![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 months ago
Closed 4 months ago
#17987 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-x86_64-i386-64bit
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 0x00007ff84e24cdc0 (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, lxml._elementpath, lxml.etree, 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, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 61)
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{
"uptime" : 110000,
"procRole" : "Background",
"version" : 2,
"userID" : 887764,
"deployVersion" : 210,
"modelCode" : "iMac19,1",
"coalitionID" : 3437,
"osVersion" : {
"train" : "macOS 15.5",
"build" : "24F74",
"releaseType" : "User"
},
"captureTime" : "2025-06-15 18:16:07.8889 +0200",
"codeSigningMonitor" : 0,
"incident" : "3D6BAD05-F271-47B1-A05A-9632BDA1A8F6",
"pid" : 70622,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-06-13 10:43:13.3803 +0200",
"procStartAbsTime" : 52820768383689,
"procExitAbsTime" : 116532978953482,
"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":"11D4ED0C-EE2A-5588-BC68-7EEBF82CD7B9","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "E46FA158-6920-516D-E229-EBF2F669647E",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["deviceNotCapable"]},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"bootSessionUUID" : "E67C21CA-B709-41C3-A630-C6E5CD696BB4",
"wakeTime" : 8,
"sleepWakeUUID" : "B6925797-47F9-4972-B99E-37F7B02B6D77",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4455211008\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1098d2000-1098d6000 [ 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":70622},
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4455211008\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1098d2000-1098d6000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.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: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/wang.peng/Downloads/6yn1.cif
Summary of feedback from opening /Users/wang.peng/Downloads/6yn1.cif
---
note | Fetching CCD CL from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/CL/CL.cif
6yn1.cif title:
Crystal structure of histone chaperone APLF acidic domain bound to the histone
H2A-H2B-H3-H4 octamer [more info...]
Chain information for 6yn1.cif #1
---
Chain | Description | UniProt
A F K P U Z e j | Histone H2A | Q6AZJ8_XENLA 13-118
B G L Q V a f k | Histone H2B | A0A1L8FQA5_XENLA 27-125
C H M R W b g l | Histone H3 | A0A310TTQ1_XENLA 38-135
D I N S X c h m | Histone H4 | H4_XENLA 20-102
E J O T Y d i n | Aprataxin and PNK-like factor | APLF_HUMAN 449-490
Non-standard residues in 6yn1.cif #1
---
CL — chloride ion
GOL — glycerol (glycerin; propane-1,2,3-triol)
6yn1.cif mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
4| author_defined_assembly
30 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 24456 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> sequence chain #1/A#1/F#1/K#1/P#1/U#1/Z#1/e#1/j
Alignment identifier is 1
> select /A,F,K,P:118
36 atoms, 32 bonds, 4 residues, 1 model selected
> select /A,F,K:16-118/P:15-118/U,Z,j:15-117/e:16-117
6360 atoms, 6440 bonds, 824 residues, 1 model selected
> close session
> open /Users/wang.peng/Downloads/8g88.cif
8g88.cif title:
Human Oct4 bound to nucleosome with human nMatn1 sequence [more info...]
Chain information for 8g88.cif #1
---
Chain | Description | UniProt
A E | Histone H3 | H32_XENLA 1-135
B F | Histone H4 | H4_XENLA 1-102
C G | Histone H2A | Q6AZJ8_XENLA 1-129
D H | Histone H2B | H2B11_XENLA 1-122
I | nMATn1 DNA top strand (168-MER) |
J | nMatn1 DNA bottom strand (168-MER) |
X | POU domain, class 5, transcription factor 1 | PO5F1_HUMAN 1-360
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 13995 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> sequence chain #1/C#1/G
Alignment identifier is 1
> sequence chain #1/A#1/E
Alignment identifier is 2
> sequence chain #1/A#1/E
Alignment identifier is 3
> select clear
> select /A,E
1593 atoms, 1617 bonds, 193 residues, 1 model selected
> close session
> open /Users/wang.peng/Downloads/3av2.cif
3av2.cif title:
The human nucleosome structure containing the histone variant H3.3 [more
info...]
Chain information for 3av2.cif #1
---
Chain | Description | UniProt
A E | Histone H3.3 | H33_HUMAN 0-135
B F | Histone H4 | H4_HUMAN 0-102
C G | Histone H2A type 1-B/E | H2A1B_HUMAN 0-129
D H | Histone H2B type 1-J | H2B1J_HUMAN 0-125
I J | 146-MER DNA |
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 11942 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> close session
> open /Users/wang.peng/Downloads/3av1.cif
3av1.cif title:
The human nucleosome structure containing the histone variant H3.2 [more
info...]
