![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 months ago
Closed 7 months ago
#17269 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-15.3.2-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00000001fc574840 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 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, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, 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, lxml._elementpath, lxml.etree, PIL._imagingmath (total: 59)
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{
"uptime" : 450000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,5",
"coalitionID" : 21145,
"osVersion" : {
"train" : "macOS 15.3.2",
"build" : "24D81",
"releaseType" : "User"
},
"captureTime" : "2025-04-01 18:03:45.1577 -0700",
"codeSigningMonitor" : 1,
"incident" : "D25CBCCD-4498-44EF-BDE7-E1F9F05F530A",
"pid" : 49198,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-04-01 11:19:55.3861 -0700",
"procStartAbsTime" : 10600421643542,
"procExitAbsTime" : 10962382130276,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"8130645D-BEAB-5776-BE53-C039A7FAE8AE","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "34646E04-77D9-22C8-5CBA-A82BA218D2EA",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "0C17CBEB-30D5-476A-8EB6-962600B7C5A8",
"wakeTime" : 239,
"sleepWakeUUID" : "7FE8AB52-28D8-4CFD-884E-5FE70CFE36B3",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4339007488\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102a00000-102a04000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":49198},
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4339007488\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102a00000-102a04000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
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===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/poojasrinivas/Library/CloudStorage/OneDrive-
> UW/Desktop/umbtoxin_paper2/models_lectindomains.cxs
Log from Mon Mar 31 14:02:19 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/poojasrinivas/Library/CloudStorage/OneDrive-
> UW/Desktop/umbtoxin_paper2/lectindomainstructures/TrypsinLectinStructures/SP+inTrypsin+5BPF-4+CBM_4_9_MER7108863.pdb
Chain information for SP+inTrypsin+5BPF-4+CBM_4_9_MER7108863.pdb #1
---
Chain | Description
A | No description available
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> lighting soft
> open /Users/poojasrinivas/Library/CloudStorage/OneDrive-
> UW/Desktop/umbtoxin_paper2/lectindomainstructures/TrypsinLectinStructures/SP+inTrypsin+6BPF-1+6BPF-1_MFD5149162.pdb
Chain information for SP+inTrypsin+6BPF-1+6BPF-1_MFD5149162.pdb #2
---
Chain | Description
A | No description available
> matchmaker #2 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 SP+inTrypsin+5BPF-4+CBM_4_9_MER7108863.pdb, chain A (#1) with
SP+inTrypsin+6BPF-1+6BPF-1_MFD5149162.pdb, chain A (#2), sequence alignment
score = 827.2
RMSD between 185 pruned atom pairs is 0.728 angstroms; (across all 574 pairs:
25.783)
> hide #1 models
> show #1 models
> open /Users/poojasrinivas/Library/CloudStorage/OneDrive-
> UW/Desktop/umbtoxin_paper2/lectindomainstructures/TrypsinLectinStructures/SP+7BPF-7+BPA-
> Ig+5BPF-11_MER8041134.cif
Chain information for SP+7BPF-7+BPA-Ig+5BPF-11_MER8041134.cif #3
---
Chain | Description
A | .
> matchmaker #3 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 SP+inTrypsin+5BPF-4+CBM_4_9_MER7108863.pdb, chain A (#1) with
SP+7BPF-7+BPA-Ig+5BPF-11_MER8041134.cif, chain A (#3), sequence alignment
score = 447.9
RMSD between 6 pruned atom pairs is 1.424 angstroms; (across all 454 pairs:
30.481)
> open /Users/poojasrinivas/Library/CloudStorage/OneDrive-
