![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 months ago
Closed 7 months ago
#17498 closed defect (can't reproduce)
Crash in QListWidgetitem.text()
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| 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-14.5-arm64-arm-64bit
ChimeraX Version: 1.9rc202411061937 (2024-11-06 19:37:44 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00000003326cb000 (most recent call first):
File "/Applications/ChimeraX-1.9-rc2024.11.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.9-rc2024.11.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.9-rc2024.11.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.9-rc2024.11.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9-rc2024.11.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000002065a0c00 (most recent call first):
File "/Applications/ChimeraX-1.9-rc2024.11.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/item_chooser.py", line 167 in
File "/Applications/ChimeraX-1.9-rc2024.11.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/item_chooser.py", line 167 in _items_change
File "/Applications/ChimeraX-1.9-rc2024.11.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/item_chooser.py", line 89 in _sleep_check
File "/Applications/ChimeraX-1.9-rc2024.11.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/item_chooser.py", line 133 in get_value
File "/Applications/ChimeraX-1.9-rc2024.11.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/item_chooser.py", line 130 in value
File "/Applications/ChimeraX-1.9-rc2024.11.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/tool.py", line 213 in structures
File "/Applications/ChimeraX-1.9-rc2024.11.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/tool.py", line 195 in add_h
File "/Applications/ChimeraX-1.9-rc2024.11.06.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-rc2024.11.06.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-rc2024.11.06.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.surface._surface, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, 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.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 54)
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"captureTime" : "2025-04-28 10:55:51.5909 +0200",
"codeSigningMonitor" : 1,
"incident" : "AEC574F8-A762-4856-8BB4-6B8E55AF3109",
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"procLaunch" : "2025-04-23 21:50:49.7337 +0200",
"procStartAbsTime" : 4902977671155,
"procExitAbsTime" : 6683309747345,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9-rc2024.11.06.app\/Contents\/MacOS\/ChimeraX",
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"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
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"vmRegionInfo" : "0x3688f2c57978 is not in any region. Bytes after previous region: 59480780142969 Bytes before following region: 45591299786376\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x0000b688f2c57978","rawCodes":[1,200699304835448],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000b688f2c57978 -> 0x00003688f2c57978 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":31914},
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9rc202411061937 (2024-11-06)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/elizabethkwon/Downloads/1czz.pdb
1czz.pdb title:
Structure of TNF receptor associated factor 2 In complex with A 17- residue
CD40 peptide [more info...]
Chain information for 1czz.pdb #1
---
Chain | Description | UniProt
A B C | TRAF2 | TRAF2_HUMAN 315-501
D E | CD40 | TNR5_HUMAN 250-258
Non-standard residues in 1czz.pdb #1
---
ACE — acetyl group
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> color bychain
> hide surfaces
> style ball
Changed 4444 atom styles
> style sphere
Changed 4444 atom styles
> style stick
Changed 4444 atom styles
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> style ball
Changed 4444 atom styles
> show cartoons
> hide atoms
> select /D/E
144 atoms, 132 bonds, 32 residues, 1 model selected
> open /Users/elizabethkwon/Downloads/2naq.pdb
2naq.pdb title:
3D NMR solution structure of NLRP3 pyd [more info...]
Chain information for 2naq.pdb
---
Chain | Description | UniProt
2.1/A 2.2/A 2.3/A 2.4/A 2.5/A 2.6/A 2.7/A 2.8/A 2.9/A 2.10/A 2.11/A 2.12/A 2.13/A 2.14/A 2.15/A 2.16/A 2.17/A 2.18/A 2.19/A 2.20/A | nacht, LRR and pyd domains-containing protein 3 | NLRP3_HUMAN 1-91
> close #1
> ui tool show "Dock Prep"
Starting dock prep
Deleting solvent
Deleting non-metal-complex ions
Deleting non-current alt locs
Summary of feedback from adding hydrogens to multiple structures
---
notes | Termini for 2naq.pdb (#2.1) chain A determined from SEQRES records
Chain-initial residues that are actual N termini: 2naq.pdb #2.1/A MET 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: 2naq.pdb #2.1/A LYS 91
Chain-final residues that are not actual C termini:
58 hydrogen bonds
No usable SEQRES records for 2naq.pdb (#2.2) chain A; guessing termini instead
Chain-initial residues that are actual N termini: 2naq.pdb #2.2/A MET 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: 2naq.pdb #2.2/A LYS 91
Chain-final residues that are not actual C termini:
61 hydrogen bonds
No usable SEQRES records for 2naq.pdb (#2.3) chain A; guessing termini instead
Chain-initial residues that are actual N termini: 2naq.pdb #2.3/A MET 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: 2naq.pdb #2.3/A LYS 91
