![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 months ago
Closed 4 months ago
#18131 closed defect (duplicate)
Crash on Mac waking from sleep
| 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-15.5-arm64-arm-64bit
ChimeraX Version: 1.10rc202506130232 (2025-06-13 02:32:35 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 0x000000020d301f00 (most recent call first):
File "/Applications/ChimeraX-1.10-rc2025.06.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 368 in event_loop
File "/Applications/ChimeraX-1.10-rc2025.06.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1057 in init
File "/Applications/ChimeraX-1.10-rc2025.06.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1220 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, chimerax.pdb_lib._load_libs, chimerax.surface._surface, psutil._psutil_osx, psutil._psutil_posix, 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, PIL._imaging, PIL._imagingmath, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 52)
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{
"uptime" : 23000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac15,3",
"coalitionID" : 2787,
"osVersion" : {
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"build" : "24F74",
"releaseType" : "User"
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"captureTime" : "2025-07-03 14:23:52.5935 -0400",
"codeSigningMonitor" : 1,
"incident" : "956BE4B2-C0CA-47F8-AAAE-6D3B64E45097",
"pid" : 3295,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-07-02 22:40:00.4561 -0400",
"procStartAbsTime" : 291305681094,
"procExitAbsTime" : 567443939911,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.10-rc2025.06.18.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.10.0","CFBundleVersion":"1.10.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"AB2DBFE5-5CBA-5275-85E6-CC563EEE01CB","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "8BF9EB06-ACC3-9188-B672-E29A3BA5029D",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["assetIsNotReady","notOptedIn","siriAssetIsNotReady"]},
"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=="},
"bootSessionUUID" : "2EB0409A-8183-4BE7-8193-83930AE9E959",
"sleepWakeUUID" : "05CC879D-FE20-4527-B26E-0DB24C962995",
"sip" : "enabled",
"vmRegionInfo" : "0x26f0dfb5d2b0 is not in any region. Bytes after previous region: 42334950904497 Bytes before following region: 62737129024848\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x0000a6f0dfb5d2b0","rawCodes":[1,183553475596976],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000a6f0dfb5d2b0 -> 0x000026f0dfb5d2b0 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":3295},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0x26f0dfb5d2b0 is not in any region. Bytes after previous region: 42334950904497 Bytes before following region: 62737129024848\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
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===== Log before crash start =====
UCSF ChimeraX version: 1.10rc202506130232 (2025-06-13)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 8USB
8usb title:
Non-substrate-engaged human 26S proteasome with Nub1/FAT10 bound to Rpn1 [more
info...]
Chain information for 8usb #1
---
Chain | Description | UniProt
A | 26S proteasome regulatory subunit 7 | PRS7_HUMAN 1-433
B | 26S proteasome regulatory subunit 4 | PRS4_HUMAN 1-440
C | 26S protease regulatory subunit 8 | PRS8_HUMAN 1-406
D | 26S proteasome regulatory subunit 6B | PRS6B_HUMAN 1-418
E | 26S protease regulatory subunit 10B | PRS10_HUMAN 1-389
F | 26S proteasome regulatory subunit 6A | PRS6A_HUMAN 1-439
G | Proteasome subunit alpha type-6 | PSA6_HUMAN 1-246
H | Proteasome subunit alpha type-2 | PSA2_HUMAN 1-234
I | Proteasome subunit alpha type-4 | PSA4_HUMAN 1-261
J | Proteasome subunit alpha type-7 | PSA7_HUMAN 1-248