> UW/Desktop/umbtoxin_paper2/lectindomainstructures/TrypsinLectinStructures/ALF_accessory+inTrypsin+RicinB-2+RicinB-2_ALO06367.pdb
Chain information for ALF_accessory+inTrypsin+RicinB-2+RicinB-2_ALO06367.pdb
#4
---
Chain | Description
A | No description available
> matchmaker #4 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 SP+inTrypsin+5BPF-4+CBM_4_9_MER7108863.pdb, chain A (#1) with
ALF_accessory+inTrypsin+RicinB-2+RicinB-2_ALO06367.pdb, chain A (#4), sequence
alignment score = 684
RMSD between 181 pruned atom pairs is 0.827 angstroms; (across all 474 pairs:
28.058)
> open /Users/poojasrinivas/Library/CloudStorage/OneDrive-
> UW/Desktop/umbtoxin_paper2/lectindomainstructures/TrypsinLectinStructures/ALF_accessory+inTrypsin+Jellyroll-
> like+Jellyroll-like+Jellyroll-like_MCU7825302.pdb
Chain information for ALF_accessory+inTrypsin+Jellyroll-like+Jellyroll-
like+Jellyroll-like_MCU7825302.pdb #5
---
Chain | Description
A | No description available
> matchmaker #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 SP+inTrypsin+5BPF-4+CBM_4_9_MER7108863.pdb, chain A (#1) with
ALF_accessory+inTrypsin+Jellyroll-like+Jellyroll-like+Jellyroll-
like_MCU7825302.pdb, chain A (#5), sequence alignment score = 684.8
RMSD between 174 pruned atom pairs is 0.841 angstroms; (across all 575 pairs:
34.961)
> open /Users/poojasrinivas/Library/CloudStorage/OneDrive-
> UW/Desktop/umbtoxin_paper2/lectindomainstructures/TrypsinLectinStructures/SP+inTrypsin+TAC4_MER7568781.pdb
Chain information for SP+inTrypsin+TAC4_MER7568781.pdb #6
---
Chain | Description
A | No description available
> matchmaker #6to #1
Missing or invalid "matchAtoms" argument: only initial part "#6" of atom
specifier valid
> matchmaker #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 SP+inTrypsin+5BPF-4+CBM_4_9_MER7108863.pdb, chain A (#1) with
SP+inTrypsin+TAC4_MER7568781.pdb, chain A (#6), sequence alignment score =
684.5
RMSD between 198 pruned atom pairs is 0.726 angstroms; (across all 357 pairs:
19.803)
> open /Users/poojasrinivas/Library/CloudStorage/OneDrive-
> UW/Desktop/umbtoxin_paper2/lectindomainstructures/TrypsinLectinStructures/SP+inTrypsin+Bulb-
> lectin+Bulb-lectin+RicinB-6_BAU81346.pdb
Chain information for SP+inTrypsin+Bulb-lectin+Bulb-
lectin+RicinB-6_BAU81346.pdb #7
---
Chain | Description
A | No description available
> matchmaker #7 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 SP+inTrypsin+5BPF-4+CBM_4_9_MER7108863.pdb, chain A (#1) with
SP+inTrypsin+Bulb-lectin+Bulb-lectin+RicinB-6_BAU81346.pdb, chain A (#7),
sequence alignment score = 827.6
RMSD between 180 pruned atom pairs is 0.755 angstroms; (across all 556 pairs:
29.281)
> open /Users/poojasrinivas/Library/CloudStorage/OneDrive-
> UW/Desktop/umbtoxin_paper2/lectindomainstructures/TrypsinLectinStructures/SP+inTrypsin+Bulb-
> lectin+Bulb-lectin+5BPF-6_MER7730173.pdb
Chain information for SP+inTrypsin+Bulb-lectin+Bulb-
lectin+5BPF-6_MER7730173.pdb #8
---
Chain | Description
A | No description available
> color white
> hide #8 models
> hide #7 models
> hide #6 models
> hide #5 models
> hide #4 models
> hide #3 models
> hide #2 models
> tile
1 model tiled
> show #1-8
> show #1-8 cartoons
> show #2 models
> show #3 models
> show #8 models
> show #7 models
> show #5 models
> show #4 models
> show #6 models
> tile
8 models tiled
> select #1-8 :1-25
1397 atoms, 1412 bonds, 200 residues, 8 models selected
> ui mousemode right select
Drag select of 27 residues
Drag select of 29 residues
> delete sel
Drag select of 25 residues
Drag select of 33 residues
Drag select of 31 residues
> delete sel
Drag select of 19 residues
> delete sel
Drag select of 14 residues
> delete sel
Drag select of 7 residues
> delete sel
Drag select of 18 residues