Chain-final residues that are not actual C termini:
64 hydrogen bonds
No usable SEQRES records for 2naq.pdb (#2.4) chain A; guessing termini instead
Chain-initial residues that are actual N termini: 2naq.pdb #2.4/A MET 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: 2naq.pdb #2.4/A LYS 91
Chain-final residues that are not actual C termini:
56 hydrogen bonds
No usable SEQRES records for 2naq.pdb (#2.5) chain A; guessing termini instead
Chain-initial residues that are actual N termini: 2naq.pdb #2.5/A MET 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: 2naq.pdb #2.5/A LYS 91
Chain-final residues that are not actual C termini:
66 hydrogen bonds
No usable SEQRES records for 2naq.pdb (#2.6) chain A; guessing termini instead
Chain-initial residues that are actual N termini: 2naq.pdb #2.6/A MET 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: 2naq.pdb #2.6/A LYS 91
Chain-final residues that are not actual C termini:
59 hydrogen bonds
No usable SEQRES records for 2naq.pdb (#2.7) chain A; guessing termini instead
Chain-initial residues that are actual N termini: 2naq.pdb #2.7/A MET 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: 2naq.pdb #2.7/A LYS 91
Chain-final residues that are not actual C termini:
58 hydrogen bonds
No usable SEQRES records for 2naq.pdb (#2.8) chain A; guessing termini instead
Chain-initial residues that are actual N termini: 2naq.pdb #2.8/A MET 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: 2naq.pdb #2.8/A LYS 91
Chain-final residues that are not actual C termini:
57 hydrogen bonds
No usable SEQRES records for 2naq.pdb (#2.9) chain A; guessing termini instead
Chain-initial residues that are actual N termini: 2naq.pdb #2.9/A MET 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: 2naq.pdb #2.9/A LYS 91
Chain-final residues that are not actual C termini:
54 hydrogen bonds
No usable SEQRES records for 2naq.pdb (#2.10) chain A; guessing termini
instead
Chain-initial residues that are actual N termini: 2naq.pdb #2.10/A MET 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: 2naq.pdb #2.10/A LYS 91
Chain-final residues that are not actual C termini:
61 hydrogen bonds
No usable SEQRES records for 2naq.pdb (#2.11) chain A; guessing termini
instead
Chain-initial residues that are actual N termini: 2naq.pdb #2.11/A MET 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: 2naq.pdb #2.11/A LYS 91
Chain-final residues that are not actual C termini:
58 hydrogen bonds
No usable SEQRES records for 2naq.pdb (#2.12) chain A; guessing termini
instead
Chain-initial residues that are actual N termini: 2naq.pdb #2.12/A MET 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: 2naq.pdb #2.12/A LYS 91
Chain-final residues that are not actual C termini:
59 hydrogen bonds
No usable SEQRES records for 2naq.pdb (#2.13) chain A; guessing termini
instead
Chain-initial residues that are actual N termini: 2naq.pdb #2.13/A MET 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: 2naq.pdb #2.13/A LYS 91
Chain-final residues that are not actual C termini:
58 hydrogen bonds
No usable SEQRES records for 2naq.pdb (#2.14) chain A; guessing termini
instead
Chain-initial residues that are actual N termini: 2naq.pdb #2.14/A MET 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: 2naq.pdb #2.14/A LYS 91
Chain-final residues that are not actual C termini:
55 hydrogen bonds
No usable SEQRES records for 2naq.pdb (#2.15) chain A; guessing termini
instead
Chain-initial residues that are actual N termini: 2naq.pdb #2.15/A MET 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: 2naq.pdb #2.15/A LYS 91
Chain-final residues that are not actual C termini:
62 hydrogen bonds
No usable SEQRES records for 2naq.pdb (#2.16) chain A; guessing termini
instead
Chain-initial residues that are actual N termini: 2naq.pdb #2.16/A MET 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: 2naq.pdb #2.16/A LYS 91
Chain-final residues that are not actual C termini:
61 hydrogen bonds
No usable SEQRES records for 2naq.pdb (#2.17) chain A; guessing termini
instead
Chain-initial residues that are actual N termini: 2naq.pdb #2.17/A MET 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: 2naq.pdb #2.17/A LYS 91
Chain-final residues that are not actual C termini:
58 hydrogen bonds
No usable SEQRES records for 2naq.pdb (#2.18) chain A; guessing termini
instead
Chain-initial residues that are actual N termini: 2naq.pdb #2.18/A MET 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: 2naq.pdb #2.18/A LYS 91
Chain-final residues that are not actual C termini:
56 hydrogen bonds
No usable SEQRES records for 2naq.pdb (#2.19) chain A; guessing termini
instead
Chain-initial residues that are actual N termini: 2naq.pdb #2.19/A MET 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: 2naq.pdb #2.19/A LYS 91
Chain-final residues that are not actual C termini:
64 hydrogen bonds
No usable SEQRES records for 2naq.pdb (#2.20) chain A; guessing termini
instead
Chain-initial residues that are actual N termini: 2naq.pdb #2.20/A MET 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: 2naq.pdb #2.20/A LYS 91
Chain-final residues that are not actual C termini:
59 hydrogen bonds
0 hydrogens added
Closest equivalent command: addcharge standardizeResidues none
Using Amber 20 recommended default charges and atom types for standard
residues
Dock prep finished
> save /Users/elizabethkwon/Desktop/2naq_cleaned.pdb
> open /Users/elizabethkwon/Downloads/3qf2.pdb
3qf2.pdb title:
Crystal structure of NALP3 pyd [more info...]
