![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 hours ago
Closed 4 hours ago
#19887 closed defect (duplicate)
Crash in swap_buffers exposing status line during Mac wakeup, macOS 26
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-26.3-arm64-arm-64bit
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error
Current thread 0x00000001f607ac40 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 248 in swap_buffers
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 561 in swap_buffers
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py", line 166 in status
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py", line 98 in _expose_event
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 414 in event_loop
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1064 in init
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, psutil._psutil_osx, psutil._psutil_posix, chimerax.surface._surface, chimerax.pdb_lib._load_libs, PIL._imaging, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lxml._elementpath, lxml.etree (total: 58)
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"procRole" : "Background",
"version" : 2,
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"modelCode" : "Mac15,12",
"coalitionID" : 20611,
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"captureTime" : "2026-02-22 22:26:48.4748 +0000",
"codeSigningMonitor" : 2,
"incident" : "26C81A81-8970-407C-8506-F990DF36B358",
"pid" : 39226,
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"cpuType" : "ARM-64",
"procLaunch" : "2026-02-22 17:25:03.7248 +0000",
"procStartAbsTime" : 14118943673667,
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"procPath" : "\/Applications\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX",
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"crashReporterKey" : "FE67BA55-D792-7881-4D27-94DE5BAD681B",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["notOptedIn","assetIsNotReady"]},
"developerMode" : 1,
"bootProgressRegister" : "0x2f000000",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRFOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkQng\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "55038E8A-416D-4FC1-8F35-A2C0AF7A83E2",
"wakeTime" : 1,
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"sip" : "enabled",
"vmRegionInfo" : "0xa00003a00 is in 0x7e6000000-0xadb400000; bytes after start: 9026157056 bytes before end: 3678389759
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
MALLOC_LARGE 5ffc00000-601ab0000 [ 30.7M] rw-\/rwx SM=PRV
GAP OF 0x1e4550000 BYTES
---> commpage (reserved) 7e6000000-adb400000 [ 11.8G] ---\/--- SM=NUL reserved VM address space (unallocated)
MALLOC_SMALL adb400000-adb800000 [ 4096K] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000002, 0x0000000a00003a00","rawCodes":[2,42949687808],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_PROTECTION_FAILURE at 0x0000000a00003a00"},
"termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"ChimeraX","byPid":39226},
"vmregioninfo" : "0xa00003a00 is in 0x7e6000000-0xadb400000; bytes after start: 9026157056 bytes before end: 3678389759
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
MALLOC_LARGE 5ffc00000-601ab0000 [ 30.7M] rw-\/rwx SM=PRV
GAP OF 0x1e4550000 BYTES
---> commpage (reserved) 7e6000000-adb400000 [ 11.8G] ---\/--- SM=NUL reserved VM address space (unallocated)
MALLOC_SMALL adb400000-adb800000 [ 4096K] rw-\/rwx SM=PRV ",
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"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
},
{
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"arch" : "arm64e",
"base" : 6593335296,
"size" : 532552,
"uuid" : "fb5569a9-cb26-36c2-aa05-e99243692b60",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
},
{
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"arch" : "arm64e",
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"size" : 33776,
"uuid" : "4dbaf982-1576-3ffc-86be-03a9d2c96be5",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
},
{
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{