> delete sel
Drag select of 46 residues
> delete sel
Drag select of 30 residues
> delete sel
Drag select of 2 residues
> delete sel
Drag select of 19 residues
> delete sel
Drag select of 12 residues
> delete sel
> lighting soft
> hide #2-8 cartoons
> select #1 :256-504
1824 atoms, 1868 bonds, 249 residues, 1 model selected
> select #1 :256-501
1795 atoms, 1837 bonds, 246 residues, 1 model selected
> color sel dodgerblue
> select #1 :505-644
1044 atoms, 1061 bonds, 140 residues, 1 model selected
> color sel tan
> select clear
[Repeated 2 time(s)]Drag select of 39 residues
> select clear
> hide #1 models
> show #2/catoons
> show #2 cartoons
> select #2:251-819
4123 atoms, 4215 bonds, 569 residues, 1 model selected
> color sel pueple
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel lavendar
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel lavender
> color sel plum
> select clear
> hide #3 models
> show #3 models
> hide #2 models
> show #1 models
> show #2 models
Drag select of 34 residues
> select clear
> show #3 cartoons
> select #3 :49-367
2352 atoms, 2397 bonds, 319 residues, 1 model selected
> select #3 :41-367
2409 atoms, 2457 bonds, 327 residues, 1 model selected
> color sel lime
> color pale green
> color sel pale green
> select #3 :368-489
924 atoms, 951 bonds, 122 residues, 1 model selected
> select #3 :368-488
917 atoms, 943 bonds, 121 residues, 1 model selected
> color sel forestgreen
> select #3 :487-700
1596 atoms, 1635 bonds, 214 residues, 1 model selected
> select #3 :487-900
1998 atoms, 2051 bonds, 265 residues, 1 model selected
> color sel dodger blue
> select clear
> open
> /Users/poojasrinivas/Downloads/fold_meu0719199_1/fold_meu0719199_1_model_0.cif
Chain information for fold_meu0719199_1_model_0.cif #9
---
Chain | Description
A | .
> matchmaker #9 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 SP+inTrypsin+5BPF-4+CBM_4_9_MER7108863.pdb, chain A (#1) with
fold_meu0719199_1_model_0.cif, chain A (#9), sequence alignment score = 3063
RMSD between 249 pruned atom pairs is 0.509 angstroms; (across all 615 pairs:
17.385)
> hide #1 models
> show #1 models
> hide #9 models
> show #4 cartoons
> select #4 :342..477
Expected a keyword
> select #4 :342-477
1032 atoms, 1052 bonds, 136 residues, 1 model selected
> select #4 :342-800
2103 atoms, 2146 bonds, 277 residues, 1 model selected
> color sel orange
> color sel gold
Drag select of 141 residues
> select clear
> hide #4 models
> show #4 models
> hide #5 models
> show #5 models
> show #5 cartoons
> select #5 :402-766
2615 atoms, 2678 bonds, 365 residues, 1 model selected
> color sel magenta
> color sel medium violet red
> select clear
> show #6 cartoons
> select clear
> select #6:274-401
910 atoms, 927 bonds, 128 residues, 1 model selected
> color sel pink
> select clear
> show #7 cartoons
> select #7 :246-370
927 atoms, 947 bonds, 125 residues, 1 model selected
> select #7 :246-370,371-485
1823 atoms, 1867 bonds, 240 residues, 1 model selected
> color sel magenta
> select #7 :485-606
887 atoms, 903 bonds, 121 residues, 1 model selected
> color sel orange
> select clear
> show #8 cartoons
> select #8 :250-368
869 atoms, 887 bonds, 119 residues, 1 model selected
> select #8 :247-368
893 atoms, 911 bonds, 122 residues, 1 model selected
> color sel magenta
> select #8 :247-491
1812 atoms, 1855 bonds, 245 residues, 1 model selected
> color sel magenta
> select #8 :492-774
2090 atoms, 2139 bonds, 283 residues, 1 model selected
> color sel dodger blue
> select clear
Drag select of 76 residues
> select clear
> close #9
> open
> /Users/poojasrinivas/Downloads/fold_meu6965693_1/fold_meu6965693_1_model_0.cif
Chain information for fold_meu6965693_1_model_0.cif #9
---
Chain | Description
A | .
