![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 weeks ago
Closed 4 weeks ago
#19104 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-26.0.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x000000020ccb4800 (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.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, 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._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.mlp._mlp, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, _pyKVFinder (total: 60)
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{
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"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,1",
"coalitionID" : 2299,
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"build" : "25A362",
"releaseType" : "User"
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"codeSigningMonitor" : 1,
"incident" : "40205B0B-88F3-42DD-9070-C8DC513F93AD",
"pid" : 29808,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-10-09 14:27:14.2563 -0700",
"procStartAbsTime" : 2071576452496,
"procExitAbsTime" : 2273302082690,
"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"},
"storeInfo" : {"deviceIdentifierForVendor":"043CD568-6CA0-5CAE-9768-7BA2D6BEA547","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "19B0A0CA-352B-89CC-7C2B-A2CF1E191A0E",
"developerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRFOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkQng\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "613746FA-EB74-4EE4-A1B7-BD2EE2669056",
"wakeTime" : 21606,
"sleepWakeUUID" : "56B5B082-3F9C-4A68-A724-26C8A146513C",
"sip" : "enabled",
"vmRegionInfo" : "0x169 is not in any region. Bytes before following region: 4337794711\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1028d8000-1028dc000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000169","rawCodes":[1,361],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000169"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":29808},
"vmregioninfo" : "0x169 is not in any region. Bytes before following region: 4337794711\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1028d8000-1028dc000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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"faultingThread" : 0,
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===== Log before crash start =====
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/JackKim/Downloads/fold_gemma_tcs_hk/fold_gemma_tcs_hk_model_0.cif
Chain information for fold_gemma_tcs_hk_model_0.cif #1
---
Chain | Description
A | .
Computing secondary structure
> close
> open
> /Users/JackKim/Downloads/fold_gemma_tcs_dimerhkwithrr/fold_gemma_tcs_dimerhkwithrr_model_0.cif
Chain information for fold_gemma_tcs_dimerhkwithrr_model_0.cif #1
---
Chain | Description
A | .
B C | .
Computing secondary structure
> set bgColor white
> color bychain
> ui mousemode right "move picked models"
> mlp
Map values for surface "fold_gemma_tcs_dimerhkwithrr_model_0.cif_A SES
surface": minimum -30.95, mean -5.611, maximum 25.89
Map values for surface "fold_gemma_tcs_dimerhkwithrr_model_0.cif_B SES
surface": minimum -30.91, mean -4.136, maximum 24.69
Map values for surface "fold_gemma_tcs_dimerhkwithrr_model_0.cif_C SES
surface": minimum -30.11, mean -4.194, maximum 24.3
To also show corresponding color key, enter the above mlp command and add key
true
> hide surfaces
> coulombic
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_gemma_tcs_dimerhkwithrr_model_0.cif_A SES surface
#1.1: minimum, -22.77, mean -1.89, maximum 9.54
Coulombic values for fold_gemma_tcs_dimerhkwithrr_model_0.cif_B SES surface
#1.2: minimum, -16.50, mean -2.08, maximum 13.20
Coulombic values for fold_gemma_tcs_dimerhkwithrr_model_0.cif_C SES surface
#1.3: minimum, -21.29, mean -2.08, maximum 13.74
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!1 models
> show #!1 models
> hide surfaces
> select #1:asp
624 atoms, 549 bonds, 78 residues, 1 model selected
> show sel target a
> select #1:asp
624 atoms, 549 bonds, 78 residues, 1 model selected
> show sel target a
> color sel black
> select #1:asp,glu
2001 atoms, 1782 bonds, 231 residues, 1 model selected
> show sel target a
> color sel black
> select add #1
13795 atoms, 13992 bonds, 1800 residues, 4 models selected
> select subtract #1
3 models selected
> open
> /Users/JackKim/Downloads/fold_gemma_ctwithparalog1/fold_gemma_ctwithparalog1_model_0.cif
Chain information for fold_gemma_ctwithparalog1_model_0.cif #2
---
Chain | Description
A | .
B | .
