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Opened 11 hours ago
#20546 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-26.5-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.
Fatal Python error: Segmentation fault
Current thread 0x00000001f4121e80 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 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.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, openmm._openmm, openmm.app.internal.compiled, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, psutil._psutil_osx, psutil._psutil_posix, lxml._elementpath, lxml.etree, chimerax.atom_search.ast (total: 62)
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"procRole" : "Background",
"version" : 2,
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"modelCode" : "Mac15,6",
"coalitionID" : 67362,
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"releaseType" : "User"
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"captureTime" : "2026-06-25 17:38:08.2248 -0700",
"codeSigningMonitor" : 2,
"incident" : "F39E0A72-8ED9-4883-BBE5-57483A85FBF1",
"pid" : 22406,
"translated" : false,
"cpuType" : "ARM-64",
"procLaunch" : "2026-06-25 17:21:56.4849 -0700",
"procStartAbsTime" : 18200955845290,
"procExitAbsTime" : 18224275246479,
"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" : "1204DDE0-2D6B-4EB9-D3AB-15EDFB620925",
"appleIntelligenceStatus" : {"reasons":["assetIsNotReady","notOptedIn"],"state":"unavailable"},
"developerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRCuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkf\/f\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
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"wakeTime" : 24361,
"sleepWakeUUID" : "CB08616B-2DA3-4C77-BE69-741BE37D1FAC",
"sip" : "enabled",
"vmRegionInfo" : "0xc is not in any region. Bytes before following region: 4308697076\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100d18000-100d1c000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x000000000000000c","rawCodes":[1,12],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000000000000000c"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":22406},
"vmregioninfo" : "0xc is not in any region. Bytes before following region: 4308697076\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100d18000-100d1c000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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"vmSummary" : "ReadOnly portion of Libraries: Total=2.1G resident=0K(0%) swapped_out_or_unallocated=2.1G(100%)\nWritable regions: Total=2.9G written=23.6M(1%) resident=1682K(0%) swapped_out=22.0M(1%) unallocated=2.9G(99%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nAttributeGraph Data 1024K 1 \nCG image 48K 3 \nColorSync 80K 4 \nCoreAnimation 2048K 117 \nCoreGraphics 48K 3 \nCoreServices 240K 1 \nCoreUI image data 5664K 50 \nFoundation 16K 1 \nKernel Alloc Once 256K 3 \nMALLOC 2.3G 122 \nMALLOC guard page 384K 24 \nMach message 64K 4 \nOpenGL GLSL 384K 4 \nSTACK GUARD 704K 44 \nStack 196.0M 45 \nStack Guard 56.0M 1 \nVM_ALLOCATE 238.2M 206 \nVM_ALLOCATE (reserved) 256.0M 3 reserved VM address space (unallocated)\n__AUTH 6147K 647 \n__AUTH_CONST 91.4M 1043 \n__CTF 824 1 \n__DATA 44.2M 1183 \n__DATA_CONST 45.5M 1233 \n__DATA_DIRTY 8459K 897 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 611.9M 187 \n__OBJC_RO 79.1M 1 \n__OBJC_RW 2599K 1 \n__TEXT 1.5G 1256 \n__TPRO_CONST 128K 2 \ndyld private memory 4144K 34 \nmapped file 330.2M 56 \npage table in kernel 1682K 1 \nshared memory 3216K 28 \n=========== ======= ======= \nTOTAL 5.7G 7210 \nTOTAL, minus reserved VM space 5.4G 7210 \n",
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"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "02fa774b3b5ce3f57cbaa6294994c6d70f5b0aa0",
"bug_type" : "309",
"roots_installed" : 0,
"trmStatus" : 1,
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "5fb4245a1bbfe8005e33a1e1",
"factorPackIds" : [
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{
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}
===== Log before crash start =====