K | Proteasome subunit alpha type-5 | PSA5_HUMAN 1-241
L | Proteasome subunit alpha type-1 | PSA1_HUMAN 1-263
M | Proteasome subunit alpha type-3 | PSA3_HUMAN 0-254
O | Proteasome subunit beta type-7 | PSB7_HUMAN -42-234
U | 26S proteasome non-ATPase regulatory subunit 1 | PSMD1_HUMAN 1-953
V | 26S proteasome non-ATPase regulatory subunit 3 | PSMD3_HUMAN 1-534
W | 26S proteasome non-ATPase regulatory subunit 12 | PSD12_HUMAN 1-456
X | 26S proteasome non-ATPase regulatory subunit 11 | PSD11_HUMAN 1-422
Y | 26S proteasome non-ATPase regulatory subunit 6 | PSMD6_HUMAN 1-389
Z | 26S proteasome non-ATPase regulatory subunit 7 | PSMD7_HUMAN 1-324
a | 26S proteasome non-ATPase regulatory subunit 13 | PSD13_HUMAN 1-376
b | 26S proteasome non-ATPase regulatory subunit 4 | PSMD4_HUMAN 1-377
c | 26S proteasome non-ATPase regulatory subunit 14 | PSDE_HUMAN 1-310
d | 26S proteasome non-ATPase regulatory subunit 8 | PSMD8_HUMAN 1-350
e | 26S proteasome complex subunit SEM1 | SEM1_HUMAN 1-70
f | 26S proteasome non-ATPase regulatory subunit 2 | PSMD2_HUMAN 1-908
g | NEDD8 ultimate buster 1 | NUB1_HUMAN 1-601
Non-standard residues in 8usb #1
---
ADP — adenosine-5'-diphosphate
ATP — adenosine-5'-triphosphate
MG — magnesium ion
ZN — zinc ion
3 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> set bgColor white
> ui mousemode right translate
> set bgColor white
> hide atoms
> show atoms
> show cartoons
> hide atoms
> lighting simple
> ui mousemode right zoom
> cd projects
Expected name of a folder to open/read; a name of 'browse' will bring up a
file browser or a keyword
> pwd
Current working directory is: /Users/emena/Desktop
> cd ../projects
Current working directory is: /Users/emena/projects
> cd crispr-bean/a_19s_6bp
Current working directory is: /Users/emena/projects/crispr-bean/a_19s_6bp
> open gene_outputs/combined_residue_scores.defattr
Summary of feedback from opening gene_outputs/combined_residue_scores.defattr
---
note | Assigned attribute 'edit_score' to 2242 residues using match mode: any
> color byattribute edit_score target r palette white:red range 0,5
8855 residues, atom edit_score range 0.007 to 17.1
> show atoms
> style stick
Changed 70140 atom styles
> select clear
> color light gray
> color byattribute edit_score target r palette white:red range 0,5
8855 residues, atom edit_score range 0.007 to 17.1
> color byattribute edit_score target r,a palette white:red range 0,5
Invalid "target" argument: Character ',' is not an allowed target, must be one
of acrsbmpfl
> color byattribute edit_score target a palette white:red range 0,5
70140 atoms, atom edit_score range 0.007 to 17.1
> color byattribute edit_score target a palette white:red range 0,3
70140 atoms, atom edit_score range 0.007 to 17.1
> show surfaces
> color byattribute edit_score target r palette white:red range 0,5
8855 residues, atom edit_score range 0.007 to 17.1
> color byattribute edit_score target r palette white:red range 0,2
8855 residues, atom edit_score range 0.007 to 17.1
> color byattribute edit_score target r palette white:red range 0,3
8855 residues, atom edit_score range 0.007 to 17.1
> color byattribute edit_score target s palette white:red range 0,3
27 surfaces, atom edit_score range 0.007 to 17.1
> transparency 30
> transparency 20
> transparency 80
> hide surfaces
> ui tool show "Side View"
> hide atoms
> show atoms
> hide atoms
> show surfaces
> hide surfaces
> show surfaces
> lighting simple
> lighting soft
> hide atoms
> hide cartoons
> show cartoons
> hide cartoons
> show atoms
> surface hidePatches
> hide atoms
> show cartoons
> lighting simple
> lighting full
> lighting flat
> show atoms
> select ~sel & ##selected
Nothing selected
> show surfaces
> hide surfaces
> hide atoms
> show atoms
> hide atoms
> lighting soft
> lighting full
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting soft