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"uuid" : "5c6605f9-666d-38b5-b38b-9305fbe0be1b",
"path" : "\/System\/Library\/Frameworks\/OpenGL.framework\/Versions\/A\/Resources\/GLEngine.bundle\/GLEngine",
"name" : "GLEngine"
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{
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"arch" : "arm64e",
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"CFBundleIdentifier" : "com.apple.opengl",
"size" : 66456,
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"path" : "\/System\/Library\/Frameworks\/OpenGL.framework\/Versions\/A\/OpenGL",
"name" : "OpenGL",
"CFBundleVersion" : "23.0.2"
},
{
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"arch" : "arm64e",
"base" : 6759870464,
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"CFBundleIdentifier" : "com.apple.QuartzCore",
"size" : 4262880,
"uuid" : "0bc5d4e0-0414-3f32-8aed-629119615d8f",
"path" : "\/System\/Library\/Frameworks\/QuartzCore.framework\/Versions\/A\/QuartzCore",
"name" : "QuartzCore",
"CFBundleVersion" : "1193.49.3"
},
{
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"arch" : "arm64e",
"base" : 6595121152,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 5540928,
"uuid" : "649000a2-3eb4-3cf5-970a-d3cb37b5780c",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "4201"
},
{
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"arch" : "arm64e",
"base" : 6620622848,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.Foundation",
"size" : 16397536,
"uuid" : "6a518869-0a98-34cb-8a15-cc28f898255e",
"path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
"name" : "Foundation",
"CFBundleVersion" : "4201"
},
{
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"arch" : "arm64e",
"base" : 6703771648,
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"path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
"name" : "SkyLight"
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Writable regions: Total=1.0G written=65.1M(6%) resident=1202K(0%) swapped_out=63.9M(6%) unallocated=936.9M(94%)
VIRTUAL REGION
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=========== ======= =======
Accelerate framework 128K 1
Activity Tracing 256K 1
AttributeGraph Data 1024K 1
CG image 160K 6
ColorSync 128K 8
CoreAnimation 1904K 72
CoreGraphics 48K 3
CoreUI image data 3808K 29
Foundation 16K 1
Kernel Alloc Once 32K 1
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MALLOC guard page 3104K 4
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Stack 215.3M 39
Stack Guard 56.0M 1
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VM_ALLOCATE (reserved) 128.0M 1 reserved VM address space (unallocated)
__AUTH 5935K 652
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__DATA 43.5M 1138
__DATA_CONST 59.5M 1184
__DATA_DIRTY 8778K 901
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__TEXT (graphics) 2720K 16
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dyld private memory 1328K 13
mapped file 322.5M 53
page table in kernel 1202K 1
shared memory 3280K 23
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TOTAL 3.7G 7032
TOTAL, minus reserved VM space 3.6G 7032
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}
===== Log before crash start =====
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/margotfield/Desktop/AF3 folders
> /fold_rhdl2_alone/fold_rhdl2_alone_model_1.cif"
Chain information for fold_rhdl2_alone_model_1.cif #1
---
Chain | Description
A | .
Computing secondary structure
> open "/Users/margotfield/Desktop/AF3 folders
> /fold_rhdl2_alone/fold_rhdl2_alone_model_2.cif"
Chain information for fold_rhdl2_alone_model_2.cif #2
---
Chain | Description
A | .
> open "/Users/margotfield/Desktop/AF3 folders
> /fold_rhdl2_alone/fold_rhdl2_alone_model_3.cif"
Chain information for fold_rhdl2_alone_model_3.cif #3
---
Chain | Description
A | .
> open "/Users/margotfield/Desktop/AF3 folders
> /fold_rhdl2_alone/fold_rhdl2_alone_model_4.cif"
Chain information for fold_rhdl2_alone_model_4.cif #4
---
Chain | Description
A | .