> tile
9 models tiled
> hide #8 models
> hide #7 models
> hide #6 models
> hide #5 models
> hide #4 models
> hide #3 models
> hide #2 models
> hide #1 models
> lighting soft
> select #9:1-40
262 atoms, 265 bonds, 40 residues, 1 model selected
> delete sel
> color #9 white
> select #9 :378-900 grey
Expected a keyword
> select #9 :378-900
3258 atoms, 3331 bonds, 435 residues, 1 model selected
> color sel grey
> select clear
> show #8 models
> show #7 models
> show #6 models
> show #5 models
> show #3 models
> show #4 models
> show #2 models
> show #1 models
> save /Users/poojasrinivas/Library/CloudStorage/OneDrive-
> UW/Desktop/umbtoxin_paper2/models_lectindomains.cxs
——— End of log from Mon Mar 31 14:02:19 2025 ———
opened ChimeraX session
> hide #9 models
> hide #8 models
> hide #7 models
> hide #6 models
> hide #5 models
> hide #4 models
> hide #3 models
> hide #2 models
> ui tool show "Side View"
> ui mousemode right select
Drag select of 172 residues
> color sel white
> select clear
> color #1 :255-501 #192F8A
Drag select of 13 residues
> select clear
> ui mousemode right translate
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> graphics silhouettes true
> color #1 white
> ui mousemode right select
Drag select of 143 residues
> color #1 #B5A688
> color sel #B5A688
> select clear
Drag select of 3 residues
> color sel #B5A688
> select clear
> save
> /Users/poojasrinivas/Desktop/umbtoxin_paper2/chimeraXscreenshots/CBM_4_MER71088631.png
> width 1800 height 1800 supersample 4 transparentBackground true
> hide #1 models
> show #2 models
> open /Users/poojasrinivas/Library/CloudStorage/OneDrive-
> UW/Desktop/umbtoxin_paper2/lectindomainstructures/TrypsinLectinStructures/SP+inTrypsin+6BPF-2_MET7413469.cif
Chain information for SP+inTrypsin+6BPF-2_MET7413469.cif #10
---
Chain | Description
A | .
Drag select of 24 residues
> delete sel
Drag select of 3 residues
> delete sel
> select clear
> hide #2 models
Drag select of 217 residues
> color sel white
> select ~sel
46124 atoms, 47132 bonds, 6307 residues, 10 models selected
> color sel #BD8FC1
> select clear
Drag select of 72 residues
> color sel white
> select clear
> save
> /Users/poojasrinivas/Desktop/umbtoxin_paper2/chimeraXscreenshots/6BPF-2_MET7413469.png
> width 1800 height 1800 supersample 4 transparentBackground true
> hide #10 models
> show #3 models
Drag select of 711 residues
> color sel white
> select clear
> select #3 :1-370
2428 atoms, 2477 bonds, 330 residues, 1 model selected
> color sel #A7D073
> select clear
> select #3/A:113
8 atoms, 7 bonds, 1 residue, 1 model selected
> save
> /Users/poojasrinivas/Desktop/umbtoxin_paper2/chimeraXscreenshots/7bpf-7_MER8041134.png
> width 1800 height 1800 supersample 4 transparentBackground true
> select clear
> save
> /Users/poojasrinivas/Desktop/umbtoxin_paper2/chimeraXscreenshots/7bpf-7_MER8041134.png
> width 1800 height 1800 supersample 4 transparentBackground true
> color #1 white
> color #3 white
Drag select of 2 residues
> ui mousemode right translate
> color #3:369-484 #3BB092
> ui mousemode right select
> select clear
> save /Users/poojasrinivas/Desktop/umbtoxin_paper2/chimeraXscreenshots/bpa-
> ig_MER8041134.png width 1800 height 1800 supersample 4 transparentBackground
> true
Drag select of 401 residues
> color sel white
> select clear
> ui mousemode right translate
> ui mousemode right select
Drag select of 266 residues
> color sel #48B4ED
> select clear
Drag select of 7 residues
> select clear
> save
> /Users/poojasrinivas/Desktop/umbtoxin_paper2/chimeraXscreenshots/5bpf11_MER8041134.png
> width 1800 height 1800 supersample 4 transparentBackground true
> hide #3 models
> show #4 models
> select add #4
4507 atoms, 4590 bonds, 618 residues, 1 model selected
> color sel white
> select clear
Drag select of 135 residues
> color sel #E64216
Drag select of 63 residues
> color sel #E64216
Drag select of 126 residues
> color sel #E64216
Drag select of 20 residues
> color sel #E64216
Drag select of 3 residues
> color sel #E64216
> select clear
