![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 months ago
Closed 3 months ago
#18321 closed defect (duplicate)
mshMIGPerform crash
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Platform | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.5-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 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 0x000000020d581f00 (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, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, lxml._elementpath, lxml.etree, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 59)
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"procRole" : "Foreground",
"version" : 2,
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"modelCode" : "Mac15,12",
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"codeSigningMonitor" : 1,
"incident" : "FCCFF855-2918-4FA1-8352-679A13040F8C",
"pid" : 81221,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-07-31 01:38:46.1045 +0800",
"procStartAbsTime" : 9184357185182,
"procExitAbsTime" : 9264635709622,
"procName" : "ChimeraX",
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"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "4F206021-E1E0-3AF2-F2BE-B563ABAFF9DA",
"appleIntelligenceStatus" : {"reasons":["regionIneligible","countryBillingIneligible","countryLocationIneligible"],"state":"unavailable"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
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"wakeTime" : 5989,
"sleepWakeUUID" : "6E097701-6185-4B14-BA99-19EC102F75DA",
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"exception" : {"codes":"0x0000000000000001, 0x0000000000000003","rawCodes":[1,3],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000003"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":81221},
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/core\/_mac_util.cpython-311-darwin.so",
"name" : "_mac_util.cpython-311-darwin.so"
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/iconengines\/libqsvgicon.dylib",
"name" : "libqsvgicon.dylib"
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/OpenGL_accelerate\/numpy_formathandler.cpython-311-darwin.so",
"name" : "numpy_formathandler.cpython-311-darwin.so"
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"uuid" : "12c53516-421d-3f7a-a81e-95bcfdb8a3ff",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/OpenGL_accelerate\/nones_formathandler.cpython-311-darwin.so",
"name" : "nones_formathandler.cpython-311-darwin.so"
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"name" : "_multiprocessing.cpython-311-darwin.so"
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"name" : "_pdbio.cpython-311-darwin.so"
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"uuid" : "3133c77c-8bf7-32a3-b5db-cbfe2e50ce9d",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic\/_ribbons.cpython-311-darwin.so",
"name" : "_ribbons.cpython-311-darwin.so"
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"name" : "_graphics.cpython-311-darwin.so"
},
{
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"uuid" : "0c6e9a11-e483-3d7d-a88f-8ad0507af167",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/mmcif.cpython-311-darwin.so",
"name" : "mmcif.cpython-311-darwin.so"
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{
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"uuid" : "1ab8e5e2-c699-3efb-8f77-d375e3793c8f",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/_mmcif.cpython-311-darwin.so",
"name" : "_mmcif.cpython-311-darwin.so"
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"uuid" : "8abbdcef-1901-3d4b-9e6b-a38214b79214",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/_imagingmath.cpython-311-darwin.so",