> open "/Users/margotfield/Desktop/AF3 folders
> /fold_rhdl2_alone/fold_rhdl2_alone_model_0.cif"
Chain information for fold_rhdl2_alone_model_0.cif #5
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #2-5 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_rhdl2_alone_model_1.cif, chain A (#1) with
fold_rhdl2_alone_model_2.cif, chain A (#2), sequence alignment score = 1243.8
RMSD between 225 pruned atom pairs is 0.307 angstroms; (across all 236 pairs:
0.696)
Matchmaker fold_rhdl2_alone_model_1.cif, chain A (#1) with
fold_rhdl2_alone_model_3.cif, chain A (#3), sequence alignment score = 1243.8
RMSD between 230 pruned atom pairs is 0.320 angstroms; (across all 236 pairs:
0.549)
Matchmaker fold_rhdl2_alone_model_1.cif, chain A (#1) with
fold_rhdl2_alone_model_4.cif, chain A (#4), sequence alignment score = 1230.6
RMSD between 231 pruned atom pairs is 0.443 angstroms; (across all 236 pairs:
0.634)
Matchmaker fold_rhdl2_alone_model_1.cif, chain A (#1) with
fold_rhdl2_alone_model_0.cif, chain A (#5), sequence alignment score = 1236.6
RMSD between 226 pruned atom pairs is 0.299 angstroms; (across all 236 pairs:
0.770)
> color bychain
> color blue
> color cornflower blue
> open "/Users/margotfield/Desktop/Chimera X sessions/rank 9 structure
> af3.cxs" format session
> view name session-start
opened ChimeraX session
> open
> /Users/margotfield/Desktop/fold_7ah0_tab_workshop/fold_7ah0_tab_workshop_model_2.cif
> format mmcif
No such file/path:
/Users/margotfield/Desktop/fold_7ah0_tab_workshop/fold_7ah0_tab_workshop_model_2.cif
> open "/Users/margotfield/Desktop/TAB workshop 7AH0 .cxs" format session
No such file/path: /Users/margotfield/Desktop/TAB workshop 7AH0 .cxs
> open "/Users/margotfield/Desktop/Chimera X sessions/rank 8 strucutre
> af3.cxs" format session
> view name session-start
opened ChimeraX session
> show #10 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!6 models
> hide #!5 models
> show #7 models
> show #8 models
> show #9 models
> show #11 models
> color (#7-11 & sel) cornflower blue
> label (#7-11 & sel) attribute name
> label height 1
> color (#!7-11 & sel) red
> color (#!7-11 & sel) dark gray
> color (#!7-11 & sel) purple
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/margotfield/Desktop/Chimera X sessions/Rank 2 structure .cxs"
Log from Fri Jan 30 11:51:21 2026UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> "/Users/margotfield/Library/Containers/com.microsoft.Outlook/Data/tmp/Outlook
> Temp/rank0002_R2BG_0245[3].cif"
Chain information for rank0002_R2BG_0245[3].cif #1
---
Chain | Description
A | No description available
B | No description available
Color rank0002_R2BG_0245[3].cif by residue attribute pLDDT_score
Computing secondary structure
> open /Users/margotfield/Desktop/fold_r2bg_0245/fold_r2bg_0245_model_0.cif
> /Users/margotfield/Desktop/fold_r2bg_0245/fold_r2bg_0245_model_1.cif
> /Users/margotfield/Desktop/fold_r2bg_0245/fold_r2bg_0245_model_2.cif
> /Users/margotfield/Desktop/fold_r2bg_0245/fold_r2bg_0245_model_3.cif
> /Users/margotfield/Desktop/fold_r2bg_0245/fold_r2bg_0245_model_4.cif
Chain information for fold_r2bg_0245_model_0.cif #2
---
Chain | Description
A | .
B | .
Chain information for fold_r2bg_0245_model_1.cif #3
---
Chain | Description
A | .
B | .
Chain information for fold_r2bg_0245_model_2.cif #4
---
Chain | Description
A | .
B | .
Chain information for fold_r2bg_0245_model_3.cif #5
---
Chain | Description
A | .
B | .
Chain information for fold_r2bg_0245_model_4.cif #6
---
Chain | Description
A | .
B | .