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/mylanmayer/Library/CloudStorage/OneDrive-
> UCSF/Documents/Integrin/Mg_Apo_Extended_Closed/extended_closed_alpha-
> beta_interactions_labeled_v2.cxs
Opened cryosparc_P6_J300_007_volume_map_sharp_z_flip.mrc as #2, grid size
300,300,300, pixel 0.834, shown at level 0.401, step 1, values float32
Log from Wed Jan 7 14:11:53 2026 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/mylanmayer/Library/CloudStorage/OneDrive-
> UCSF/Desktop/extended_closed_initial_model_ordered_chainA_goodBGOL_real_space_refined_002_isolde_v3.pdb
Chain information for
extended_closed_initial_model_ordered_chainA_goodBGOL_real_space_refined_002_isolde_v3.pdb
#1
---
Chain | Description
A | No description available
B | No description available
G | No description available
L | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
W | No description available
X | No description available
Y | No description available
c | No description available
f | No description available
i | No description available
> style stick
Changed 15637 atom styles
> open
> /Users/mylanmayer/Downloads/cryosparc_P6_J300_007_volume_map_sharp_z_flip.mrc
Opened cryosparc_P6_J300_007_volume_map_sharp_z_flip.mrc as #2, grid size
300,300,300, pixel 0.834, shown at level 0.183, step 2, values float32
> volume #2 color #bf9fb5
> volume #2 color #bfae74
> volume #2 color #ffe89b
> volume #2 color #ffe5af
> volume #2 color #ffd1d6
> volume #2 step 1
> volume #2 level 0.3579
> volume #2 color #ffd1d676
> volume #2 color #ffd1d675
> open /Users/mylanmayer/Library/CloudStorage/OneDrive-
> UCSF/Desktop/extended_closed_initial_model_ordered_chainA_goodBGOL_real_space_refined_002_isolde_v3.pdb
Chain information for
extended_closed_initial_model_ordered_chainA_goodBGOL_real_space_refined_002_isolde_v3.pdb
#3
---
Chain | Description
A | No description available
B | No description available
G | No description available
L | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
W | No description available
X | No description available
Y | No description available
c | No description available
f | No description available
i | No description available
> hide #!1 models
> show #!1 models
> select add #3
15637 atoms, 15784 bonds, 1 pseudobond, 1031 residues, 2 models selected
> close #1
> select subtract #3
Nothing selected
> style stick
Changed 15637 atom styles
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 8 residues in model #3 to IUPAC-IUB
standards.
Chain information for
extended_closed_initial_model_ordered_chainA_goodBGOL_real_space_refined_002_isolde_v3.pdb
---
Chain | Description
1.2/A | No description available
1.2/B | No description available
1.2/G | No description available
1.2/L | No description available
1.2/O | No description available
1.2/P | No description available
1.2/Q | No description available
1.2/R | No description available
1.2/S | No description available
1.2/W | No description available
1.2/X | No description available
1.2/Y | No description available
1.2/c | No description available
1.2/f | No description available
1.2/i | No description available
> clipper associate #2 toModel #1
Opened cryosparc_P6_J300_007_volume_map_sharp_z_flip.mrc as #1.1.1.1, grid
size 300,300,300, pixel 0.834, shown at step 1, values float32
> isolde sim start /A-i
ISOLDE: started sim
> select clear
> volume #1.1.1.1 level 0.6323
> volume #1.1.1.1 level 0.3786
> volume #1.1.1.1 level 0.2676
> volume #1.1.1.1 level 0.2993
> ui mousemode right "isolde tug residue"
> isolde sim pause
> isolde tutorial
> isolde shorthand
Initialising ISOLDE-specific command aliases:
Alias Equivalent full command
-------------------------------------------------
st isolde step {arguments}
aw isolde add water {arguments}
awsf isolde add water {arguments} sim false
al isolde add ligand {arguments}
aa isolde add aa $1 sel {arguments}
ht isolde mod his sel {arguments}
so setattr sel atoms occupancy {arguments}
ab isolde adjust bfactors {arguments}
ss isolde sim start sel
rt isolde release torsions sel {arguments}
rd isolde release distances sel {arguments}
ra rd; rt
pf isolde pepflip sel
cf isolde cisflip sel
cbb color bfactor {arguments}
cbo color byattr occupancy {arguments}