"name" : "_imagingmath.cpython-311-darwin.so"
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"uuid" : "644b1794-90c5-3838-9ffa-b772683aeb37",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/alignment_algs\/_sw.cpython-311-darwin.so",
"name" : "_sw.cpython-311-darwin.so"
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{
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"base" : 5147541504,
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"uuid" : "02f24514-9c56-3aa2-806f-b6eae4e7cf23",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/alignment_algs\/libalign_algs.dylib",
"name" : "libalign_algs.dylib"
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{
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"base" : 5837127680,
"size" : 16384,
"uuid" : "4e700338-6839-3c7c-9f41-a201e7f185e5",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/dssp\/_dssp.cpython-311-darwin.so",
"name" : "_dssp.cpython-311-darwin.so"
},
{
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"uuid" : "93fd54d8-5d5e-319d-94c5-2702d533d751",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/alignment_algs\/_nw.cpython-311-darwin.so",
"name" : "_nw.cpython-311-darwin.so"
},
{
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"uuid" : "d7bd530c-3353-37a6-b81f-ee3179d65811",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lz4\/_version.cpython-311-darwin.so",
"name" : "_version.cpython-311-darwin.so"
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"uuid" : "87eed069-25fc-30f6-aa30-1e54859d92e2",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lz4\/frame\/_frame.cpython-311-darwin.so",
"name" : "_frame.cpython-311-darwin.so"
},
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"uuid" : "c1a3c2d3-b21b-3231-839d-fcbc83ca2028",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/core\/_serialize.cpython-311-darwin.so",
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/msgpack\/_cmsgpack.cpython-311-darwin.so",
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"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
},
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"name" : "HIServices"
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=3.3G written=136.7M(4%) resident=2522K(0%) swapped_out=134.2M(4%) unallocated=3.2G(96%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG image 1088K 53 \nColorSync 656K 33 \nCoreAnimation 4464K 197 \nCoreGraphics 80K 5 \nCoreImage 64K 4 \nCoreServices 624K 2 \nCoreUI image data 5712K 59 \nDispatch continuations 64.0M 1 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 2.5G 1972 \nMALLOC guard page 288K 18 \nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 624K 39 \nStack 200.8M 40 \nStack Guard 56.0M 1 \nVM_ALLOCATE 409.4M 425 \nVM_ALLOCATE (reserved) 128.0M 1 reserved VM address space (unallocated)\n__AUTH 5521K 698 \n__AUTH_CONST 77.4M 945 \n__CTF 824 1 \n__DATA 34.3M 1092 \n__DATA_CONST 37.0M 1109 \n__DATA_DIRTY 2778K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 647.1M 158 \n__OBJC_RO 61.4M 1 \n__OBJC_RW 2396K 1 \n__TEXT 1.3G 1103 \n__TEXT (graphics) 29.8M 26 \n__TPRO_CONST 128K 2 \ndyld private memory 3616K 30 \nmapped file 645.6M 114 \npage table in kernel 2522K 1 \nshared memory 3264K 29 \n=========== ======= ======= \nTOTAL 6.2G 8519 \nTOTAL, minus reserved VM space 6.0G 8519 \n",
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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/daisy/Library/Containers/com.tencent.xinWeChat/Data/Library/Application
> Support/com.tencent.xinWeChat/2.0b4.0.9/4ab61b2092f657967c9150833138310e/Message/MessageTemp/217b9cf35a6b26eec7e599641c75feb8/File/TAX-4