Computing secondary structure
[Repeated 4 time(s)]
> hide #1 models
> ui tool show Matchmaker
> matchmaker #2-6 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker rank0002_R2BG_0245[3].cif, chain B (#1) with
fold_r2bg_0245_model_0.cif, chain A (#2), sequence alignment score = 1216.8
RMSD between 221 pruned atom pairs is 0.643 angstroms; (across all 236 pairs:
1.002)
Matchmaker rank0002_R2BG_0245[3].cif, chain B (#1) with
fold_r2bg_0245_model_1.cif, chain A (#3), sequence alignment score = 1216.8
RMSD between 212 pruned atom pairs is 0.651 angstroms; (across all 236 pairs:
1.126)
Matchmaker rank0002_R2BG_0245[3].cif, chain B (#1) with
fold_r2bg_0245_model_2.cif, chain A (#4), sequence alignment score = 1195.2
RMSD between 220 pruned atom pairs is 0.575 angstroms; (across all 236 pairs:
1.071)
Matchmaker rank0002_R2BG_0245[3].cif, chain B (#1) with
fold_r2bg_0245_model_3.cif, chain A (#5), sequence alignment score = 1216.8
RMSD between 215 pruned atom pairs is 0.638 angstroms; (across all 236 pairs:
1.168)
Matchmaker rank0002_R2BG_0245[3].cif, chain B (#1) with
fold_r2bg_0245_model_4.cif, chain A (#6), sequence alignment score = 1204.2
RMSD between 220 pruned atom pairs is 0.626 angstroms; (across all 236 pairs:
1.171)
> color #2-6 bychain
> show #1 models
> hide #1 models
> open
> /Users/margotfield/Desktop/fold_rhdl2_alone/fold_rhdl2_alone_model_0.cif
> /Users/margotfield/Desktop/fold_rhdl2_alone/fold_rhdl2_alone_model_1.cif
> /Users/margotfield/Desktop/fold_rhdl2_alone/fold_rhdl2_alone_model_2.cif
> /Users/margotfield/Desktop/fold_rhdl2_alone/fold_rhdl2_alone_model_3.cif
> /Users/margotfield/Desktop/fold_rhdl2_alone/fold_rhdl2_alone_model_4.cif
Chain information for fold_rhdl2_alone_model_0.cif #7
---
Chain | Description
A | .
Chain information for fold_rhdl2_alone_model_1.cif #8
---
Chain | Description
A | .
Chain information for fold_rhdl2_alone_model_2.cif #9
---
Chain | Description
A | .
Chain information for fold_rhdl2_alone_model_3.cif #10
---
Chain | Description
A | .
Chain information for fold_rhdl2_alone_model_4.cif #11
---
Chain | Description
A | .
Computing secondary structure
[Repeated 4 time(s)]
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #6 models
> ui tool show Matchmaker
> matchmaker #8-11 to #7
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 fold_rhdl2_alone_model_0.cif, chain A (#7) with
fold_rhdl2_alone_model_1.cif, chain A (#8), sequence alignment score = 1236.6
RMSD between 226 pruned atom pairs is 0.299 angstroms; (across all 236 pairs:
0.770)
Matchmaker fold_rhdl2_alone_model_0.cif, chain A (#7) with
fold_rhdl2_alone_model_2.cif, chain A (#9), sequence alignment score = 1236.6
RMSD between 230 pruned atom pairs is 0.415 angstroms; (across all 236 pairs:
0.661)
Matchmaker fold_rhdl2_alone_model_0.cif, chain A (#7) with
fold_rhdl2_alone_model_3.cif, chain A (#10), sequence alignment score = 1236.6
RMSD between 227 pruned atom pairs is 0.260 angstroms; (across all 236 pairs:
0.743)
Matchmaker fold_rhdl2_alone_model_0.cif, chain A (#7) with
fold_rhdl2_alone_model_4.cif, chain A (#11), sequence alignment score = 1236.6
RMSD between 229 pruned atom pairs is 0.508 angstroms; (across all 236 pairs:
0.773)
> color #7-11 bychain
> color #7-11 cyan
> show #6 models
> show #5 models
> show #4 models
> show #3 models
> show #2 models
> ui tool show Matchmaker
> matchmaker #1,3-11 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 fold_r2bg_0245_model_0.cif, chain A (#2) with
rank0002_R2BG_0245[3].cif, chain B (#1), sequence alignment score = 1216.8
RMSD between 221 pruned atom pairs is 0.643 angstroms; (across all 236 pairs:
1.002)
Matchmaker fold_r2bg_0245_model_0.cif, chain A (#2) with
fold_r2bg_0245_model_1.cif, chain A (#3), sequence alignment score = 1242