> open gene_outputs/combined_residue_scores_libAB.defattr
Summary of feedback from opening
gene_outputs/combined_residue_scores_libAB.defattr
---
note | Assigned attribute 'edit_score' to 2296 residues using match mode: any
> color byattribute edit_score target s palette white:red range 0,3
27 surfaces, atom edit_score range 0.007 to 17.1
> color byattribute edit_score target a palette white:red range 0,3
70140 atoms, atom edit_score range 0.007 to 17.1
> color byattribute edit_score target c palette white:red range 0,3
8855 residues, atom edit_score range 0.007 to 17.1
> show atoms
> set bgColor white
> hide atoms
> show cartoons
> show atoms
> hide atoms
> lighting simple
> lighting soft
> lighting full
> set bgColor white
> lighting simple
> show atoms
> hide atoms
> select :/edit_score>1
Expected an objects specifier or a keyword
> select #1 & :edit_score>1
Expected a keyword
> select :/edit_score>1
Expected an objects specifier or a keyword
> select attr edit_score > 1
Expected an objects specifier or a keyword
> select #1 & attr edit_score > 1
Expected a keyword
> select #1 & attr edit_score > 1
Expected a keyword
> select attr:edit_score>1
Expected an objects specifier or a keyword
> list attributes
Unknown command: list attributes
> list
Unknown command: modelcif list
> showattr sel
Unknown command: showattr sel
> select attr:edit_score>1
Expected an objects specifier or a keyword
> select :/edit_score>1
Expected an objects specifier or a keyword
> select #.edit_score > 1
Expected an objects specifier or a keyword
> show cartoons
> show atoms
> hide atoms
> ui tool show "Model Panel"
> setattr show #1
Missing or invalid "attrValue" argument: Expected a text string
> setattr show #1
Missing or invalid "attrValue" argument: Expected a text string
> info #1 attributes
Expected a keyword
> attributes list #1
Unknown command: attributes list #1
> attributes show #1
Unknown command: attributes show #1
> info models
model id #1 type AtomicStructure name 8usb
model id #1.1 type PseudobondGroup name "metal coordination bonds"
model id #1.2 type PseudobondGroup name "missing structure"
model id #1.3 type MolecularSurface name "8usb_A SES surface"
model id #1.4 type MolecularSurface name "8usb_B SES surface"
model id #1.5 type MolecularSurface name "8usb_C SES surface"
model id #1.6 type MolecularSurface name "8usb_D SES surface"
model id #1.7 type MolecularSurface name "8usb_E SES surface"
model id #1.8 type MolecularSurface name "8usb_F SES surface"
model id #1.9 type MolecularSurface name "8usb_G SES surface"
model id #1.10 type MolecularSurface name "8usb_H SES surface"
model id #1.11 type MolecularSurface name "8usb_I SES surface"
model id #1.12 type MolecularSurface name "8usb_J SES surface"
model id #1.13 type MolecularSurface name "8usb_K SES surface"
model id #1.14 type MolecularSurface name "8usb_L SES surface"
model id #1.15 type MolecularSurface name "8usb_M SES surface"
model id #1.16 type MolecularSurface name "8usb_O SES surface"
model id #1.17 type MolecularSurface name "8usb_U SES surface"
model id #1.18 type MolecularSurface name "8usb_V SES surface"
model id #1.19 type MolecularSurface name "8usb_W SES surface"
model id #1.20 type MolecularSurface name "8usb_X SES surface"
model id #1.21 type MolecularSurface name "8usb_Y SES surface"
model id #1.22 type MolecularSurface name "8usb_Z SES surface"
model id #1.23 type MolecularSurface name "8usb_a SES surface"
model id #1.23.1 type ClipCap name "cap near"
model id #1.24 type MolecularSurface name "8usb_b SES surface"
model id #1.25 type MolecularSurface name "8usb_c SES surface"
model id #1.26 type MolecularSurface name "8usb_d SES surface"
model id #1.27 type MolecularSurface name "8usb_e SES surface"
model id #1.28 type MolecularSurface name "8usb_f SES surface"