> Model/WT-4cGMP-Open-coot-9-final.pdb"
Chain information for WT-4cGMP-Open-coot-9-final.pdb #1
---
Chain | Description
A B C D | No description available
> open
> "/Users/daisy/Library/Containers/com.tencent.xinWeChat/Data/Library/Application
> Support/com.tencent.xinWeChat/2.0b4.0.9/4ab61b2092f657967c9150833138310e/Message/MessageTemp/217b9cf35a6b26eec7e599641c75feb8/File/TAX-4
> Model/apo-WT-zx-coot-10-final.pdb"
Chain information for apo-WT-zx-coot-10-final.pdb #2
---
Chain | Description
A B C D | No description available
> open
> "/Users/daisy/Library/Containers/com.tencent.xinWeChat/Data/Library/Application
> Support/com.tencent.xinWeChat/2.0b4.0.9/4ab61b2092f657967c9150833138310e/Message/MessageTemp/217b9cf35a6b26eec7e599641c75feb8/File/TAX-4
> Model/3WT-1EA-3cGMP-Open-coot-28-Final.pdb"
Chain information for 3WT-1EA-3cGMP-Open-coot-28-Final.pdb #3
---
Chain | Description
A B C | No description available
D | No description available
> open
> "/Users/daisy/Library/Containers/com.tencent.xinWeChat/Data/Library/Application
> Support/com.tencent.xinWeChat/2.0b4.0.9/4ab61b2092f657967c9150833138310e/Message/MessageTemp/217b9cf35a6b26eec7e599641c75feb8/File/TAX-4
> Model/3EA-1WT-1cGMP-Clsoed-coot-24-Final.pdb"
Chain information for 3EA-1WT-1cGMP-Clsoed-coot-24-Final.pdb #4
---
Chain | Description
A | No description available
B C D | No description available
> open "/Users/daisy/Library/Mobile
> Documents/com~apple~CloudDocs/Documents/TAX4/Finnal PDB and map/3WT-EA
> close/3WT-EA close.pdb"
Chain information for 3WT-EA close.pdb #5
---
Chain | Description
A B C | No description available
D | No description available
> ui tool show Matchmaker
> matchmaker #2/A to #1/A pairing ss
Computing secondary structure
Parameters
---
Chain pairing | ss
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 WT-4cGMP-Open-coot-9-final.pdb, chain A (#1) with apo-WT-zx-
coot-10-final.pdb, chain A (#2), sequence alignment score = 2609
RMSD between 285 pruned atom pairs is 0.573 angstroms; (across all 513 pairs:
3.486)
> matchmaker #3/A to #1/A pairing ss
Computing secondary structure
Parameters
---
Chain pairing | ss
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 WT-4cGMP-Open-coot-9-final.pdb, chain A (#1) with 3WT-1EA-3cGMP-
Open-coot-28-Final.pdb, chain A (#3), sequence alignment score = 2669.9
RMSD between 486 pruned atom pairs is 0.607 angstroms; (across all 518 pairs:
0.860)
> matchmaker #4/A to #1/A pairing ss
Computing secondary structure
Parameters
---
Chain pairing | ss
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 WT-4cGMP-Open-coot-9-final.pdb, chain A (#1) with 3EA-1WT-1cGMP-
Clsoed-coot-24-Final.pdb, chain A (#4), sequence alignment score = 2587.4
RMSD between 416 pruned atom pairs is 0.938 angstroms; (across all 513 pairs:
1.681)
> matchmaker #4/A to #1/A pairing ss
Computing secondary structure
Parameters
---
Chain pairing | ss
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 WT-4cGMP-Open-coot-9-final.pdb, chain A (#1) with 3EA-1WT-1cGMP-
Clsoed-coot-24-Final.pdb, chain A (#4), sequence alignment score = 2587.4
RMSD between 416 pruned atom pairs is 0.938 angstroms; (across all 513 pairs:
1.681)
> matchmaker #5/A to #1/A pairing ss
Computing secondary structure
Parameters
---
Chain pairing | ss
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 WT-4cGMP-Open-coot-9-final.pdb, chain A (#1) with 3WT-EA close.pdb,
chain A (#5), sequence alignment score = 2452
RMSD between 477 pruned atom pairs is 0.828 angstroms; (across all 514 pairs:
1.248)
> hide #!4 models
> hide #3 models
> hide #!2 models
> hide #1 models
> show #1 models
> show #!2 models
> hide #!2 models
> hide #!5 models
> hide #1 models