Computing secondary structure
> hide #!1 models
> view #2 clip false
> coulombic #2
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_gemma_ctwithparalog1_model_0.cif_A SES surface #2.1:
minimum, -29.47, mean -4.77, maximum 12.93
Coulombic values for fold_gemma_ctwithparalog1_model_0.cif_B SES surface #2.2:
minimum, -15.79, mean -1.23, maximum 15.45
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!2 surfaces
> color #!2 bychain
> coulombic #!2
Coulombic values for fold_gemma_ctwithparalog1_model_0.cif_A SES surface #2.1:
minimum, -29.47, mean -4.77, maximum 12.93
Coulombic values for fold_gemma_ctwithparalog1_model_0.cif_B SES surface #2.2:
minimum, -15.79, mean -1.23, maximum 15.45
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!2 models
> show #!2 models
> ui tool show "AlphaFold Error Plot"
> alphafold pae #2 file
> /Users/JackKim/Downloads/fold_gemma_ctwithparalog1/fold_gemma_ctwithparalog1_full_data_0.json
> color #2/A:99-112 lime
> color #2/B:166-193 magenta
> hide #!2 surfaces
> color #2/A:105 lime
> color #2/B:283 magenta
> color #2/A:99-111 lime
> color #2/B:259-285 magenta
> open
> /Users/JackKim/Downloads/fold_gemma_ctwithparalog2/fold_gemma_ctwithparalog2_model_0.cif
Chain information for fold_gemma_ctwithparalog2_model_0.cif #3
---
Chain | Description
A | .
B | .
Computing secondary structure
> mmaker #3 to #2
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_gemma_ctwithparalog1_model_0.cif, chain B (#2) with
fold_gemma_ctwithparalog2_model_0.cif, chain B (#3), sequence alignment score
= 2088
RMSD between 346 pruned atom pairs is 0.520 angstroms; (across all 421 pairs:
11.405)
> ui tool show "AlphaFold Error Plot"
> alphafold pae #3 file
> /Users/JackKim/Downloads/fold_gemma_ctwithparalog2/fold_gemma_ctwithparalog2_full_data_0.json
> ui tool show "AlphaFold Error Plot"
> alphafold pae #3 file
> /Users/JackKim/Downloads/fold_gemma_ctwithparalog2/fold_gemma_ctwithparalog2_full_data_0.json
> hide #!2 models
> color #3/A:235-248 lime
> color #3/B:166-193 magenta
> color #3/A:236-248 lime
> color #3/B:261-285 magenta
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #3 models
> show #3 models
> color #3/A:208-209 lime
> color #3/B:181 magenta
> color #3 bychain
> coulombic #3
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_gemma_ctwithparalog2_model_0.cif_A SES surface #3.1:
minimum, -23.72, mean -2.47, maximum 16.68
Coulombic values for fold_gemma_ctwithparalog2_model_0.cif_B SES surface #3.2:
minimum, -16.04, mean -1.17, maximum 14.69
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!3 surfaces
> log metadata #3
No models had metadata
> log chains #3
Chain information for fold_gemma_ctwithparalog2_model_0.cif #3
---
Chain | Description
A | .
B | .
> select #3/A:100-
Expected an objects specifier or a keyword
> select #3/A:100-200
791 atoms, 802 bonds, 101 residues, 1 model selected
> select #3/A:100-250
1201 atoms, 1219 bonds, 151 residues, 1 model selected
> sequence chain #3/A
Alignment identifier is 3/A
> select #3/A:100
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:100-290
1529 atoms, 1554 bonds, 191 residues, 1 model selected
> select #3/A:121
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:121-290
1360 atoms, 1384 bonds, 170 residues, 1 model selected
> select add #3/B
4721 atoms, 4829 bonds, 591 residues, 2 models selected
> coulombic sel
Coulombic values for fold_gemma_ctwithparalog2_model_0.cif_A SES surface #3.1:
minimum, -23.72, mean -2.47, maximum 16.68
Coulombic values for fold_gemma_ctwithparalog2_model_0.cif_B SES surface #3.2:
minimum, -16.04, mean -1.17, maximum 14.69
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!3 models
> select add #3
5632 atoms, 5756 bonds, 711 residues, 3 models selected
> select subtract #3
2 models selected
> select #3/A:pro
84 atoms, 86 bonds, 12 residues, 1 model selected
> select #3/A:70
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:70-120
393 atoms, 397 bonds, 51 residues, 1 model selected
> show #!3 models
> select add #3
5632 atoms, 5756 bonds, 711 residues, 2 models selected
> select subtract #3
2 models selected
> select #3/A:1
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:1-7
46 atoms, 45 bonds, 7 residues, 1 model selected
> hide sel surfaces
> select add #3
5632 atoms, 5756 bonds, 711 residues, 2 models selected
> select subtract #3
2 models selected
> hide #!3 surfaces
> select #3/A:1
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:1-17
122 atoms, 123 bonds, 17 residues, 1 model selected
> select #3/A:1
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:1-35
261 atoms, 266 bonds, 35 residues, 1 model selected
> select #3/A:1
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:1-44
339 atoms, 346 bonds, 44 residues, 1 model selected
> coulombic sel
Coulombic values for fold_gemma_ctwithparalog2_model_0.cif_A SES surface #3.1:
minimum, -23.72, mean -2.47, maximum 16.68
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!3 models
> select add #3
5632 atoms, 5756 bonds, 711 residues, 2 models selected
> select subtract #3
2 models selected
> open
> /Users/JackKim/Downloads/fold_gemma_tcwithparalog2_nosp_postlinker/fold_gemma_tcwithparalog2_nosp_postlinker_model_0.cif
Chain information for fold_gemma_tcwithparalog2_nosp_postlinker_model_0.cif #4
---
Chain | Description
A | .