> select #4/A:480
7 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> save
> /Users/poojasrinivas/Desktop/umbtoxin_paper2/chimeraXscreenshots/ricinb2_alo06367.png
> width 1800 height 1800 supersample 4 transparentBackground true
> hide #4 models
> show #5 models
Drag select of 748 residues
> color sel white
> select clear
> select #5 :402-766
2615 atoms, 2678 bonds, 365 residues, 1 model selected
> color sel #D165A5
> select #5/A:413
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> save
> /Users/poojasrinivas/Desktop/umbtoxin_paper2/chimeraXscreenshots/jellyrolllike_mcu7825302.png
> width 1800 height 1800 supersample 4 transparentBackground true
> hide #5 models
> show #6 models
> color #6 white
> select clear
Drag select of 126 residues
> color #6 #EFA0C6
> color sel #EFA0C6
> select clear
> save
> /Users/poojasrinivas/Desktop/umbtoxin_paper2/chimeraXscreenshots/tac4_mer7568781.png
> width 1800 height 1800 supersample 4 transparentBackground true
> hide #6 models
> show #7 models
> color #7 white
> color #7 :246-485 #DE007B
> select #7/A:246
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> select #7/A:485
6 atoms, 5 bonds, 1 residue, 1 model selected
> color #7/A :246-485 #D19EC8
> select clear
> save
> /Users/poojasrinivas/Desktop/umbtoxin_paper2/chimeraXscreenshots/bulblectins.png
> width 1800 height 1800 supersample 4 transparentBackground true
> hide #7 models
> show #1 models
> color #1 white
Drag select of 144 residues
Drag select of 2 residues
> select add #1/A:559
1087 atoms, 8 bonds, 145 residues, 1 model selected
> color sel $B7D123
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel #B7D123
> select clear
> save
> /Users/poojasrinivas/Desktop/umbtoxin_paper2/chimeraXscreenshots/cmb4.png
> width 1800 height 1800 supersample 4 transparentBackground true
> color #1/white
> color #1 white
Drag select of 250 residues
Drag select of 2 residues
> select subtract #1/A:503
1817 atoms, 249 residues, 1 model selected
Drag select of 2 residues
Drag select of 4 residues
> select subtract #1/A:250
1799 atoms, 246 residues, 1 model selected
Drag select of 3 residues
> color sel #65C2EE
> select clear
> save
> /Users/poojasrinivas/Desktop/umbtoxin_paper2/chimeraXscreenshots/5bpf.png
> width 1800 height 1800 supersample 4 transparentBackground true
> hide #1 models
> show #2 models
> color #2 white
Drag select of 572 residues
Drag select of 1 residues
> color sel #E266A3
> select clear
> select #2/A:673
6 atoms, 5 bonds, 1 residue, 1 model selected
> save
> /Users/poojasrinivas/Desktop/umbtoxin_paper2/chimeraXscreenshots/6bpf.png
> width 1800 height 1800 supersample 4 transparentBackground true
> select clear
> show #3 models
> hide #2 models
> color #3/white
> color #3 white
> color #3 :369-484 #3BB092
> save
> /Users/poojasrinivas/Desktop/umbtoxin_paper2/chimeraXscreenshots/BPAig.png
> width 1800 height 1800 supersample 4 transparentBackground true
> hide #3 models
> show #4 models
> select clear
Drag select of 104 residues
Drag select of 171 residues
> select #4 :342-900
2103 atoms, 2146 bonds, 277 residues, 1 model selected
> color sel BF371B
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel #BF371B
> select clear
> save
> /Users/poojasrinivas/Desktop/umbtoxin_paper2/chimeraXscreenshots/ricinb2.png
> width 1800 height 1800 supersample 4 transparentBackground true
> hide #4 models
> show #5 models
> color #5/A :402-900
> select #5/A :402-900
2615 atoms, 2678 bonds, 365 residues, 1 model selected
> color sel #3280C7
> select clear
> save
> /Users/poojasrinivas/Desktop/umbtoxin_paper2/chimeraXscreenshots/jellyroll.png
> width 1800 height 1800 supersample 4 transparentBackground true
> hide #5 models
> show #6 models
Drag select of 121 residues
Drag select of 119 residues
Drag select of 126 residues
> color sel #9A4193
> select clear
> save
> /Users/poojasrinivas/Desktop/umbtoxin_paper2/chimeraXscreenshots/tac4.png
> width 1800 height 1800 supersample 4 transparentBackground true
> hide #6 models
> show #7 models
> hide #7 models
> show #8 models