> show #!4 models
> show #1 models
> select: 421
Unknown command: select: 421
> select :421
220 atoms, 200 bonds, 20 residues, 5 models selected
> show sel & #1#!4 atoms
> select clear
> show #3 models
> hide #3 models
> show #3 models
> show #!5 models
> show #!2 models
> select :421
220 atoms, 200 bonds, 20 residues, 5 models selected
> show sel atoms
> ui tool show "Side View"
> select clear
> color #2 light gray
> color byhetero
> color #5 lavender
> color #5 Lavender
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #5 bubblegum
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #5 #d783ffff
> color #3 #ff9300ff
> color #3 #ff7e79ff
> color byattribute hetero
No known/registered numeric attribute hetero
> color byhetero
> open "/Users/daisy/Library/Mobile
> Documents/com~apple~CloudDocs/Documents/TAX4/Finnal PDB and map/2WT-2EA
> close/2WT-2EA close.pdb"
Chain information for 2WT-2EA close.pdb #6
---
Chain | Description
A B C | No description available
D | No description available
> ui tool show Matchmaker
> matchmaker #6/A to #1/A pairing ss
Computing secondary structure
Parameters
---
Chain pairing | ss
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 WT-4cGMP-Open-coot-9-final.pdb, chain A (#1) with 2WT-2EA
close.pdb, chain A (#6), sequence alignment score = 2481.4
RMSD between 386 pruned atom pairs is 1.019 angstroms; (across all 514 pairs:
1.896)
> select :421
264 atoms, 240 bonds, 24 residues, 6 models selected
> show sel atoms
> color #6 #941751ff
> color #6 #0096ffff
> color #6 #76d6ffff
> color byhetero
> select clear
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #1 models
> hide #3 models
> hide #!4 models
> hide #!5 models
> select #2/D:456
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel bychain
> select #2/A:299
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:302
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #2/A:299
13 atoms, 11 bonds, 2 residues, 1 model selected
> select add #2/A:304
20 atoms, 18 bonds, 3 residues, 1 model selected
> select add #2/A:305
28 atoms, 25 bonds, 4 residues, 1 model selected
> select subtract #2/A:304
21 atoms, 18 bonds, 3 residues, 1 model selected
> show sel atoms
> select #2/A:300
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #2/A:301
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> color byhetero
> select #2/D:420
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/D:421
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/D:421
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/D:420
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #2/D:419
10 atoms, 8 bonds, 2 residues, 1 model selected
> select add #2/D:417
18 atoms, 15 bonds, 3 residues, 1 model selected
> select add #2/D:418
24 atoms, 20 bonds, 4 residues, 1 model selected
> select add #2/D:416
32 atoms, 27 bonds, 5 residues, 1 model selected
> select add #2/D:415
38 atoms, 32 bonds, 6 residues, 1 model selected
> select add #2/D:414
46 atoms, 39 bonds, 7 residues, 1 model selected
> select add #2/D:413
54 atoms, 46 bonds, 8 residues, 1 model selected
> show sel atoms
> show #3 models
> show #!4 models
> show #!5 models
> show #!6 models
> select: 413-421
Unknown command: select: 413-421
> select :413-421
1560 atoms, 1536 bonds, 216 residues, 6 models selected
> show sel & #3#!2,4-6 atoms
> select :456
336 atoms, 360 bonds, 24 residues, 6 models selected
> select #3/B:452
11 atoms, 11 bonds, 1 residue, 1 model selected
> select :452
264 atoms, 264 bonds, 24 residues, 6 models selected
> show sel & #3#!2,4-6 atoms
> select :456
336 atoms, 360 bonds, 24 residues, 6 models selected
> show sel & #3#!2,4-6 atoms
> select :452
264 atoms, 264 bonds, 24 residues, 6 models selected