B | .
Computing secondary structure
> color #4 bychain
> coulombic #4
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_gemma_tcwithparalog2_nosp_postlinker_model_0.cif_A
SES surface #4.1: minimum, -24.82, mean -3.75, maximum 11.30
Coulombic values for fold_gemma_tcwithparalog2_nosp_postlinker_model_0.cif_B
SES surface #4.2: minimum, -35.75, mean -1.60, maximum 16.40
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!4 surfaces
> coulombic #!4
Coulombic values for fold_gemma_tcwithparalog2_nosp_postlinker_model_0.cif_A
SES surface #4.1: minimum, -24.82, mean -3.75, maximum 11.30
Coulombic values for fold_gemma_tcwithparalog2_nosp_postlinker_model_0.cif_B
SES surface #4.2: minimum, -35.75, mean -1.60, maximum 16.40
To also show corresponding color key, enter the above coulombic command and
add key true
> ui tool show "Side View"
> view #4 clip false
> hide #!4 surfaces
> show #!3 models
> mmaker #3 to #4
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_gemma_tcwithparalog2_nosp_postlinker_model_0.cif, chain B (#4)
with fold_gemma_ctwithparalog2_model_0.cif, chain B (#3), sequence alignment
score = 1995.9
RMSD between 334 pruned atom pairs is 0.360 angstroms; (across all 400 pairs:
12.027)
> hide #!3-4 surfaces
> open /Users/JackKim/Downloads/fold_gemma_ct/fold_gemma_ct_model_0.cif
Chain information for fold_gemma_ct_model_0.cif #5
---
Chain | Description
A | .
Computing secondary structure
> mmaker #5 to #4
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_gemma_tcwithparalog2_nosp_postlinker_model_0.cif, chain B (#4)
with fold_gemma_ct_model_0.cif, chain A (#5), sequence alignment score =
1986.3
RMSD between 335 pruned atom pairs is 0.444 angstroms; (across all 400 pairs:
2.328)
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> hide #!4 models
> coulombic #5
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_gemma_ct_model_0.cif_A SES surface #5.1: minimum,
-16.73, mean -1.52, maximum 13.89
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!5 surfaces
> show #!4 models
> select add #5
3361 atoms, 3445 bonds, 421 residues, 1 model selected
> color sel red
> select subtract #5
1 model selected
> hide #!4 models
> show #!5 surfaces
> hide #!5 surfaces
> coulombic #!5
Coulombic values for fold_gemma_ct_model_0.cif_A SES surface #5.1: minimum,
-16.73, mean -1.52, maximum 13.89
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!5 surfaces
> show #5 target a
> coulombic #!5
Coulombic values for fold_gemma_ct_model_0.cif_A SES surface #5.1: minimum,
-16.73, mean -1.52, maximum 13.89
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!5 surfaces
> ui mousemode right distance
> distance #5/A:299@CB #5/A:308@CG
Distance between fold_gemma_ct_model_0.cif #5/A SER 299 CB and ASP 308 CG:
7.316Å
> coulombic #!5
Coulombic values for fold_gemma_ct_model_0.cif_A SES surface #5.1: minimum,
-16.73, mean -1.52, maximum 13.89
To also show corresponding color key, enter the above coulombic command and
add key true
> color #3/A:28-29 lime
> color #3/B:124-125 magenta
> hide #!5 surfaces
> coulombic #!5
Coulombic values for fold_gemma_ct_model_0.cif_A SES surface #5.1: minimum,
-16.73, mean -1.52, maximum 13.89
To also show corresponding color key, enter the above coulombic command and
add key true
> ui mousemode right "move picked models"
> hide #!5 surfaces
> ui mousemode right distance
> distance #5/A:307@CB #5/A:406@OH