cbc color {arguments} bychain; color {arguments} byhet
cs clipper set contourSensitivity {arguments}
> st first
> isolde shorthand
Registered ISOLDE-specific command aliases:
Alias Equivalent full command
-------------------------------------------------
st isolde step {arguments}
aw isolde add water {arguments}
awsf isolde add water {arguments} sim false
al isolde add ligand {arguments}
aa isolde add aa $1 sel {arguments}
ht isolde mod his sel {arguments}
so setattr sel atoms occupancy {arguments}
ab isolde adjust bfactors {arguments}
ss isolde sim start sel
rt isolde release torsions sel {arguments}
rd isolde release distances sel {arguments}
ra rd; rt
pf isolde pepflip sel
cf isolde cisflip sel
cbb color bfactor {arguments}
cbo color byattr occupancy {arguments}
cbc color {arguments} bychain; color {arguments} byhet
cs clipper set contourSensitivity {arguments}
> st 775
Unrecognised residue argument! If specified, must be either a residue,
"first", "last", "next" or "prev"
> st 775
Unrecognised residue argument! If specified, must be either a residue,
"first", "last", "next" or "prev"
> st #1.2/A:775
[Repeated 1 time(s)]
> isolde sim resume
> volume #1.1.1.1 level 0.2517
> isolde pepflip /A:777
> ui tool show "Ramachandran Plot"
> isolde pepflip /A:777
> st prev
[Repeated 1 time(s)]
> st
[Repeated 2 time(s)]
> st prev
> isolde pepflip /A:775
> st
> st prev
> isolde pepflip #!1.2/A:775
[Repeated 1 time(s)]
> st prev
> st
[Repeated 1 time(s)]
> isolde pepflip /A:776
[Repeated 1 time(s)]
> isolde cisflip /A:776
[Repeated 1 time(s)]
> st
[Repeated 2 time(s)]
> st prev
[Repeated 3 time(s)]
> isolde pepflip /A:775
> st prev
> st
[Repeated 1 time(s)]
> volume #1.1.1.1 level 0.3469
> st prev
[Repeated 1 time(s)]
> st
[Repeated 2 time(s)]
> isolde pepflip /A:777
[Repeated 1 time(s)]
> isolde cisflip /A:777
[Repeated 1 time(s)]
> isolde pepflip /A:776
[Repeated 1 time(s)]
> isolde pepflip /A:778
[Repeated 4 time(s)]
> isolde pepflip #!1.2/A:779
[Repeated 1 time(s)]
> isolde pepflip /A:780
> volume #1.1.1.1 level 0.3151
> st
[Repeated 1 time(s)]
> '
incomplete quoted text
> st
[Repeated 5 time(s)]
> volume #1.1.1.1 level 0.2993
> st
> isolde pepflip /A:786
> st prev
> volume #1.1.1.1 level 0.2834
> st
[Repeated 6 time(s)]
> volume #1.1.1.1 level 0.3469
> st
[Repeated 14 time(s)]
> isolde sim pause
> st
> volume #1.1.1.1 level 0.4103
> st
[Repeated 42 time(s)]
> '
incomplete quoted text
> st
[Repeated 6 time(s)]
> st prev
> ui mousemode right "isolde tug atom"
> isolde sim resume
> st prev
> st
[Repeated 47 time(s)]
> isolde sim pause
> st
[Repeated 3 time(s)]
> isolde sim resume
> st
[Repeated 2 time(s)]
> ui mousemode right "isolde tug residue"
> st
[Repeated 19 time(s)]
> ui mousemode right "isolde tug residue"
[Repeated 1 time(s)]
> ui mousemode right "isolde tug atom"
> st
[Repeated 2 time(s)]
> isolde sim pause
> st
[Repeated 13 time(s)]
> st #1.2/A:775
> st \
Unrecognised residue argument! If specified, must be either a residue,
"first", "last", "next" or "prev"
> st
[Repeated 1 time(s)]
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde pepflip /A:779
> isolde pepflip /A:778
> isolde cisflip /A:779
> st
> st prev
> volume #1.1.1.1 level 0.3469
> isolde pepflip /A:776
[Repeated 1 time(s)]
> isolde cisflip /A:776
[Repeated 1 time(s)]
> isolde cisflip /A:777
[Repeated 1 time(s)]
> isolde pepflip #!1.2/A:779
[Repeated 1 time(s)]
> st prev
> isolde sim pause
> save /Users/mylanmayer/Library/CloudStorage/OneDrive-
> UCSF/Desktop/extended_closed_initial_model_ordered_chainA_goodBGOL_real_space_refined_002_isolde_v4.pdb
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 5 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> close
> open /Users/mylanmayer/Library/CloudStorage/OneDrive-
> UCSF/Desktop/extended_closed_initial_model_ordered_chainA_goodBGOL_real_space_refined_002_isolde_v4.pdb
Chain information for
extended_closed_initial_model_ordered_chainA_goodBGOL_real_space_refined_002_isolde_v4.pdb
#1
---
Chain | Description
A | No description available
B | No description available
G | No description available
L | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