model id #1.29 type MolecularSurface name "8usb_g SES surface"
> info atomattr
atomattr alt_loc
atomattr alt_locs
atomattr aniso_u
atomattr aniso_u6
atomattr atomspec
atomattr bfactor
atomattr bonds
atomattr color
atomattr coord
atomattr coord_index
atomattr cpp_pointer
atomattr custom_attrs
atomattr default_radius
atomattr deleted
atomattr display
atomattr display_radius
atomattr draw_mode
atomattr effective_coord
atomattr element
atomattr has_custom_attrs
atomattr hide
atomattr idatm_type
atomattr is_ribose
atomattr is_side_chain
atomattr is_side_connector
atomattr is_side_only
atomattr name
atomattr neighbors
atomattr num_alt_locs
atomattr num_bonds
atomattr num_explicit_bonds
atomattr occupancy
atomattr pb_coord
atomattr pb_scene_coord
atomattr radius
atomattr residue
atomattr ribbon_coord
atomattr scene_coord
atomattr selected
atomattr serial_number
atomattr session
atomattr structure
atomattr structure_category
atomattr visible
> open gene_outputs/combined_residue_scores_libAB.defattr
Summary of feedback from opening
gene_outputs/combined_residue_scores_libAB.defattr
---
note | Assigned attribute 'edit_score' to 2296 residues using match mode: any
> info resattr
resattr alt_loc
resattr alt_locs
resattr atoms
resattr atomspec
resattr center
resattr chain
resattr chain_id
resattr chi1
resattr chi2
resattr chi3
resattr chi4
resattr cpp_pointer
resattr custom_attrs
resattr deleted
resattr description
resattr edit_score
resattr has_custom_attrs
resattr insertion_code
resattr is_helix
resattr is_strand
resattr label_one_letter_code
resattr label_specifier
resattr mmcif_chain_id
resattr name
resattr neighbors
resattr num_atoms
resattr number
resattr omega
resattr one_letter_code
resattr phi
resattr polymer_type
resattr principal_atom
resattr psi
resattr ribbon_adjust
resattr ribbon_color
resattr ribbon_display
resattr ribbon_hide_backbone
resattr ring_color
resattr ring_display
resattr selected
resattr session
resattr ss_id
resattr ss_type
resattr standard_aa_name
resattr structure
resattr sym_chi1
resattr sym_chi2
resattr sym_chi3
resattr sym_chi4
resattr thin_rings
resattr worm_radius
> select :/edit_score > 0.8
Expected an objects specifier or a keyword
> color byattribute :/edit_score palette rainbow
No known/registered numeric attribute :/edit_score
> select #1 :/edit_score > 0.8
Expected a keyword
> select :#1/edit_score > 0.8
Expected an objects specifier or a keyword
> select:#1/edit_score > 0.8
Unknown command: select:#1/edit_score > 0.8
> undo
> select (attribute edit_score > 0.8)
Expected an objects specifier or a keyword
> select #1 & (attribute edit_score > 0.8)
Expected a keyword
> select :/edit_score > 0.8
Expected an objects specifier or a keyword
> select attribute:edit_score > 0.8
Expected an objects specifier or a keyword
> select #1 & attribute:edit_score > 0.8
Expected a keyword
> attribute list
Unknown command: attribute list
> select :/edit_score > 0.8
Expected an objects specifier or a keyword
> select attribute:edit_score > 0.8
Expected an objects specifier or a keyword
> select #1 & @ca & attribute edit_score > 0.8
Expected a keyword
> select #1 & :. & attribute edit_score > 0.8
Expected a keyword
> select (:/edit_score > 0.8)
Expected an objects specifier or a keyword
> select (#1:/edit_score > 0.8)
Expected an objects specifier or a keyword
> select attribute edit_score > 0.8 target r
Expected an objects specifier or a keyword
> select (#1 & attribute edit_score > 0.8 target r)
Expected an objects specifier or a keyword
> hide atoms
> show atoms
> color byhetero
> hide atoms
> save /Users/emena/projects/crispr-bean/a_19s_6bp/8USB_libAB.cxs
> ui tool show Distances
> show atoms
> select add /D:239@OH
1 atom, 1 bond, 1 residue, 1 model selected
Exactly two atoms must be selected!
> select /c:52@OE1
1 atom, 1 residue, 1 model selected
Exactly two atoms must be selected!