> hide sel & #3#!2,4-6 atoms
> show #1 models
> select up
3662 atoms, 3782 bonds, 387 residues, 6 models selected
> select :456
336 atoms, 360 bonds, 24 residues, 6 models selected
> show sel atoms
> select :413-421
1560 atoms, 1536 bonds, 216 residues, 6 models selected
> show sel atoms
> select :299
168 atoms, 144 bonds, 24 residues, 6 models selected
> show sel atoms
> select :301-302
288 atoms, 264 bonds, 48 residues, 6 models selected
> show sel atoms
> select :301-305
840 atoms, 840 bonds, 120 residues, 6 models selected
> show sel atoms
> hide sel atoms
> select :301-302
288 atoms, 264 bonds, 48 residues, 6 models selected
> show sel atoms
> select :305
192 atoms, 168 bonds, 24 residues, 6 models selected
> show sel atoms
> hide #!6 models
> hide #!5 models
> hide #3 models
> hide #!2 models
> hide #!4 models
> show #!2 models
> show #3 models
> show #!4 models
> show #!5 models
> show #!6 models
> select :298
216 atoms, 192 bonds, 24 residues, 6 models selected
> show sel atoms
> select :305
192 atoms, 168 bonds, 24 residues, 6 models selected
> hide sel atoms
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #3 models
> hide #!2 models
> save /Users/daisy/Desktop/00001.cxs
> select #1/B:456@NE1
1 atom, 1 residue, 1 model selected
> select #1/B:421@NH1
1 atom, 1 residue, 1 model selected
> select add #1/B:456@NE1
2 atoms, 2 residues, 1 model selected
> distance #1/B:421@NH1 #1/B:456@NE1
Distance between WT-4cGMP-Open-coot-9-final.pdb #1/B ARG 421 NH1 and TRP 456
NE1: 3.205Å
> select #1/B:421@NH2
1 atom, 1 residue, 1 model selected
> select add #1/A:299@OG1
2 atoms, 2 residues, 1 model selected
> select subtract #1/A:299@OG1
1 atom, 1 residue, 1 model selected
> select add #1/A:299@OG1
2 atoms, 2 residues, 1 model selected
> distance #1/B:421@NH2 #1/A:299@OG1
Distance between WT-4cGMP-Open-coot-9-final.pdb #1/B ARG 421 NH2 and /A THR
299 OG1: 4.342Å
> select #1/A:299@OG1
1 atom, 1 residue, 1 model selected
> select #1/A:299@OG1
1 atom, 1 residue, 1 model selected
> select clear
> select #1/B:421@NH2
1 atom, 1 residue, 1 model selected
> select add #1/A:298@OE2
2 atoms, 2 residues, 1 model selected
> select subtract #1/A:298@OE2
1 atom, 1 residue, 1 model selected
> select add #1/A:298@OE2
2 atoms, 2 residues, 1 model selected
> select subtract #1/A:298@OE2
1 atom, 1 residue, 1 model selected
> select add #1/A:298@OE2
2 atoms, 2 residues, 1 model selected
> select #1/A:298@OE2
1 atom, 1 residue, 1 model selected
> select add #1/B:421@NH2
2 atoms, 2 residues, 1 model selected
> select subtract #1/B:421@NH2
1 atom, 1 residue, 1 model selected
> select add #1/B:421@NH2
2 atoms, 2 residues, 1 model selected
> select subtract #1/B:421@NH2
1 atom, 1 residue, 1 model selected
> select add #1/B:421@NH2
2 atoms, 2 residues, 1 model selected
> distance #1/A:298@OE2 #1/B:421@NH2
Distance between WT-4cGMP-Open-coot-9-final.pdb #1/A GLU 298 OE2 and /B ARG
421 NH2: 2.313Å
> select #1/A:295
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #1/A:295@OE2
1 atom, 1 bond, 1 residue, 1 model selected
> select subtract #1/A:295@OE2
1 bond, 1 model selected
> select add #1/A:295@OE2
1 atom, 1 bond, 1 residue, 1 model selected
> select clear
> select #1/B:421@NE
1 atom, 1 residue, 1 model selected
> select #1/A:295@OE2
1 atom, 1 residue, 1 model selected
> select add #1/B:421@NE
2 atoms, 2 residues, 1 model selected
> distance #1/A:295@OE2 #1/B:421@NE
Distance between WT-4cGMP-Open-coot-9-final.pdb #1/A GLU 295 OE2 and /B ARG
421 NE: 4.807Å
> select #1/B:456@NE1
1 atom, 1 residue, 1 model selected
> select add #1/B:421@NE
2 atoms, 1 pseudobond, 2 residues, 2 models selected
> select subtract #1/B:421@NE
1 atom, 1 residue, 1 model selected