Chain information for 3av1.cif #1
---
Chain | Description | UniProt
A E | Histone H3.2 | H32_HUMAN 0-135
B F | Histone H4 | H4_HUMAN 0-102
C G | Histone H2A type 1-B/E | H2A1B_HUMAN 0-129
D H | Histone H2B type 1-J | H2B1J_HUMAN 0-125
I J | 146-MER DNA |
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 11941 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> open Q71DI3 fromDatabase uniprot associate #1/A,E
Summary of feedback from opening Q71DI3 fetched from uniprot
---
notes | Fetching compressed Q71DI3 UniProt info from https://www.uniprot.org/uniprot/Q71DI3.xml
Alignment identifier is Q71DI3
Associated 3av1.cif chain A to Q71DI3 with 0 mismatches
Associated 3av1.cif chain E to Q71DI3 with 0 mismatches
Opened UniProt Q71DI3
> open Q71DI3 fromDatabase uniprot associate #1/A,E
Summary of feedback from opening Q71DI3 fetched from uniprot
---
notes | Destroying pre-existing alignment with identifier Q71DI3
Alignment identifier is Q71DI3
Associated 3av1.cif chain A to Q71DI3 with 0 mismatches
Associated 3av1.cif chain E to Q71DI3 with 0 mismatches
Opened UniProt Q71DI3
> select ::name="CYS"
12 atoms, 10 bonds, 2 residues, 1 model selected
> show sel target ab
Drag select of 9 residues
> select ::name="CYS"
12 atoms, 10 bonds, 2 residues, 1 model selected
> select clear
> select /A:110@SG
1 atom, 1 residue, 1 model selected
> select add /A:110
6 atoms, 6 bonds, 1 residue, 1 model selected
> ui tool show Distances
Exactly two atoms must be selected!
> select clear
> select /A:110@SG
1 atom, 1 residue, 1 model selected
> select add /E:110@SG
2 atoms, 2 residues, 1 model selected
> distance /A:110@SG /E:110@SG
Distance between /A CYS 110 SG and /E CYS 110 SG: 6.121Å
> select /C/G
1636 atoms, 1635 bonds, 230 residues, 1 model selected
> color sel light gray
> select clear
> select /D/H
1452 atoms, 1466 bonds, 193 residues, 1 model selected
> color sel gray
> select clear
> select /A/E
1648 atoms, 1633 bonds, 1 pseudobond, 233 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light yellow
> select clear
> select /A/E
1648 atoms, 1633 bonds, 1 pseudobond, 233 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light green
> select clear
> select /B/F
1320 atoms, 1306 bonds, 190 residues, 1 model selected
> color sel lime
> select clear
> save "/Users/wang.peng/Documents/MPI/Projects/MINFLUX
> transcription/Chromotain remodelling/Chimera & Alphafold/pdb_3av1.cxs"
> save /Users/wang.peng/Desktop/image1.png supersample 3
> select ::name="CYS"
12 atoms, 10 bonds, 1 pseudobond, 2 residues, 2 models selected
> color (#!1 & sel) yellow
> select clear
> set bgColor white
> set bgColor black
> save /Users/wang.peng/Desktop/image1.png supersample 3
> select ::name="CYS"
12 atoms, 10 bonds, 1 pseudobond, 2 residues, 2 models selected
> color (#!1 & sel) red
> select clear
> save /Users/wang.peng/Desktop/image2.png supersample 3
> select /C/G
1636 atoms, 1635 bonds, 230 residues, 1 model selected
> color sel white
> select clear
> save /Users/wang.peng/Desktop/image3.png supersample 3
> save /Users/wang.peng/Desktop/image4.png supersample 3
> save "/Users/wang.peng/Documents/MPI/Projects/MINFLUX
> transcription/Chromotain remodelling/Chimera & Alphafold/pdb_3av1.cxs"
> ui tool show "Blast Protein"
> ui tool show "Show Sequence Viewer"
> sequence chain /C /G
Alignment identifier is 1
> select clear
> select /C,G:16-22,26-37,45-73,79-97,112-116
1108 atoms, 1112 bonds, 144 residues, 1 model selected
> select clear
> select /C,G:46
8 atoms, 6 bonds, 2 residues, 1 model selected
> select /C,G:46-97
818 atoms, 826 bonds, 104 residues, 1 model selected
> select /C,G:16