> select add /D:239@OH
2 atoms, 1 bond, 2 residues, 1 model selected
> select add /E:77@CD
3 atoms, 1 bond, 3 residues, 2 models selected
Exactly two atoms must be selected!
No distances to delete!
> select /c:129@OG1
1 atom, 1 residue, 1 model selected
> select add /C:72@OH
2 atoms, 2 residues, 2 models selected
> distance /c:129@OG1 /C:72@OH
Distance between /c THR 129 OG1 and /C TYR 72 OH: 34.277Å
> show sel surfaces
> select clear
> show surfaces
> hide surfaces
> select #1: 593, 595
28 atoms, 24 bonds, 4 residues, 1 model selected
> select #1/U: 593, 595
14 atoms, 12 bonds, 2 residues, 1 model selected
> select #1/U: 590, 593
18 atoms, 17 bonds, 2 residues, 1 model selected
> style sel sphere
Changed 18 atom styles
> style sel stick
Changed 18 atom styles
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.10rc202506130232 (2025-06-13)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/emena/projects/crispr-bean/a_19s_6bp/8USB_libAB.cxs
Log from Thu Jul 3 00:04:57 2025UCSF ChimeraX version: 1.10rc202506130232
(2025-06-13)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 8USB
8usb title:
Non-substrate-engaged human 26S proteasome with Nub1/FAT10 bound to Rpn1 [more
info...]
Chain information for 8usb #1
---
Chain | Description | UniProt
A | 26S proteasome regulatory subunit 7 | PRS7_HUMAN 1-433
B | 26S proteasome regulatory subunit 4 | PRS4_HUMAN 1-440
C | 26S protease regulatory subunit 8 | PRS8_HUMAN 1-406
D | 26S proteasome regulatory subunit 6B | PRS6B_HUMAN 1-418
E | 26S protease regulatory subunit 10B | PRS10_HUMAN 1-389
F | 26S proteasome regulatory subunit 6A | PRS6A_HUMAN 1-439
G | Proteasome subunit alpha type-6 | PSA6_HUMAN 1-246
H | Proteasome subunit alpha type-2 | PSA2_HUMAN 1-234
I | Proteasome subunit alpha type-4 | PSA4_HUMAN 1-261
J | Proteasome subunit alpha type-7 | PSA7_HUMAN 1-248
K | Proteasome subunit alpha type-5 | PSA5_HUMAN 1-241
L | Proteasome subunit alpha type-1 | PSA1_HUMAN 1-263
M | Proteasome subunit alpha type-3 | PSA3_HUMAN 0-254
O | Proteasome subunit beta type-7 | PSB7_HUMAN -42-234
U | 26S proteasome non-ATPase regulatory subunit 1 | PSMD1_HUMAN 1-953
V | 26S proteasome non-ATPase regulatory subunit 3 | PSMD3_HUMAN 1-534
W | 26S proteasome non-ATPase regulatory subunit 12 | PSD12_HUMAN 1-456
X | 26S proteasome non-ATPase regulatory subunit 11 | PSD11_HUMAN 1-422
Y | 26S proteasome non-ATPase regulatory subunit 6 | PSMD6_HUMAN 1-389
Z | 26S proteasome non-ATPase regulatory subunit 7 | PSMD7_HUMAN 1-324
a | 26S proteasome non-ATPase regulatory subunit 13 | PSD13_HUMAN 1-376
b | 26S proteasome non-ATPase regulatory subunit 4 | PSMD4_HUMAN 1-377
c | 26S proteasome non-ATPase regulatory subunit 14 | PSDE_HUMAN 1-310
d | 26S proteasome non-ATPase regulatory subunit 8 | PSMD8_HUMAN 1-350
e | 26S proteasome complex subunit SEM1 | SEM1_HUMAN 1-70
f | 26S proteasome non-ATPase regulatory subunit 2 | PSMD2_HUMAN 1-908
g | NEDD8 ultimate buster 1 | NUB1_HUMAN 1-601
Non-standard residues in 8usb #1
---
ADP — adenosine-5'-diphosphate
ATP — adenosine-5'-triphosphate
MG — magnesium ion
ZN — zinc ion
3 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> set bgColor white
> ui mousemode right translate
> set bgColor white
> hide atoms
> show atoms
> show cartoons
> hide atoms
> lighting simple
> ui mousemode right zoom
> cd projects
Expected name of a folder to open/read; a name of 'browse' will bring up a
file browser or a keyword
> pwd
Current working directory is: /Users/emena/Desktop
> cd ../projects
Current working directory is: /Users/emena/projects
> cd crispr-bean/a_19s_6bp
Current working directory is: /Users/emena/projects/crispr-bean/a_19s_6bp
> open gene_outputs/combined_residue_scores.defattr
Summary of feedback from opening gene_outputs/combined_residue_scores.defattr
---
note | Assigned attribute 'edit_score' to 2242 residues using match mode: any
> color byattribute edit_score target r palette white:red range 0,5
8855 residues, atom edit_score range 0.007 to 17.1
> show atoms
> style stick