W | No description available
X | No description available
Y | No description available
c | No description available
f | No description available
i | No description available
> style stick
Changed 15637 atom styles
> open /Users/mylanmayer/Library/CloudStorage/OneDrive-
> UCSF/Desktop/extended_closed_initial_model_ordered_chainA_goodBGOL_real_space_refined_002_isolde_v4.pdb
> format pdb
Chain information for
extended_closed_initial_model_ordered_chainA_goodBGOL_real_space_refined_002_isolde_v4.pdb
#2
---
Chain | Description
A | No description available
B | No description available
G | No description available
L | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
W | No description available
X | No description available
Y | No description available
c | No description available
f | No description available
i | No description available
> style stick
Changed 31274 atom styles
> select add #2
15637 atoms, 15784 bonds, 1 pseudobond, 1031 residues, 2 models selected
> close #2
> open
> /Users/mylanmayer/Downloads/cryosparc_P6_J300_007_volume_map_sharp_z_flip.mrc
Opened cryosparc_P6_J300_007_volume_map_sharp_z_flip.mrc as #2, grid size
300,300,300, pixel 0.834, shown at level 0.183, step 2, values float32
> volume #2 step 1
> volume #2 level 0.3676
> label #1-2 attribute name
> ~label #1-2 atoms
> ~label #1-2 residues
> ui tool show "Change Chain IDs"
> select O
1569 atoms, 1031 residues, 1 model selected
> hide #!2 models
> select clear
> select /L
284 atoms, 286 bonds, 22 residues, 1 model selected
> select /O
721 atoms, 725 bonds, 46 residues, 1 model selected
> select /B
4445 atoms, 4490 bonds, 285 residues, 1 model selected
> select clear
> select /L,O
1005 atoms, 1013 bonds, 68 residues, 1 model selected
> select /L,O,B
5450 atoms, 5503 bonds, 353 residues, 1 model selected
> select /L,O,B,G
6585 atoms, 6646 bonds, 427 residues, 1 model selected
> select /L,O,B,B
5450 atoms, 5503 bonds, 353 residues, 1 model selected
> select /L,O,B,G
6585 atoms, 6646 bonds, 427 residues, 1 model selected
> select /L,O,B,G,D
6585 atoms, 6646 bonds, 427 residues, 1 model selected
> select /L,O,B,G,D,N
6585 atoms, 6646 bonds, 427 residues, 1 model selected
> ui tool show "Change Chain IDs"
> changechains sel B
Proposed chain ID change would produce multiple residues with the samechain-
ID/number/insertion-code combo (B/4/)
> select /L,O,B,G,D,N
6585 atoms, 6646 bonds, 427 residues, 1 model selected
> ui tool show "Change Chain IDs"
> ui tool show "Show Sequence Viewer"
> ui tool show "Change Chain IDs"
> changechains sel z
Proposed chain ID change would produce multiple residues with the samechain-
ID/number/insertion-code combo (z/7/)
> show #!2 models
> color #2 #b2b2b274 models
> color #2 #bf8e7474 models
> color #2 #bf8e7475 models
> set bgColor white
> ui mousemode right zoom
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> volume #2 level 0.2166
> volume #2 level 0.4011
> color sel byhetero
> select H
7723 atoms, 1031 residues, 1 model selected
> hide sel target a
> ui mousemode right translate
> select /L,O,B,G,D,N
6585 atoms, 6646 bonds, 427 residues, 1 model selected
> color sel red
> select clear
> select /A
8399 atoms, 8492 bonds, 1 pseudobond, 556 residues, 2 models selected
> color (#!1 & sel) cornflower blue
> select clear
> hide #!1 models
> show #!1 models
> hide #!2 models
> open /Users/mylanmayer/Library/CloudStorage/OneDrive-
> UCSF/Documents/Integrin/bent_model_9-19-25.pdb
Chain information for bent_model_9-19-25.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | 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
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | 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
> style stick
Changed 27059 atom styles
> hide #!1 models
> select /L,O,B,G,D,N
10660 atoms, 10783 bonds, 958 residues, 2 models selected
> color (#!3 & sel) orange
> color (#!3 & sel) orange red
> color (#!3 & sel) orange
> select /F,J,C,A,I,E,K,M,H
14970 atoms, 15187 bonds, 4 pseudobonds, 1415 residues, 4 models selected
> color (#!3 & sel) cyan
> select clear
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> select #1/B:223@CD