14 atoms, 12 bonds, 2 residues, 1 model selected
> select /C,G:16-22
100 atoms, 98 bonds, 14 residues, 1 model selected
> select /C,G:17
22 atoms, 20 bonds, 2 residues, 1 model selected
> select /C,G:16-17
36 atoms, 34 bonds, 4 residues, 1 model selected
> select /C,G:114
14 atoms, 12 bonds, 2 residues, 1 model selected
> select /C,G:114-116
46 atoms, 44 bonds, 6 residues, 1 model selected
> select /C,G:89
16 atoms, 14 bonds, 2 residues, 1 model selected
> select /C,G:89-94
100 atoms, 98 bonds, 12 residues, 1 model selected
> select /C,G:87
16 atoms, 14 bonds, 2 residues, 1 model selected
> select /C,G:87-97
188 atoms, 186 bonds, 22 residues, 1 model selected
> select /C:64
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A/E
1648 atoms, 1633 bonds, 1 pseudobond, 233 residues, 2 models selected
> ui tool show "Color Actions"
> color sel orange
> select clear
> select /B/F
1320 atoms, 1306 bonds, 190 residues, 1 model selected
> color sel yellow
> select clear
> select ::name="CYS"
12 atoms, 10 bonds, 1 pseudobond, 2 residues, 2 models selected
> color (#!1 & sel) red
> select clear
> save /Users/wang.peng/Desktop/image1.png supersample 3
> save /Users/wang.peng/Desktop/image2.png supersample 3
> save "/Users/wang.peng/Documents/MPI/Projects/MINFLUX
> transcription/Chromotain remodelling/Chimera & Alphafold/pdb_3av1.cxs"
> save /Users/wang.peng/Desktop/image3.png supersample 3
> select clear
> select /C:14-118/G:15-118
1615 atoms, 1635 bonds, 209 residues, 1 model selected
> select clear
> select /C:14-118/G:15-118
1615 atoms, 1635 bonds, 209 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /D /H
Alignment identifier is 1
> select clear
> select /D:32-124/H:33-124
1444 atoms, 1466 bonds, 185 residues, 1 model selected
> select /A/E
1648 atoms, 1633 bonds, 1 pseudobond, 233 residues, 2 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain /A /E
Alignment identifier is 1
> select /E:135
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:39-134/E:37-135
1610 atoms, 1633 bonds, 1 pseudobond, 195 residues, 2 models selected
> select /A,E:110-111
22 atoms, 20 bonds, 1 pseudobond, 4 residues, 2 models selected
> select /A,E:110-111
22 atoms, 20 bonds, 1 pseudobond, 4 residues, 2 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain /B /F
Alignment identifier is 2
> select /B,F:102
10 atoms, 8 bonds, 2 residues, 1 model selected
> select /B:25-102/F:19-102
1292 atoms, 1306 bonds, 162 residues, 1 model selected
> save "/Users/wang.peng/Documents/MPI/Projects/MINFLUX
> transcription/Chromotain remodelling/Chimera & Alphafold/pdb_3av1.cxs"
> save "/Users/wang.peng/Documents/MPI/Projects/MINFLUX
> transcription/Chromotain remodelling/Chimera & Alphafold/pdb_3av1 (H3.2
> C110A).cxs"
> select /A:110
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel target a
> select /F:53
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /E:110
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel target a
> select /E:110
6 atoms, 5 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
Populating font family aliases took 114 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.
> ui tool show Rotamers
> ui tool show "Show Sequence Viewer"
> sequence chain /A /E
Alignment identifier is 1
> select /A,E:110
12 atoms, 10 bonds, 1 pseudobond, 2 residues, 2 models selected
> select /A,E:110
12 atoms, 10 bonds, 1 pseudobond, 2 residues, 2 models selected
> ui tool show Rotamers
> swapaa interactive sel SER rotLib Dunbrack
/A CYS 110: phi -68.4, psi -38.4 trans
Changed 9 bond radii
No rotamers selected. Click the 'Calculate' button (not 'OK') to add a column
to the table.