Changed 70140 atom styles
> select clear
> color light gray
> color byattribute edit_score target r palette white:red range 0,5
8855 residues, atom edit_score range 0.007 to 17.1
> color byattribute edit_score target r,a palette white:red range 0,5
Invalid "target" argument: Character ',' is not an allowed target, must be one
of acrsbmpfl
> color byattribute edit_score target a palette white:red range 0,5
70140 atoms, atom edit_score range 0.007 to 17.1
> color byattribute edit_score target a palette white:red range 0,3
70140 atoms, atom edit_score range 0.007 to 17.1
> show surfaces
> color byattribute edit_score target r palette white:red range 0,5
8855 residues, atom edit_score range 0.007 to 17.1
> color byattribute edit_score target r palette white:red range 0,2
8855 residues, atom edit_score range 0.007 to 17.1
> color byattribute edit_score target r palette white:red range 0,3
8855 residues, atom edit_score range 0.007 to 17.1
> color byattribute edit_score target s palette white:red range 0,3
27 surfaces, atom edit_score range 0.007 to 17.1
> transparency 30
> transparency 20
> transparency 80
> hide surfaces
> ui tool show "Side View"
> hide atoms
> show atoms
> hide atoms
> show surfaces
[Repeated 1 time(s)]
> hide surfaces
> show surfaces
> lighting simple
> lighting soft
> hide atoms
> hide cartoons
> show cartoons
> hide cartoons
> show atoms
[Repeated 1 time(s)]
> surface hidePatches
> hide atoms
> show cartoons
> lighting simple
> lighting full
> lighting flat
> show atoms
> select ~sel & ##selected
Nothing selected
> show surfaces
> hide surfaces
> hide atoms
> show atoms
> hide atoms
> lighting soft
> lighting full
> lighting soft
[Repeated 1 time(s)]
> lighting full
[Repeated 1 time(s)]
> lighting flat
[Repeated 1 time(s)]
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting soft
> open gene_outputs/combined_residue_scores_libAB.defattr
Summary of feedback from opening
gene_outputs/combined_residue_scores_libAB.defattr
---
note | Assigned attribute 'edit_score' to 2296 residues using match mode: any
> color byattribute edit_score target s palette white:red range 0,3
27 surfaces, atom edit_score range 0.007 to 17.1
> color byattribute edit_score target a palette white:red range 0,3
70140 atoms, atom edit_score range 0.007 to 17.1
> color byattribute edit_score target c palette white:red range 0,3
8855 residues, atom edit_score range 0.007 to 17.1
> show atoms
> set bgColor white
> hide atoms
> show cartoons
> show atoms
> hide atoms
> lighting simple
> lighting soft
> lighting full
> set bgColor white
> lighting simple
> show atoms
> hide atoms
> select :/edit_score>1
Expected an objects specifier or a keyword
> select #1 & :edit_score>1
Expected a keyword
> select :/edit_score>1
Expected an objects specifier or a keyword
> select attr edit_score > 1
Expected an objects specifier or a keyword
> select #1 & attr edit_score > 1
Expected a keyword
> select #1 & attr edit_score > 1
Expected a keyword
> select attr:edit_score>1
Expected an objects specifier or a keyword
> list attributes
Unknown command: list attributes
> list
Unknown command: modelcif list
> showattr sel
Unknown command: showattr sel
> select attr:edit_score>1
Expected an objects specifier or a keyword
> select :/edit_score>1
Expected an objects specifier or a keyword
> select #.edit_score > 1
Expected an objects specifier or a keyword
> show cartoons
> show atoms
> hide atoms
> ui tool show "Model Panel"
> setattr show #1
Missing or invalid "attrValue" argument: Expected a text string
> setattr show #1
Missing or invalid "attrValue" argument: Expected a text string
> info #1 attributes
Expected a keyword
> attributes list #1
Unknown command: attributes list #1
> attributes show #1
Unknown command: attributes show #1
> info models
model id #1 type AtomicStructure name 8usb
model id #1.1 type PseudobondGroup name "metal coordination bonds"
model id #1.2 type PseudobondGroup name "missing structure"
model id #1.3 type MolecularSurface name "8usb_A SES surface"