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/A:551@CG
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/B:217@CB
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/A:523@CD
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/B:195@CG
1 atom, 1 residue, 1 model selected
> select #1/B:195@CD
1 atom, 1 residue, 1 model selected
> select #1/B:195@CG
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/A:617@CZ
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/A:47@CD
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/A:641@CZ
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/B:194@CG
1 atom, 1 residue, 1 model selected
> color sel dim gray
Drag select of 16 atoms, 15 bonds
> select clear
> select #1/A:50@CZ
1 atom, 1 residue, 1 model selected
Drag select of 2 bonds
> select clear
> select #1/A:50@CZ
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/B:193@CB
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/B:188@CE
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/B:212@CZ
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/A:76@CZ
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/B:190@C
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/A:69@CH2
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/B:191@C
1 atom, 1 residue, 1 model selected
> color sel dim gray
[Repeated 1 time(s)]
> select #1/B:191@C
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/B:92@SD
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/A:378@SD
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/A:404@CZ2
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/A:517@SD
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/B:250@CG
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/A:487@CG1
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/B:218@CB
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/B:219@CA
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/A:461@CZ
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/B:181@C
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/A:490@CZ
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/B:184@C
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/A:436@CZ
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/B:145@CG
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/A:142@CD
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/B:96@CB
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/B:98@CB
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/A:143@CE2
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/A:140@C
1 atom, 1 residue, 1 model selected
> select #1/A:138@CD
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/A:141@CG
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/B:101@CE
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/A:439@CZ
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/B:185@C
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/A:383@CE1
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/B:189@CG
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/A:399@CB
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/A:374@CZ
1 atom, 1 residue, 1 model selected
> select #1/B:144@CG
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/A:434@CB
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/B:146@CB
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/A:553@CZ
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/B:184@CA
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select /A:76
28 atoms, 26 bonds, 2 residues, 2 models selected
> select /B:92
25 atoms, 23 bonds, 2 residues, 2 models selected
> save /Users/mylanmayer/Documents/Integrin/extended_closed_alpha-
> beta_interactions_labeled.cxs
> select clear
> select #1/A:432@C
1 atom, 1 residue, 1 model selected
Drag select of 2 bonds
> select clear
> select #1/A:432@C
1 atom, 1 residue, 1 model selected
> select #1/A:432@CG
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/B:239@CD
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/A:521@CE
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/B:250@C
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select #1/A:486@CD