> hbonds #!1 & ~#!1/A:110 & ~solvent reveal true restrict #1.2 & ~@c,ca,n
3 hydrogen bonds found
No rotamers selected
> swapaa #!1/A:110 SER criteria 1 rotLib Dunbrack
Using Dunbrack library
3av1.cif #!1/A CYS 110: phi -68.4, psi -38.4 trans
Applying SER rotamer (chi angles: -65.9) to 3av1.cif #!1/A SER 110
> close session
> open "/Users/wang.peng/Documents/MPI/Projects/MINFLUX
> transcription/Chromotain remodelling/Chimera & Alphafold/pdb_3av1 (H3.2
> C110A).cxs" format session
opened ChimeraX session
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain /I /J
Alignment identifier is 3
> select /I:146/J:292
40 atoms, 42 bonds, 2 residues, 1 model selected
> select /I:1-146/J:147-292
5980 atoms, 6708 bonds, 358 pseudobonds, 292 residues, 2 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain /C /G
Alignment identifier is 3
> ui tool show "Show Sequence Viewer"
> sequence chain /D /H
Alignment identifier is 1
> ui tool show "Show Sequence Viewer"
> sequence chain /A /E
Alignment identifier is 2
> ui tool show "Show Sequence Viewer"
> sequence chain /B /F
Alignment identifier is 4
> select clear
> select /C:14-118/G:15-118
1615 atoms, 1635 bonds, 209 residues, 1 model selected
> close session
> open "/Users/wang.peng/Documents/MPI/Projects/MINFLUX
> transcription/Chromotain remodelling/Chimera & Alphafold/pdb_3av1.cxs"
> format session
opened ChimeraX session
> select clear
> select /B:25-102/F:19-102
1292 atoms, 1306 bonds, 162 residues, 1 model selected
> select clear
> select /F:19
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /F:19-23
46 atoms, 45 bonds, 5 residues, 1 model selected
> select /B:25/F:24-25
24 atoms, 22 bonds, 3 residues, 1 model selected
> select /B:25-27/F:24-27
58 atoms, 56 bonds, 7 residues, 1 model selected
> select clear
> select /F:19-20
20 atoms, 19 bonds, 2 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /I /J
Alignment identifier is 3
> select /I:146/J:292
40 atoms, 42 bonds, 2 residues, 1 model selected
> select /I:1-146/J:147-292
5980 atoms, 6708 bonds, 358 pseudobonds, 292 residues, 2 models selected
> close session
> open "/Users/wang.peng/Documents/MPI/Projects/MINFLUX
> transcription/Chromotain remodelling/Chimera &
> Alphafold/fold_human_histone_pdb_3av1_sequences/fold_human_histone_pdb_3av1_sequences_model_0.cif"
Chain information for fold_human_histone_pdb_3av1_sequences_model_0.cif #1
---
Chain | Description
A B | .
C D | .
E F | .
G H | .
I | .
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 10702 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> select /A:1-130
996 atoms, 1008 bonds, 130 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /A /B
Alignment identifier is 1
> select /A-B:130
20 atoms, 18 bonds, 2 residues, 1 model selected
> select /A-B:122-130
144 atoms, 146 bonds, 18 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /E /F
Alignment identifier is 2
> select /E-F:111
12 atoms, 10 bonds, 2 residues, 1 model selected
> select /E-F:111
12 atoms, 10 bonds, 2 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /A /B
Alignment identifier is 1
> sequence chain /C /D
Alignment identifier is 2
> sequence chain /E /F
Alignment identifier is 3
> sequence chain /G /H
Alignment identifier is 4
> select /E-F:93-136
700 atoms, 706 bonds, 88 residues, 1 model selected
> select /E-F
2162 atoms, 2190 bonds, 272 residues, 1 model selected
> color sel orange
> select clear
> select /G-H:103
10 atoms, 8 bonds, 2 residues, 1 model selected
> select /G-H
1600 atoms, 1616 bonds, 206 residues, 1 model selected
> color sel yellow
> select clear
> select /C-D:39-49,57-84,92-102,105-124
1092 atoms, 1100 bonds, 140 residues, 1 model selected
> select /C-D:126
20 atoms, 18 bonds, 2 residues, 1 model selected
> select /C-D
1954 atoms, 1984 bonds, 252 residues, 1 model selected
> color sel gray
> select /A-B:130
20 atoms, 18 bonds, 2 residues, 1 model selected
> select /A-B
1992 atoms, 2016 bonds, 260 residues, 1 model selected
> color sel white
> select clear
> select ::name="CYS"
12 atoms, 10 bonds, 2 residues, 1 model selected
> color sel red
> show sel target ab
> select clear
> select /F:111@SG
1 atom, 1 residue, 1 model selected
> select add /E:111@SG
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance /F:111@SG /E:111@SG
Distance between /F CYS 111 SG and /E CYS 111 SG: 6.229Å
> distance style color #fa1f08
> distance style color #fa1f07
> save /Users/wang.peng/Desktop/image1.png supersample 3
> select clear
> save /Users/wang.peng/Desktop/image2.png supersample 3
> save "/Users/wang.peng/Documents/MPI/Projects/MINFLUX
> transcription/Chromotain remodelling/Chimera &
> Alphafold/fold_human_histone_pdb_3av1_sequences.cxs"
> close session
> open "/Users/wang.peng/Documents/MPI/Projects/MINFLUX
> transcription/Chromotain remodelling/Chimera &
> Alphafold/fold_human_histone_uniprot_q96qv6_q99880_p68431_p62805/fold_human_histone_uniprot_q96qv6_q99880_p68431_p62805_model_0.cif"
Chain information for
fold_human_histone_uniprot_q96qv6_q99880_p68431_p62805_model_0.cif #1
---
Chain | Description
A B | .
