface zone #2 nearAtoms sel distance 2.29
> surface zone #2 nearAtoms sel distance 2.19
> surface zone #2 nearAtoms sel distance 2.09
> surface zone #2 nearAtoms sel distance 1.99
> surface zone #2 nearAtoms sel distance 1.89
> surface zone #2 nearAtoms sel distance 2
[Repeated 1 time(s)]
> select clear
> lighting full
> lighting soft
> color #2 #d6d6d6ff models
> color #2 #ebebebff models
> color #2 #d6d6d6ff models
> color #2 #ebebebff models
> color #2 silver models
> select #2
2 models selected
> select clear
> color #2 #d6d6d6ff models
> color #2 white models
> color #2 #ebebebff models
> color #2 #d6d6d6ff models
> hide #!2 models
> show #!2 models
> hide #!2 models
Drag select of 202 atoms, 41 residues, 177 bonds
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> label height 1
> show #!2 models
> color #2 silver models
> select clear
> color #2 #76d6ffff models
> color #2 #00fdffff models
> color #2 #00f900ff models
> color #2 #00fa92ff models
> color #2 #7a81ffff models
> color #2 #919191ff models
> color #2 #929292ff models
> color #2 silver models
> color #2 darkgrey models
> color #2 silver models
> hide #1.2 models
> save "/Users/minggu/Google Drive/My
> Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/Rawpng/20250428_QcrB.png"
> width 936 height 739 supersample 4
> save "/Users/minggu/Google Drive/My
> Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/chimerax/20250428_QcrB.cxs"
> includeMaps true
> volume #2 showOutlineBox true
> show #1.2 models
Drag select of 202 atoms, 41 residues, 177 bonds, 2
20250417_qcr_caa3_composite.mrc
> hide sel cartoons
> hide sel atoms
> select clear
> select #1/C,c
4232 atoms, 4345 bonds, 9 pseudobonds, 516 residues, 2 models selected
> show sel cartoons
> show sel atoms
> style sel stick
Changed 4232 atom styles
> color (#!1 & sel) byhetero
> surface zone #2 nearAtoms sel distance 2
> hide sel cartoons
> hide sel atoms
> select #1/C:36-65
248 atoms, 258 bonds, 30 residues, 1 model selected
> show sel cartoons
> show sel atoms
> surface zone #2 nearAtoms sel distance 2
> select clear
> save "/Users/minggu/Google Drive/My
> Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/chimerax/20250428_QcrC.cxs"
> includeMaps true
Drag select of 158 atoms, 30 residues, 141 bonds, 2
20250417_qcr_caa3_composite.mrc
> show sel atoms
> color (#!1 & sel) byhetero
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> label height 1
> select clear
> hide #1.2 models
> save "/Users/minggu/Google Drive/My
> Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/Rawpng/20250428_QcrC.png"
> width 936 height 739 supersample 4
> show #1.2 models
Drag select of 158 atoms, 30 residues, 141 bonds, 2
20250417_qcr_caa3_composite.mrc
> hide sel atoms
> hide sel cartoons
> select clear
> select #1/N
2694 atoms, 2752 bonds, 7 pseudobonds, 337 residues, 2 models selected
> show sel
> hide sel atoms
> show sel cartoons
> show sel atoms
> style sel stick
Changed 2694 atom styles
> color (#!1 & sel) byhetero
> surface zone #2 nearAtoms sel distance 2
> hide sel cartoons
> hide sel atoms
> select #1/N:85-116
260 atoms, 265 bonds, 32 residues, 1 model selected
> show sel cartoons
> show sel atoms
> surface zone #2 nearAtoms sel distance 2
> select clear
Drag select of 166 atoms, 32 residues, 140 bonds, 2
20250417_qcr_caa3_composite.mrc
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> label height 1
> select clear
> hide #1.2 models
> select #1/N:85-116
260 atoms, 265 bonds, 32 residues, 1 model selected
> surface zone #2 nearAtoms sel distance 1
> surface zone #2 nearAtoms sel distance 1.9
[Repeated 1 time(s)]
> surface zone #2 nearAtoms sel distance 1
> surface zone #2 nearAtoms sel distance 1.8
[Repeated 1 time(s)]