> select add #1/B:421@NE
2 atoms, 2 residues, 1 model selected
> distance #1/B:456@NE1 #1/B:421@NE
Distance between WT-4cGMP-Open-coot-9-final.pdb #1/B TRP 456 NE1 and ARG 421
NE: 4.599Å
> ui tool show Distances
> ~distance #1/B:456@NE1 #1/B:421@NE
> ~distance #1/A:295@OE2 #1/B:421@NE
> hide sel atoms
> select add #1/A:295@OE1
1 atom, 5 bonds, 1 residue, 1 model selected
> select add #1/A:295@OE2
2 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel atoms
> select add #1/A:295@CD
3 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel atoms
> select add #1/A:295@CG
4 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel atoms
> select add #1/A:295@CB
5 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> hide #1 models
> show #1 models
> select #1/D:456@NE1
1 atom, 1 residue, 1 model selected
> select add #1/D:421@NH1
2 atoms, 2 residues, 1 model selected
> distance #1/D:456@NE1 #1/D:421@NH1
Distance between WT-4cGMP-Open-coot-9-final.pdb #1/D TRP 456 NE1 and ARG 421
NH1: 3.330Å
> select #1/C:299@OG1
1 atom, 1 residue, 1 model selected
> select add #1/D:421@NH2
2 atoms, 2 residues, 1 model selected
> distance #1/C:299@OG1 #1/D:421@NH2
Distance between WT-4cGMP-Open-coot-9-final.pdb #1/C THR 299 OG1 and /D ARG
421 NH2: 4.330Å
> select #1/C:298@OE2
1 atom, 1 residue, 1 model selected
> select add #1/D:421@NH2
2 atoms, 2 residues, 1 model selected
> distance #1/C:298@OE2 #1/D:421@NH2
Distance between WT-4cGMP-Open-coot-9-final.pdb #1/C GLU 298 OE2 and /D ARG
421 NH2: 2.313Å
> select clear
> select #1/A:456@NE1
1 atom, 1 residue, 1 model selected
> select add #1/A:421@NH1
2 atoms, 2 residues, 1 model selected
> select subtract #1/A:421@NH1
1 atom, 1 residue, 1 model selected
> select add #1/A:421@NH1
2 atoms, 2 residues, 1 model selected
> distance #1/A:456@NE1 #1/A:421@NH1
Distance between WT-4cGMP-Open-coot-9-final.pdb #1/A TRP 456 NE1 and ARG 421
NH1: 2.939Å
> select #1/D:299@OG1
1 atom, 1 residue, 1 model selected
> select add #1/A:421@NH2
2 atoms, 2 residues, 1 model selected
> distance #1/D:299@OG1 #1/A:421@NH2
Distance between WT-4cGMP-Open-coot-9-final.pdb #1/D THR 299 OG1 and /A ARG
421 NH2: 4.018Å
> select #1/D:298@OE1
1 atom, 1 residue, 1 model selected
> select add #1/A:421@NH2
2 atoms, 2 residues, 1 model selected
> distance #1/D:298@OE1 #1/A:421@NH2
Distance between WT-4cGMP-Open-coot-9-final.pdb #1/D GLU 298 OE1 and /A ARG
421 NH2: 3.663Å
> select clear
> select #1/C:421@NH1
1 atom, 1 residue, 1 model selected
> select add #1/C:456@NE1
2 atoms, 2 residues, 1 model selected
> distance #1/C:421@NH1 #1/C:456@NE1
Distance between WT-4cGMP-Open-coot-9-final.pdb #1/C ARG 421 NH1 and TRP 456
NE1: 2.877Å
> select #1/B:299@OG1
1 atom, 1 residue, 1 model selected
> select add #1/C:421@NH1
2 atoms, 1 pseudobond, 2 residues, 2 models selected
> select #1/B:299@OG1
1 atom, 1 residue, 1 model selected
> select add #1/C:421@NH1
2 atoms, 2 residues, 1 model selected
> distance #1/B:299@OG1 #1/C:421@NH1
Distance between WT-4cGMP-Open-coot-9-final.pdb #1/B THR 299 OG1 and /C ARG
421 NH1: 4.568Å
> select #1/C:421@NH2
1 atom, 1 residue, 1 model selected
> select add #1/B:298@OE2
2 atoms, 2 residues, 1 model selected
> distance #1/C:421@NH2 #1/B:298@OE2
Distance between WT-4cGMP-Open-coot-9-final.pdb #1/C ARG 421 NH2 and /B GLU
298 OE2: 2.518Å
> select clear
> hide #1 models
> show #!2 models
> select #2/C:421@NH2
1 atom, 1 residue, 1 model selected
> select add #2/D:298@OE2
2 atoms, 2 residues, 1 model selected
> select subtract #2/D:298@OE2
1 atom, 1 residue, 1 model selected
> select add #2/D:298@OE2
2 atoms, 2 residues, 1 model selected
> distance #2/C:421@NH2 #2/D:298@OE2