RMSD between 228 pruned atom pairs is 0.473 angstroms; (across all 236 pairs:
0.841)
Matchmaker fold_r2bg_0245_model_0.cif, chain A (#2) with
fold_r2bg_0245_model_2.cif, chain A (#4), sequence alignment score = 1220.4
RMSD between 226 pruned atom pairs is 0.502 angstroms; (across all 236 pairs:
1.034)
Matchmaker fold_r2bg_0245_model_0.cif, chain A (#2) with
fold_r2bg_0245_model_3.cif, chain A (#5), sequence alignment score = 1242
RMSD between 225 pruned atom pairs is 0.452 angstroms; (across all 236 pairs:
1.001)
Matchmaker fold_r2bg_0245_model_0.cif, chain A (#2) with
fold_r2bg_0245_model_4.cif, chain A (#6), sequence alignment score = 1229.4
RMSD between 223 pruned atom pairs is 0.474 angstroms; (across all 236 pairs:
1.030)
Matchmaker fold_r2bg_0245_model_0.cif, chain A (#2) with
fold_rhdl2_alone_model_0.cif, chain A (#7), sequence alignment score = 1225.8
RMSD between 213 pruned atom pairs is 0.635 angstroms; (across all 236 pairs:
1.429)
Matchmaker fold_r2bg_0245_model_0.cif, chain A (#2) with
fold_rhdl2_alone_model_1.cif, chain A (#8), sequence alignment score = 1233
RMSD between 219 pruned atom pairs is 0.549 angstroms; (across all 236 pairs:
1.220)
Matchmaker fold_r2bg_0245_model_0.cif, chain A (#2) with
fold_rhdl2_alone_model_2.cif, chain A (#9), sequence alignment score = 1233
RMSD between 213 pruned atom pairs is 0.601 angstroms; (across all 236 pairs:
1.313)
Matchmaker fold_r2bg_0245_model_0.cif, chain A (#2) with
fold_rhdl2_alone_model_3.cif, chain A (#10), sequence alignment score = 1233
RMSD between 215 pruned atom pairs is 0.574 angstroms; (across all 236 pairs:
1.082)
Matchmaker fold_r2bg_0245_model_0.cif, chain A (#2) with
fold_rhdl2_alone_model_4.cif, chain A (#11), sequence alignment score = 1219.8
RMSD between 217 pruned atom pairs is 0.529 angstroms; (across all 236 pairs:
1.173)
> save "/Users/margotfield/Desktop/Rank 2 structure .cxs"
——— End of log from Fri Jan 30 11:51:21 2026 ———
> view name session-start
opened ChimeraX session
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M3
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac15,12
Model Number: MXCU3LL/A
Chip: Apple M3
Total Number of Cores: 8 (4 Performance and 4 Efficiency)
Memory: 16 GB
System Firmware Version: 13822.81.10
OS Loader Version: 13822.81.10
Software:
System Software Overview:
System Version: macOS 26.3 (25D125)
Kernel Version: Darwin 25.3.0
Time since boot: 35 minutes, 25 seconds
Graphics/Displays:
Apple M3:
Chipset Model: Apple M3
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.1
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
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: 1.0.1
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: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.12
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
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: 1.19.1
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: 2.5.2
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: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
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: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
roman-numerals-py: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
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
sse-starlette: 3.2.0
stack-data: 0.6.3
starlette: 0.52.1
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
urllib3: 2.6.3
uvicorn: 0.40.0
wcwidth: 0.3.2
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
Change History (2)
comment:1 by , 5 hours ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash in swap_buffers exposing status line during Mac wakeup, macOS 26 |
comment:2 by , 4 hours ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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