> show #3 models
> hide #8 models
> color #3 white
> select clear
> color #3 :1-366
> color #3 :1-366 #DE939C
> save
> /Users/poojasrinivas/Desktop/umbtoxin_paper2/chimeraXscreenshots/7bpf7.png
> width 1800 height 1800 supersample 4 transparentBackground true
> hide #3 models
> show #9 models
> hide #9 models
> show #9 models
> color #9 :378-812 #F69F29
> color #9 1_376
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #9 1-376 white
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #9 :1-376 white
> save
> /Users/poojasrinivas/Desktop/umbtoxin_paper2/chimeraXscreenshots/lameling.png
> width 1800 height 1800 supersample 4 transparentBackground true
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/poojasrinivas/Library/CloudStorage/OneDrive-
> UW/Desktop/umbtoxin_paper2/models_lectindomains.cxs
Log from Mon Mar 31 14:02:19 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/poojasrinivas/Library/CloudStorage/OneDrive-
> UW/Desktop/umbtoxin_paper2/lectindomainstructures/TrypsinLectinStructures/SP+inTrypsin+5BPF-4+CBM_4_9_MER7108863.pdb
Chain information for SP+inTrypsin+5BPF-4+CBM_4_9_MER7108863.pdb #1
---
Chain | Description
A | No description available
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> lighting soft
> open /Users/poojasrinivas/Library/CloudStorage/OneDrive-
> UW/Desktop/umbtoxin_paper2/lectindomainstructures/TrypsinLectinStructures/SP+inTrypsin+6BPF-1+6BPF-1_MFD5149162.pdb
Chain information for SP+inTrypsin+6BPF-1+6BPF-1_MFD5149162.pdb #2
---
Chain | Description
A | No description available
> matchmaker #2 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 SP+inTrypsin+5BPF-4+CBM_4_9_MER7108863.pdb, chain A (#1) with
SP+inTrypsin+6BPF-1+6BPF-1_MFD5149162.pdb, chain A (#2), sequence alignment
score = 827.2
RMSD between 185 pruned atom pairs is 0.728 angstroms; (across all 574 pairs:
25.783)
> hide #1 models
> show #1 models
> open /Users/poojasrinivas/Library/CloudStorage/OneDrive-
> UW/Desktop/umbtoxin_paper2/lectindomainstructures/TrypsinLectinStructures/SP+7BPF-7+BPA-
> Ig+5BPF-11_MER8041134.cif
Chain information for SP+7BPF-7+BPA-Ig+5BPF-11_MER8041134.cif #3
---
Chain | Description
A | .
> matchmaker #3 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 SP+inTrypsin+5BPF-4+CBM_4_9_MER7108863.pdb, chain A (#1) with
SP+7BPF-7+BPA-Ig+5BPF-11_MER8041134.cif, chain A (#3), sequence alignment
score = 447.9
RMSD between 6 pruned atom pairs is 1.424 angstroms; (across all 454 pairs:
30.481)
> open /Users/poojasrinivas/Library/CloudStorage/OneDrive-
> UW/Desktop/umbtoxin_paper2/lectindomainstructures/TrypsinLectinStructures/ALF_accessory+inTrypsin+RicinB-2+RicinB-2_ALO06367.pdb
Chain information for ALF_accessory+inTrypsin+RicinB-2+RicinB-2_ALO06367.pdb
#4
---
Chain | Description
A | No description available
> matchmaker #4 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 SP+inTrypsin+5BPF-4+CBM_4_9_MER7108863.pdb, chain A (#1) with
ALF_accessory+inTrypsin+RicinB-2+RicinB-2_ALO06367.pdb, chain A (#4), sequence
alignment score = 684
RMSD between 181 pruned atom pairs is 0.827 angstroms; (across all 474 pairs:
28.058)
> open /Users/poojasrinivas/Library/CloudStorage/OneDrive-
> UW/Desktop/umbtoxin_paper2/lectindomainstructures/TrypsinLectinStructures/ALF_accessory+inTrypsin+Jellyroll-
> like+Jellyroll-like+Jellyroll-like_MCU7825302.pdb
Chain information for ALF_accessory+inTrypsin+Jellyroll-like+Jellyroll-
like+Jellyroll-like_MCU7825302.pdb #5
---
Chain | Description
A | No description available
> matchmaker #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 SP+inTrypsin+5BPF-4+CBM_4_9_MER7108863.pdb, chain A (#1) with
ALF_accessory+inTrypsin+Jellyroll-like+Jellyroll-like+Jellyroll-
like_MCU7825302.pdb, chain A (#5), sequence alignment score = 684.8
RMSD between 174 pruned atom pairs is 0.841 angstroms; (across all 575 pairs:
34.961)
> open /Users/poojasrinivas/Library/CloudStorage/OneDrive-
> UW/Desktop/umbtoxin_paper2/lectindomainstructures/TrypsinLectinStructures/SP+inTrypsin+TAC4_MER7568781.pdb