model id #1.4 type MolecularSurface name "8usb_B SES surface"
model id #1.5 type MolecularSurface name "8usb_C SES surface"
model id #1.6 type MolecularSurface name "8usb_D SES surface"
model id #1.7 type MolecularSurface name "8usb_E SES surface"
model id #1.8 type MolecularSurface name "8usb_F SES surface"
model id #1.9 type MolecularSurface name "8usb_G SES surface"
model id #1.10 type MolecularSurface name "8usb_H SES surface"
model id #1.11 type MolecularSurface name "8usb_I SES surface"
model id #1.12 type MolecularSurface name "8usb_J SES surface"
model id #1.13 type MolecularSurface name "8usb_K SES surface"
model id #1.14 type MolecularSurface name "8usb_L SES surface"
model id #1.15 type MolecularSurface name "8usb_M SES surface"
model id #1.16 type MolecularSurface name "8usb_O SES surface"
model id #1.17 type MolecularSurface name "8usb_U SES surface"
model id #1.18 type MolecularSurface name "8usb_V SES surface"
model id #1.19 type MolecularSurface name "8usb_W SES surface"
model id #1.20 type MolecularSurface name "8usb_X SES surface"
model id #1.21 type MolecularSurface name "8usb_Y SES surface"
model id #1.22 type MolecularSurface name "8usb_Z SES surface"
model id #1.23 type MolecularSurface name "8usb_a SES surface"
model id #1.23.1 type ClipCap name "cap near"
model id #1.24 type MolecularSurface name "8usb_b SES surface"
model id #1.25 type MolecularSurface name "8usb_c SES surface"
model id #1.26 type MolecularSurface name "8usb_d SES surface"
model id #1.27 type MolecularSurface name "8usb_e SES surface"
model id #1.28 type MolecularSurface name "8usb_f SES surface"
model id #1.29 type MolecularSurface name "8usb_g SES surface"
> info atomattr
atomattr alt_loc
atomattr alt_locs
atomattr aniso_u
atomattr aniso_u6
atomattr atomspec
atomattr bfactor
atomattr bonds
atomattr color
atomattr coord
atomattr coord_index
atomattr cpp_pointer
atomattr custom_attrs
atomattr default_radius
atomattr deleted
atomattr display
atomattr display_radius
atomattr draw_mode
atomattr effective_coord
atomattr element
atomattr has_custom_attrs
atomattr hide
atomattr idatm_type
atomattr is_ribose
atomattr is_side_chain
atomattr is_side_connector
atomattr is_side_only
atomattr name
atomattr neighbors
atomattr num_alt_locs
atomattr num_bonds
atomattr num_explicit_bonds
atomattr occupancy
atomattr pb_coord
atomattr pb_scene_coord
atomattr radius
atomattr residue
atomattr ribbon_coord
atomattr scene_coord
atomattr selected
atomattr serial_number
atomattr session
atomattr structure
atomattr structure_category
atomattr visible
> open gene_outputs/combined_residue_scores_libAB.defattr
Summary of feedback from opening
gene_outputs/combined_residue_scores_libAB.defattr
---
note | Assigned attribute 'edit_score' to 2296 residues using match mode: any
> info resattr
resattr alt_loc
resattr alt_locs
resattr atoms
resattr atomspec
resattr center
resattr chain
resattr chain_id
resattr chi1
resattr chi2
resattr chi3
resattr chi4
resattr cpp_pointer
resattr custom_attrs
resattr deleted
resattr description
resattr edit_score
resattr has_custom_attrs
resattr insertion_code
resattr is_helix
resattr is_strand
resattr label_one_letter_code
resattr label_specifier
resattr mmcif_chain_id
resattr name
resattr neighbors
resattr num_atoms
resattr number
resattr omega
resattr one_letter_code
resattr phi
resattr polymer_type
resattr principal_atom
resattr psi
resattr ribbon_adjust
resattr ribbon_color
resattr ribbon_display
resattr ribbon_hide_backbone
resattr ring_color
resattr ring_display
resattr selected
resattr session
resattr ss_id
resattr ss_type
resattr standard_aa_name
resattr structure
resattr sym_chi1
resattr sym_chi2
resattr sym_chi3
resattr sym_chi4
resattr thin_rings
resattr worm_radius
> select :/edit_score > 0.8
Expected an objects specifier or a keyword
> color byattribute :/edit_score palette rainbow
No known/registered numeric attribute :/edit_score
> select #1 :/edit_score > 0.8
Expected a keyword
> select :#1/edit_score > 0.8