1 atom, 1 residue, 1 model selected
> select #1/A:487@CD1
1 atom, 1 residue, 1 model selected
> select add #1/B:246@OE1
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> ui mousemode right zoom
> ui mousemode right clip
[Repeated 1 time(s)]
> ui mousemode right zoom
> save /Users/mylanmayer/Documents/Integrin/extended_closed_alpha-
> beta_interactions_labeled_v2.cxs
——— End of log from Wed Jan 7 14:11:53 2026 ———
opened ChimeraX session
> ui tool show "Side View"
> ui tool show Contacts
Drag select of 564 atoms, 1 pseudobonds, 579 bonds
Drag select of 1073 atoms, 1 pseudobonds, 1099 bonds
> contacts sel restrict both distanceOnly 3.5 resSeparation 5 intraMol false
> ignoreHiddenModels true reveal true
40 distances
> ui mousemode right zoom
> ui mousemode right translate
> select clear
> ui mousemode right zoom
> ui mousemode right translate
> select add #1
15637 atoms, 15784 bonds, 41 pseudobonds, 1031 residues, 3 models selected
> color sel byhetero
> select subtract #1
Nothing selected
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> select add #1
15637 atoms, 15784 bonds, 41 pseudobonds, 1031 residues, 3 models selected
> select subtract #1
Nothing selected
> select add #1
15637 atoms, 15784 bonds, 41 pseudobonds, 1031 residues, 3 models selected
> show sel cartoons
> hide sel atoms
> select subtract #1
Nothing selected
===== Log before crash end =====
Log:
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
> /Volumes/4_IND_EM/southworth_lab/mmayer/processing/mmayer_20260204_TgM83-1_homo/relion/Class3D/selected_singlets_singlet-2_initial_model/run_it050_class003.mrc
Opened run_it050_class003.mrc as #1, grid size 288,288,288, pixel 0.728, shown
at level 0.0034, step 2, values float32
> open
> /Volumes/4_IND_EM/southworth_lab/mmayer/processing/mmayer_20260204_TgM83-1_homo/relion/Class3D/selected_singlets_singlet-2_initial_model/run_it050_class002.mrc
Opened run_it050_class002.mrc as #2, grid size 288,288,288, pixel 0.728, shown
at level 0.00709, step 2, values float32
> open
> /Volumes/4_IND_EM/southworth_lab/mmayer/processing/mmayer_20260204_TgM83-1_homo/relion/Class3D/selected_singlets_singlet-2_initial_model/run_it050_class001.mrc
Opened run_it050_class001.mrc as #3, grid size 288,288,288, pixel 0.728, shown
at level 0.00677, step 2, values float32
> ui tool show Registration
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M3 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: Mac15,6
Model Number: MRX73LL/A
Chip: Apple M3 Pro
Total Number of Cores: 12 (6 Performance and 6 Efficiency)
Memory: 18 GB
System Firmware Version: 18000.120.36
OS Loader Version: 18000.120.36
Software:
System Software Overview:
System Version: macOS 26.5 (25F71)
Kernel Version: Darwin 25.5.0
Time since boot: 30 days, 1 hour, 1 minute
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 18
Vendor: Apple (0x106b)
Metal Support: Metal 4
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: No
Connection Type: Internal
DELL P2424HEB:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
autocommand: 2.2.2
babel: 2.16.0
backports.tarfile: 1.2.0
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-Clipper: 0.24.0
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-ISOLDE: 1.9
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
importlib_metadata: 8.0.0
importlib_resources: 6.4.0
inflect: 7.3.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
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: 3.9.2
matplotlib-inline: 0.1.7
more-itertools: 10.3.0
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: 1.26.4
openvr: 1.26.701
ordered-set: 4.1.0
packaging: 23.2
packaging: 24.1
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
platformdirs: 4.2.2
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
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
tifffile: 2024.7.24
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4.2
traitlets: 5.14.3
typeguard: 4.3.0
typing_extensions: 4.12.2
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: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
zipp: 3.19.2
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