Chain information for SP+inTrypsin+TAC4_MER7568781.pdb #6
---
Chain | Description
A | No description available
> matchmaker #6to #1
Missing or invalid "matchAtoms" argument: only initial part "#6" of atom
specifier valid
> matchmaker #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 SP+inTrypsin+5BPF-4+CBM_4_9_MER7108863.pdb, chain A (#1) with
SP+inTrypsin+TAC4_MER7568781.pdb, chain A (#6), sequence alignment score =
684.5
RMSD between 198 pruned atom pairs is 0.726 angstroms; (across all 357 pairs:
19.803)
> open /Users/poojasrinivas/Library/CloudStorage/OneDrive-
> UW/Desktop/umbtoxin_paper2/lectindomainstructures/TrypsinLectinStructures/SP+inTrypsin+Bulb-
> lectin+Bulb-lectin+RicinB-6_BAU81346.pdb
Chain information for SP+inTrypsin+Bulb-lectin+Bulb-
lectin+RicinB-6_BAU81346.pdb #7
---
Chain | Description
A | No description available
> matchmaker #7 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 SP+inTrypsin+5BPF-4+CBM_4_9_MER7108863.pdb, chain A (#1) with
SP+inTrypsin+Bulb-lectin+Bulb-lectin+RicinB-6_BAU81346.pdb, chain A (#7),
sequence alignment score = 827.6
RMSD between 180 pruned atom pairs is 0.755 angstroms; (across all 556 pairs:
29.281)
> open /Users/poojasrinivas/Library/CloudStorage/OneDrive-
> UW/Desktop/umbtoxin_paper2/lectindomainstructures/TrypsinLectinStructures/SP+inTrypsin+Bulb-
> lectin+Bulb-lectin+5BPF-6_MER7730173.pdb
Chain information for SP+inTrypsin+Bulb-lectin+Bulb-
lectin+5BPF-6_MER7730173.pdb #8
---
Chain | Description
A | No description available
> color white
> hide #8 models
> hide #7 models
> hide #6 models
> hide #5 models
> hide #4 models
> hide #3 models
> hide #2 models
> tile
1 model tiled
> show #1-8
> show #1-8 cartoons
> show #2 models
> show #3 models
> show #8 models
> show #7 models
> show #5 models
> show #4 models
> show #6 models
> tile
8 models tiled
> select #1-8 :1-25
1397 atoms, 1412 bonds, 200 residues, 8 models selected
> ui mousemode right select
Drag select of 27 residues
Drag select of 29 residues
> delete sel
Drag select of 25 residues
Drag select of 33 residues
Drag select of 31 residues
> delete sel
Drag select of 19 residues
> delete sel
Drag select of 14 residues
> delete sel
Drag select of 7 residues
> delete sel
Drag select of 18 residues
> delete sel
Drag select of 46 residues
> delete sel
Drag select of 30 residues
> delete sel
Drag select of 2 residues
> delete sel
Drag select of 19 residues
> delete sel
Drag select of 12 residues
> delete sel
> lighting soft
> hide #2-8 cartoons
> select #1 :256-504
1824 atoms, 1868 bonds, 249 residues, 1 model selected
> select #1 :256-501
1795 atoms, 1837 bonds, 246 residues, 1 model selected
> color sel dodgerblue
> select #1 :505-644
1044 atoms, 1061 bonds, 140 residues, 1 model selected
> color sel tan
> select clear
[Repeated 2 time(s)]Drag select of 39 residues
> select clear
> hide #1 models
> show #2/catoons
> show #2 cartoons
> select #2:251-819
4123 atoms, 4215 bonds, 569 residues, 1 model selected
> color sel pueple
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel lavendar
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel lavender
> color sel plum
> select clear
> hide #3 models
> show #3 models
> hide #2 models
> show #1 models
> show #2 models
Drag select of 34 residues
> select clear
> show #3 cartoons
> select #3 :49-367
2352 atoms, 2397 bonds, 319 residues, 1 model selected
> select #3 :41-367
2409 atoms, 2457 bonds, 327 residues, 1 model selected
> color sel lime
> color pale green
> color sel pale green
> select #3 :368-489
924 atoms, 951 bonds, 122 residues, 1 model selected
> select #3 :368-488
917 atoms, 943 bonds, 121 residues, 1 model selected
> color sel forestgreen
> select #3 :487-700
1596 atoms, 1635 bonds, 214 residues, 1 model selected
> select #3 :487-900
1998 atoms, 2051 bonds, 265 residues, 1 model selected
> color sel dodger blue
> select clear
> open
> /Users/poojasrinivas/Downloads/fold_meu0719199_1/fold_meu0719199_1_model_0.cif
Chain information for fold_meu0719199_1_model_0.cif #9
---
Chain | Description
A | .