C D | .
E F | .
G H | .
I | .
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 10722 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> select /A:1-131
1003 atoms, 1016 bonds, 131 residues, 1 model selected
> select /A:1-131
1003 atoms, 1016 bonds, 131 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /A /B
Alignment identifier is 1
> select /A-B:131
20 atoms, 18 bonds, 2 residues, 1 model selected
> select /A-B
2006 atoms, 2032 bonds, 262 residues, 1 model selected
> color sel white
> ui tool show "Show Sequence Viewer"
> sequence chain /C /D
Alignment identifier is 1
> select /C-D:126
20 atoms, 18 bonds, 2 residues, 1 model selected
> select /C-D
1960 atoms, 1988 bonds, 252 residues, 1 model selected
> color sel gray
> ui tool show "Show Sequence Viewer"
> sequence chain /E /F
Alignment identifier is 1
> select /E-F:93-94
34 atoms, 32 bonds, 4 residues, 1 model selected
> select /E-F:46-94
824 atoms, 832 bonds, 98 residues, 1 model selected
> select /E-F:92-136
710 atoms, 716 bonds, 90 residues, 1 model selected
> select /E-F
2162 atoms, 2190 bonds, 272 residues, 1 model selected
> color sel orange
> ui tool show "Show Sequence Viewer"
> sequence chain /G /H
Alignment identifier is 1
> select /G-H:103
10 atoms, 8 bonds, 2 residues, 1 model selected
> select /G-H
1600 atoms, 1616 bonds, 206 residues, 1 model selected
> color sel yellow
> select clear
> select ::name="CYS"
24 atoms, 20 bonds, 4 residues, 1 model selected
> color sel red
> select clear
> select /E:111
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add /F:111
12 atoms, 10 bonds, 2 residues, 1 model selected
> show sel target ab
> ui tool show Distances
Exactly two atoms must be selected!
> select clear
> select /E:111@SG
1 atom, 1 residue, 1 model selected
> select add /F:111@SG
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance /E:111@SG /F:111@SG
Distance between /E CYS 111 SG and /F CYS 111 SG: 6.207Å
> save "/Users/wang.peng/Documents/MPI/Projects/MINFLUX
> transcription/Chromotain remodelling/Chimera &
> Alphafold/fold_human_histone_uniprot_q96qv6_q99880_p68431_p62805.cxs"
> save /Users/wang.peng/Desktop/image3.png supersample 3
> save /Users/wang.peng/Desktop/image4.png supersample 3
===== Log before crash end =====
Log:
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
OpenGL version: 4.1 ATI-7.0.3
OpenGL renderer: AMD Radeon Pro 580X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: en_US.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: iMac
Model Identifier: iMac19,1
Processor Name: 6-Core Intel Core i5
Processor Speed: 3,7 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 9 MB
Memory: 16 GB
System Firmware Version: 2075.100.3.0.3
OS Loader Version: 583~1350
SMC Version (system): 2.46f12
Software:
System Software Overview:
System Version: macOS 15.5 (24F74)
Kernel Version: Darwin 24.5.0
Time since boot: 3 days, 20 hours, 36 minutes
Graphics/Displays:
Radeon Pro 580X:
Chipset Model: Radeon Pro 580X
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x67df
Revision ID: 0x00c0
ROM Revision: 113-D0008A-042
VBIOS Version: 113-D0008A1X-009
EFI Driver Version: 01.B1.042
Metal Support: Metal 2
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 5K (5120 x 2880)
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL U2725QE:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: DPR9B34
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: Thunderbolt/DisplayPort
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
html2text: 2024.2.26
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 , 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 |
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