Expected an objects specifier or a keyword
> select:#1/edit_score > 0.8
Unknown command: select:#1/edit_score > 0.8
> undo
> select (attribute edit_score > 0.8)
Expected an objects specifier or a keyword
> select #1 & (attribute edit_score > 0.8)
Expected a keyword
> select :/edit_score > 0.8
Expected an objects specifier or a keyword
> select attribute:edit_score > 0.8
Expected an objects specifier or a keyword
> select #1 & attribute:edit_score > 0.8
Expected a keyword
> attribute list
Unknown command: attribute list
> select :/edit_score > 0.8
Expected an objects specifier or a keyword
> select attribute:edit_score > 0.8
Expected an objects specifier or a keyword
> select #1 & @ca & attribute edit_score > 0.8
Expected a keyword
> select #1 & :. & attribute edit_score > 0.8
Expected a keyword
> select (:/edit_score > 0.8)
Expected an objects specifier or a keyword
> select (#1:/edit_score > 0.8)
Expected an objects specifier or a keyword
> select attribute edit_score > 0.8 target r
Expected an objects specifier or a keyword
> select (#1 & attribute edit_score > 0.8 target r)
Expected an objects specifier or a keyword
> hide atoms
> show atoms
> color byhetero
> hide atoms
> save /Users/emena/projects/crispr-bean/a_19s_6bp/8USB_libAB.cxs
——— End of log from Thu Jul 3 00:04:57 2025 ———
> view name session-start
opened ChimeraX session
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M3
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,3
Model Number: Z1A90001BLL/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.121.1
OS Loader Version: 11881.121.1
Software:
System Software Overview:
System Version: macOS 15.5 (24F74)
Kernel Version: Darwin 24.5.0
Time since boot: 19 hours, 8 minutes
Graphics/Displays:
Apple M3:
Chipset Model: Apple M3
Type: GPU
Bus: Built-In
Total Number of Cores: 10
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
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.4.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.4.0
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.18
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: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
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
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10rc202506130232
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: 2.5.1
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: 1.6.2
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
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: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
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: 1.1.3
ChimeraX-ProfileGrids: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
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: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
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: 1.45.1
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: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.9.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.58.4
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
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
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.0
tzdata: 2025.2
urllib3: 2.4.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Change History (2)
comment:1 by , 4 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 4 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
The ChimeraX bug report panel says what we know about this crash
"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."
We thought this was fixed in Qt version 6.8 which is used in ChimeraX 1.10 that you were using and your bug report is the first in several months that shows the same crash can happen in Qt 6.8. We don't have a solution for this. If you know certains steps that lead to this ChimeraX crash, for instance, unplugging or plugging in an external monitor we'd be interested in hearing what those are.
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Reported by Elijah