Distance between fold_gemma_ct_model_0.cif #5/A PHE 307 CB and TYR 406 OH:
5.114Å
> coulombic #!5
Coulombic values for fold_gemma_ct_model_0.cif_A SES surface #5.1: minimum,
-16.73, mean -1.52, maximum 13.89
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!5 surfaces
> show #!5 surfaces
> hide #!5 surfaces
> help show
> show target a
> show
> ui mousemode right select
> select #5/A:297
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel target a
> show 5/A:297 targ a
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show 5/A:297
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show (#!5 & sel-residues & sidechain) target ab
> select add #5
3361 atoms, 3445 bonds, 2 pseudobonds, 421 residues, 3 models selected
> select subtract #5
1 model selected
> select add #5
3361 atoms, 3445 bonds, 2 pseudobonds, 421 residues, 2 models selected
> show (#!5 & sel-residues & sidechain) target ab
> select clear
> ui mousemode right "move picked models"
> select add #5
3361 atoms, 3445 bonds, 2 pseudobonds, 421 residues, 2 models selected
> hide (#!5 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!5 & sel-residues)
> show (#!5 & sel-residues & backbone) target ab
> undo
> show (#!5 & sel-residues & sidechain) target ab
> ui tool show "Find Cavities"
> kvfinder #5
21 cavities found for fold_gemma_ct_model_0.cif #5
fold_gemma_ct_model_0.cif Cavities
---
ID | | Volume | Area | Points
5.2.11 | | 427.46 | 385.91 | 1979
5.2.13 | | 218.81 | 176.32 | 1013
5.2.12 | | 98.28 | 116.04 | 455
5.2.18 | | 77.54 | 62.26 | 359
5.2.20 | | 69.34 | 80.24 | 321
5.2.2 | | 63.29 | 101.07 | 293
5.2.10 | | 52.06 | 71.27 | 241
5.2.14 | | 48.82 | 66.04 | 226
5.2.5 | | 43.63 | 55.54 | 202
5.2.16 | | 38.23 | 56.98 | 177
5.2.19 | | 32.83 | 36.2 | 152
5.2.17 | | 19.87 | 36.19 | 92
5.2.1 | | 18.36 | 32.45 | 85
5.2.15 | | 17.28 | 36.68 | 80
5.2.4 | | 12.74 | 24.49 | 59
5.2.8 | | 11.88 | 23.99 | 55
5.2.9 | | 10.15 | 18.37 | 47
5.2.7 | | 8.86 | 18.71 | 41
5.2.21 | | 8.64 | 18.4 | 40
5.2.6 | | 7.13 | 16.3 | 33
5.2.3 | | 5.18 | 12.46 | 24
Populating font family aliases took 79 ms. Replace uses of missing font family
"Times" with one that exists to avoid this cost.
> undo
> close #6
> select add #5
9335 atoms, 3445 bonds, 442 residues, 24 models selected
> select subtract #5
1 model selected
> close #5
> open /Users/JackKim/Downloads/fold_gemma_ct/fold_gemma_ct_model_0.cif
Chain information for fold_gemma_ct_model_0.cif #5
---
Chain | Description
A | .
Computing secondary structure
> coulombic #5
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_gemma_ct_model_0.cif_A SES surface #5.1: minimum,
-16.73, mean -1.52, maximum 13.89
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!5 surfaces
> style #!5 sphere
Changed 3361 atom styles
> show #!5 atoms
> style #!5 stick
Changed 3361 atom styles
> style #!5 ball
Changed 3361 atom styles
> style #!5 sphere
Changed 3361 atom styles
> style #!5 ball
Changed 3361 atom styles
> nucleotides #!5 atoms
> style nucleic & #!5 stick
Changed 0 atom styles
> hide #!5 atoms
> color #!5 byhetero
> show #!5 atoms
> style #!5 stick
Changed 3361 atom styles
> interfaces #!5 & ~solvent
0 buried areas:
Volume zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.
> select add #5
3361 atoms, 3445 bonds, 421 residues, 1 model selected
Volume zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.
> select subtract #5
1 model selected
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 0 maps.