> surface zone #2 nearAtoms sel distance 1
> surface zone #2 nearAtoms sel distance 1.7
> surface zone #2 nearAtoms sel distance 1
> surface zone #2 nearAtoms sel distance 2
[Repeated 1 time(s)]
> select clear
No atoms selected for zoning
[Repeated 1 time(s)]
> select #1/N:85-116
260 atoms, 265 bonds, 32 residues, 1 model selected
> surface zone #2 nearAtoms sel distance 1.9
> surface zone #2 nearAtoms sel distance 1.8
> surface zone #2 nearAtoms sel distance 1.7
> surface zone #2 nearAtoms sel distance 1.8
> surface zone #2 nearAtoms sel distance 1.9
> surface zone #2 nearAtoms sel distance 2
> surface zone #2 nearAtoms sel distance 2.1
> surface zone #2 nearAtoms sel distance 2.2
> select clear
> save "/Users/minggu/Google Drive/My
> Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/Rawpng/20250428_CtaC.png"
> width 936 height 739 supersample 4
> select clear
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> save "/Users/minggu/Google Drive/My
> Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/chimerax/20250428_CtaC.cxs"
> includeMaps true
> show #1.2 models
> select #1/M
4965 atoms, 5133 bonds, 15 pseudobonds, 608 residues, 2 models selected
> ui mousemode right select
Drag select of 166 atoms, 32 residues, 140 bonds, 2
20250417_qcr_caa3_composite.mrc
> hide sel atoms
> hide sel cartoons
> select clear
> select #1/M
4965 atoms, 5133 bonds, 15 pseudobonds, 608 residues, 2 models selected
> show sel cartoons
> ui mousemode right zoom
> show sel atoms
> style sel stick
Changed 4965 atom styles
> color (#!1 & sel) byhetero
> surface zone #2 nearAtoms sel distance 2.2
> select clear
> ui tool show "Side View"
> ui mousemode right select
Drag select of 3124 atoms, 603 residues, 15 pseudobonds, 2752 bonds, 2
20250417_qcr_caa3_composite.mrc
> hide sel atoms
> hide sel cartoons
> select clear
> select #1/M:25-52
220 atoms, 224 bonds, 28 residues, 1 model selected
> show sel cartoons
> show sel atoms
> surface zone #2 nearAtoms sel distance 2.2
Drag select of 47 atoms, 13 residues, 40 bonds, 2
20250417_qcr_caa3_composite.mrc
> select clear
> ui mousemode right zoom
No atoms selected for zoning
[Repeated 3 time(s)]
> select #1/M:25-52
220 atoms, 224 bonds, 28 residues, 1 model selected
> surface zone #2 nearAtoms sel distance 2
> select clear
> save "/Users/minggu/Google Drive/My
> Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/chimerax/20250428_CtaD.cxs"
> includeMaps true
> save "/Users/minggu/Google Drive/My
> Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/Rawpng/20250428_CtaD.png"
> width 936 height 739 supersample 4
> ui mousemode right select
Drag select of 132 atoms, 28 residues, 113 bonds, 2
20250417_qcr_caa3_composite.mrc
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> label height 1
> select clear
> ui mousemode right zoom
> ui mousemode right select
Drag select of 132 atoms, 28 residues, 113 bonds, 2
20250417_qcr_caa3_composite.mrc
> hide sel atoms
> hide sel cartoons
> select clear
[Repeated 1 time(s)]
> select #1/L
1845 atoms, 1894 bonds, 209 residues, 1 model selected
> show sel cartoons
> select clear
> select #1/L
1845 atoms, 1894 bonds, 209 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 1845 atom styles
> color sel byhetero
> ui mousemode right zoom
> surface zone #2 nearAtoms sel distance 2
> select clear
> select #1/L:175-206
273 atoms, 285 bonds, 32 residues, 1 model selected
> select #1/L
1845 atoms, 1894 bonds, 209 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> hide sel cartoons
> select #1/L:175-206
273 atoms, 285 bonds, 32 residues, 1 model selected
> show sel cartoons
> show sel atoms
> surface zone #2 nearAtoms sel distance 2
> select clear
> save "/Users/minggu/Google Drive/My
> Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/Rawpng/20250428_CtaE.png"
> width 936 height 739 supersample 4
> save "/Users/minggu/Google Drive/My
> Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/chimerax/20250428_CtaE.cxs"
> includeMaps true
> ui mousemode right select
Drag select of 177 atoms, 32 residues, 159 bonds, 2
20250417_qcr_caa3_composite.mrc
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> label height 1
> select clear
Drag select of 177 atoms, 32 residues, 159 bonds, 2
20250417_qcr_caa3_composite.mrc
> hide sel atoms
> hide sel cartoons
> select clear
> select #1/K
1045 atoms, 1069 bonds, 112 residues, 1 model selected
> show sel cartoons
> ui mousemode right zoom
> show sel atoms
> style sel stick
Changed 1045 atom styles
> color sel byhetero
> surface zone #2 nearAtoms sel distance 2
> hide sel atoms
> hide sel cartoons
> select #1/K:52-101
409 atoms, 424 bonds, 50 residues, 1 model selected
> surface zone #2 nearAtoms sel distance 2
> show sel cartoons
> show sel atoms
> undo
[Repeated 3 time(s)]
> hide sel atoms
> hide sel cartoons
> select #1/K:52-110
492 atoms, 512 bonds, 59 residues, 1 model selected
> surface zone #2 nearAtoms sel distance 2
> show sel cartoons
> show sel atoms
> select clear
> select #1/K:83-110
231 atoms, 241 bonds, 28 residues, 1 model selected
> undo
[Repeated 4 time(s)]
> redo
> show sel atoms
> undo
[Repeated 1 time(s)]
> select #1/K:83-110
231 atoms, 241 bonds, 28 residues, 1 model selected
> surface zone #2 nearAtoms sel distance 2
> show sel cartoons
> show sel atoms
> select clear
> select #1/K:83-110
231 atoms, 241 bonds, 28 residues, 1 model selected
> surface zone #2 nearAtoms sel distance 1.9
> surface zone #2 nearAtoms sel distance 1.8
> surface zone #2 nearAtoms sel distance 1.9
> surface zone #2 nearAtoms sel distance 2
> surface zone #2 nearAtoms sel distance 2.1
> surface zone #2 nearAtoms sel distance 2.2
> surface zone #2 nearAtoms sel distance 2.3
> surface zone #2 nearAtoms sel distance 2
[Repeated 1 time(s)]
> select clear
> select #1/K:83-110
231 atoms, 241 bonds, 28 residues, 1 model selected
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> label height 1
> select clear
> hide #1.2 models
> save "/Users/minggu/Google Drive/My
> Drive/QCR_Caa3/figure/Fig.S6_representative_dendity_map/chimerax/20250428_CtaF.cxs"
> includeMaps true
——— End of log from Tue Apr 29 10:13:06 2025 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,9
Model Number: MPHF3LL/A
Chip: Apple M2 Pro
Total Number of Cores: 12 (8 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.101.1
OS Loader Version: 11881.101.1
Software:
System Software Overview:
System Version: macOS 15.4.1 (24E263)
Kernel Version: Darwin 24.4.0
Time since boot: 11 days, 16 hours, 41 minutes
Graphics/Displays:
Apple M2 Pro:
Chipset Model: Apple M2 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 19
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: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
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: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.10.0
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 2.2.1
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
plotly: 5.24.1
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pyKVFinder: 0.7.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tenacity: 9.0.0
tifffile: 2024.7.24
tinyarray: 1.2.4
toml: 0.10.2
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 7 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash moving window between screens |
comment:2 by , 7 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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