> matchmaker #9 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 SP+inTrypsin+5BPF-4+CBM_4_9_MER7108863.pdb, chain A (#1) with
fold_meu0719199_1_model_0.cif, chain A (#9), sequence alignment score = 3063
RMSD between 249 pruned atom pairs is 0.509 angstroms; (across all 615 pairs:
17.385)
> hide #1 models
> show #1 models
> hide #9 models
> show #4 cartoons
> select #4 :342..477
Expected a keyword
> select #4 :342-477
1032 atoms, 1052 bonds, 136 residues, 1 model selected
> select #4 :342-800
2103 atoms, 2146 bonds, 277 residues, 1 model selected
> color sel orange
> color sel gold
Drag select of 141 residues
> select clear
> hide #4 models
> show #4 models
> hide #5 models
> show #5 models
> show #5 cartoons
> select #5 :402-766
2615 atoms, 2678 bonds, 365 residues, 1 model selected
> color sel magenta
> color sel medium violet red
> select clear
> show #6 cartoons
> select clear
> select #6:274-401
910 atoms, 927 bonds, 128 residues, 1 model selected
> color sel pink
> select clear
> show #7 cartoons
> select #7 :246-370
927 atoms, 947 bonds, 125 residues, 1 model selected
> select #7 :246-370,371-485
1823 atoms, 1867 bonds, 240 residues, 1 model selected
> color sel magenta
> select #7 :485-606
887 atoms, 903 bonds, 121 residues, 1 model selected
> color sel orange
> select clear
> show #8 cartoons
> select #8 :250-368
869 atoms, 887 bonds, 119 residues, 1 model selected
> select #8 :247-368
893 atoms, 911 bonds, 122 residues, 1 model selected
> color sel magenta
> select #8 :247-491
1812 atoms, 1855 bonds, 245 residues, 1 model selected
> color sel magenta
> select #8 :492-774
2090 atoms, 2139 bonds, 283 residues, 1 model selected
> color sel dodger blue
> select clear
Drag select of 76 residues
> select clear
> close #9
> open
> /Users/poojasrinivas/Downloads/fold_meu6965693_1/fold_meu6965693_1_model_0.cif
Chain information for fold_meu6965693_1_model_0.cif #9
---
Chain | Description
A | .
> tile
9 models tiled
> hide #8 models
> hide #7 models
> hide #6 models
> hide #5 models
> hide #4 models
> hide #3 models
> hide #2 models
> hide #1 models
> lighting soft
> select #9:1-40
262 atoms, 265 bonds, 40 residues, 1 model selected
> delete sel
> color #9 white
> select #9 :378-900 grey
Expected a keyword
> select #9 :378-900
3258 atoms, 3331 bonds, 435 residues, 1 model selected
> color sel grey
> select clear
> show #8 models
> show #7 models
> show #6 models
> show #5 models
> show #3 models
> show #4 models
> show #2 models
> show #1 models
> save /Users/poojasrinivas/Library/CloudStorage/OneDrive-
> UW/Desktop/umbtoxin_paper2/models_lectindomains.cxs
——— End of log from Mon Mar 31 14:02:19 2025 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,5
Model Number: MPHG3LL/A
Chip: Apple M2 Max
Total Number of Cores: 12 (8 performance and 4 efficiency)
Memory: 32 GB
System Firmware Version: 11881.81.4
OS Loader Version: 11881.81.4
Software:
System Software Overview:
System Version: macOS 15.3.2 (24D81)
Kernel Version: Darwin 24.3.0
Time since boot: 16 days, 18 hours, 28 minutes
Graphics/Displays:
Apple M2 Max:
Chipset Model: Apple M2 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 30
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
DELL P2721Q:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
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: 2.2.4
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: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
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-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
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: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
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: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
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idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 7 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 7 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
This crash is caused by a Qt window toolkit bug on Mac with multiple displays. The crash sometimes happens when plugging in or unplugging a display or waking from sleep or moving windows between displays. We have not seen this crash in the current ChimeraX daily build which uses a newer Qt version so you might want to try that.
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Reported by Pooja Srinivas