Distance between apo-WT-zx-coot-10-final.pdb #2/C ARG 421 NH2 and /D GLU 298
OE2: 3.218Å
> select #2/C:421@NH2
1 atom, 1 residue, 1 model selected
> select add #2/D:299@OG1
2 atoms, 2 residues, 1 model selected
> distance #2/C:421@NH2 #2/D:299@OG1
Distance between apo-WT-zx-coot-10-final.pdb #2/C ARG 421 NH2 and /D THR 299
OG1: 3.485Å
> select add #2/C:456@NE1
3 atoms, 3 residues, 1 model selected
> select clear
> select #2/C:456@NE1
1 atom, 1 residue, 1 model selected
> select add #2/C:421@NH2
2 atoms, 1 pseudobond, 2 residues, 2 models selected
> distance #2/C:456@NE1 #2/C:421@NH2
Distance between apo-WT-zx-coot-10-final.pdb #2/C TRP 456 NE1 and ARG 421 NH2:
5.925Å
> select clear
> select #2/C:456@NE1
1 atom, 1 residue, 1 model selected
> select clear
> select #2/C:421@NE
1 atom, 1 residue, 1 model selected
> select add #2/C:456@NE1
2 atoms, 2 residues, 1 model selected
> distance #2/C:421@NE #2/C:456@NE1
Distance between apo-WT-zx-coot-10-final.pdb #2/C ARG 421 NE and TRP 456 NE1:
4.569Å
> select clear
> select #2/C:298@OE1
1 atom, 1 residue, 1 model selected
> select add #2/B:421@NE
2 atoms, 2 residues, 1 model selected
> distance #2/C:298@OE1 #2/B:421@NE
Distance between apo-WT-zx-coot-10-final.pdb #2/C GLU 298 OE1 and /B ARG 421
NE: 3.456Å
> select add #2/C:299@OG1
3 atoms, 3 residues, 1 model selected
> select add #2/B:421@NH2
4 atoms, 3 residues, 1 model selected
> select clear
> select #2/B:421@NH2
1 atom, 1 residue, 1 model selected
> select add #2/C:299@OG1
2 atoms, 2 residues, 1 model selected
> distance #2/B:421@NH2 #2/C:299@OG1
Distance between apo-WT-zx-coot-10-final.pdb #2/B ARG 421 NH2 and /C THR 299
OG1: 7.036Å
> select clear
> select #2/B:421@NH2
1 atom, 1 residue, 1 model selected
> select add #2/C:298@OE1
2 atoms, 2 residues, 1 model selected
> distance #2/B:421@NH2 #2/C:298@OE1
Distance between apo-WT-zx-coot-10-final.pdb #2/B ARG 421 NH2 and /C GLU 298
OE1: 4.335Å
> select #2/B:421@NH1
1 atom, 1 residue, 1 model selected
> select add #2/B:456@NE1
2 atoms, 2 residues, 1 model selected
> select clear
> select #2/B:456@NE1
1 atom, 1 residue, 1 model selected
> select add #2/B:421@NH2
2 atoms, 2 residues, 1 model selected
> distance #2/B:456@NE1 #2/B:421@NH2
Distance between apo-WT-zx-coot-10-final.pdb #2/B TRP 456 NE1 and ARG 421 NH2:
3.135Å
> hide #!7 models
> show #!7 models
> hide #7.1 models
> show #7.1 models
> hide #7.1 models
> show #7.1 models
> hide #!7 models
> show #!7 models
> distance style symbol false
> distance style symbol true
===== 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 - 89.4
OpenGL renderer: Apple M3
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 Air
Model Identifier: Mac15,12
Model Number: Z1HY00019CH/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 24 GB
System Firmware Version: 11881.121.1
OS Loader Version: 11881.121.1
Software:
System Software Overview:
System Version: macOS 15.5 (24F74)
Kernel Version: Darwin 24.5.0
Time since boot: 8天16小时2分钟
Graphics/Displays:
Apple M3:
Chipset Model: Apple M3
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
XSN-27Q:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 75.00Hz
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: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
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
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
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 , 3 months ago
| Component: | Unassigned → Platform |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → mshMIGPerform crash |
comment:2 by , 3 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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As per #18238, hopefully fixed in newer versions of Qt