> ui tool show "Map Coordinates"
> select add #4
4634 atoms, 4742 bonds, 579 residues, 1 model selected
> select subtract #4
2 models selected
> select add #5
3361 atoms, 3445 bonds, 421 residues, 1 model selected
> select subtract #5
1 model selected
> cartoon suppressBackboneDisplay false
> show @n,ca,c,o
> show #5 @n,ca,c,o
> coulombic #!5
Coulombic values for fold_gemma_ct_model_0.cif_A SES surface #5.1: minimum,
-16.73, mean -1.52, maximum 13.89
To also show corresponding color key, enter the above coulombic command and
add key true
> view matrix models #5,1,0,0,0.67653,0,1,0,0.026663,0,0,1,-0.9568
> hide #!5 surfaces
> coulombic #!5
Coulombic values for fold_gemma_ct_model_0.cif_A SES surface #5.1: minimum,
-16.73, mean -1.52, maximum 13.89
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!5 surfaces
> hide #!5 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!1 models
> hide #targ a
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #1 target a
> color #!1 bychain
> hide #!1 models
> show #!3 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> color #3/A:235-248 lime
> color #3/B:167-191 magenta
> show #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> hide target a
> hide #!3 models
> hide #!2 models
> hide #!5 models
> mmaker #3 to #4
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_gemma_tcwithparalog2_nosp_postlinker_model_0.cif, chain B (#4)
with fold_gemma_ctwithparalog2_model_0.cif, chain B (#3), sequence alignment
score = 1995.9
RMSD between 334 pruned atom pairs is 0.360 angstroms; (across all 400 pairs:
12.027)
> view #4 clip false
No displayed objects specified.
> hide #!4 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!4 models
> view #2 clip false
No displayed objects specified.
> select add #4
4634 atoms, 4742 bonds, 579 residues, 1 model selected
> view #4 clip false
No displayed objects specified.
> show #!4 target m
> view #4 clip false
No displayed objects specified.
> select subtract #4
2 models selected
> view #4 clip false
No displayed objects specified.
> select add #4
4634 atoms, 4742 bonds, 579 residues, 1 model selected
> view #4 clip false
No displayed objects specified.
> ui tool show "AlphaFold Error Plot"
> alphafold pae #3 file
> /Users/JackKim/Downloads/fold_gemma_ctwithparalog2/fold_gemma_ctwithparalog2_full_data_0.json
> color #3/A:240-260 lime
> color #3/B:43-146 magenta
> color #3/A:218 lime
> color #3/B:116 magenta
> color #2/A:107-113 lime
> color #2/B:89-164 magenta
> color #2/A:101-122 lime
> color #2/B:129-186 magenta
> color #2/A:159 lime
> color #2/B:81-82 magenta
> ui tool show "AlphaFold Error Plot"
> alphafold pae #4 file
> /Users/JackKim/Downloads/fold_gemma_tcwithparalog2_nosp_postlinker/fold_gemma_tcwithparalog2_nosp_postlinker_full_data_0.json
> color #4/A:125-137 lime
> color #4/B:146-171 magenta
> select subtract #4
2 models selected
> open "/Users/JackKim/Downloads/fold_2025_10_09_16_08
> 2/fold_2025_10_09_16_08_model_0.cif"
Chain information for fold_2025_10_09_16_08_model_0.cif #6
---
Chain | Description
A | .
Computing secondary structure
> hide #!4 models
> color #6 purple
> coulombic #6
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_2025_10_09_16_08_model_0.cif_A SES surface #6.1:
minimum, -23.84, mean -2.17, maximum 10.84
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!6 surfaces
> ui tool show "AlphaFold Error Plot"
> alphafold pae #6 file "/Users/JackKim/Downloads/fold_2025_10_09_16_08
> 2/fold_2025_10_09_16_08_full_data_0.json"
> alphafold pae #6 colorDomains true
> select #6:asp
272 atoms, 240 bonds, 34 residues, 1 model selected
> show sel target a
> coulombic sel
Coulombic values for fold_2025_10_09_16_08_model_0.cif_A SES surface #6.1:
minimum, -23.84, mean -2.17, maximum 10.84
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> select add #6
2271 atoms, 2311 bonds, 290 residues, 2 models selected
> select subtract #6
1 model selected
> coulombic #!6
Coulombic values for fold_2025_10_09_16_08_model_0.cif_A SES surface #6.1:
minimum, -23.84, mean -2.17, maximum 10.84
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!6 surfaces
===== Log before crash end =====
Log:
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
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M1 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: MacBookPro18,1
Model Number: Z14V0016JLL/A
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 GB
System Firmware Version: 13822.1.2
OS Loader Version: 13822.1.2
Software:
System Software Overview:
System Version: macOS 26.0.1 (25A362)
Kernel Version: Darwin 25.0.0
Time since boot: 3 days, 23 hours, 57 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
HP 27er:
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
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.10.6
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
narwhals: 2.5.0
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 2.3.3
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
plotly: 6.3.0
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pyKVFinder: 0.8.3
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
tomlkit: 0.13.3
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 4 weeks 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 weeks ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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