Chain information for 3qf2.pdb #1
---
Chain | Description | UniProt
A B | nacht, LRR and pyd domains-containing protein 3 | NALP3_HUMAN 3-112
> close #2
> ui tool show "Dock Prep"
Starting dock prep
Deleting solvent
Deleting non-metal-complex ions
Deleting non-current alt locs
Summary of feedback from adding hydrogens to 3qf2.pdb #1
---
notes | Termini for 3qf2.pdb (#1) chain A determined from SEQRES records
Termini for 3qf2.pdb (#1) chain B determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: /A SER 5, /B SER 5
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A TRP 94, /B GLU 110
171 hydrogen bonds
Adding 'H' to /A SER 5
Adding 'H' to /B SER 5
/A TRP 94 is not terminus, removing H atom from 'C'
/B GLU 110 is not terminus, removing H atom from 'C'
1587 hydrogens added
Closest equivalent command: addcharge standardizeResidues none
Using Amber 20 recommended default charges and atom types for standard
residues
Dock prep finished
> save /Users/elizabethkwon/Desktop/3qf2_cleaned.pdb relModel #1
> open
> /Users/elizabethkwon/Documents/TFM_Internship/MS_Project/drugs:ligands/paclitaxel.sdf
> open "/Users/elizabethkwon/Documents/TFM_Internship/MS_Project/HLA-
> DRB1_paclitaxel/1 chain/CB-
> Dock2/1jk8_cleaned_paclitaxel_out_1.-7.4.complex.pdb"
Summary of feedback from opening
/Users/elizabethkwon/Documents/TFM_Internship/MS_Project/HLA-DRB1_paclitaxel/1
chain/CB-Dock2/1jk8_cleaned_paclitaxel_out_1.-7.4.complex.pdb
---
warning | Ignored bad PDB record found on line 1
REMARK The PDB FILE IS CREATED BY CY's PROGRAM CurvatureSurface AT Mon Mar 31
09:12:35 2025
Chain information for 1jk8_cleaned_paclitaxel_out_1.-7.4.complex.pdb
---
Chain | Description
4.1/B | No description available
Computing secondary structure
> open /Users/elizabethkwon/Downloads/Structure2D_COMPOUND_CID_36314.sdf
PubChem entry 36314
> select ::name="UNL"
405 atoms, 429 bonds, 4 residues, 4 models selected
> close #2-3
> close #5
> select ~sel
5626 atoms, 5704 bonds, 386 residues, 3 models selected
> delete atoms sel
> delete bonds sel
> save
> /Users/elizabethkwon/Documents/TFM_Internship/MS_Project/drugs:ligands/paclitaxel_3d.mol2
> open /Users/elizabethkwon/Desktop/3qf2_cleaned.pdb
3qf2_cleaned.pdb title:
Crystal structure of NALP3 pyd [more info...]
Chain information for 3qf2_cleaned.pdb #1
---
Chain | Description | UniProt
A B | nacht, LRR and pyd domains-containing protein 3 | NALP3_HUMAN 3-112
> select #1/A
1485 atoms, 1503 bonds, 90 residues, 1 model selected
> open /Users/elizabethkwon/Downloads/8etr.pdb
8etr.pdb title:
Cryoem structure of NLRP3 nacht domain In complex with G2394 [more info...]
Chain information for 8etr.pdb #2
---
Chain | Description | UniProt
A | nacht, LRR and pyd domains-containing protein 3 | NLRP3_HUMAN 134-676
Non-standard residues in 8etr.pdb #2
---
ADP — adenosine-5'-diphosphate
MG — magnesium ion
WTN — (6S,8R)-N-[(1,2,3,5,6,7-hexahydro-S-
indacen-4-yl)carbamoyl]-6-(methylamino)-6,7-dihydro-5H-pyrazolo[5,1-B][1,3]oxazine-3-sulfonamide
> hide #!4 models
> show #!4 models
> close #4
> close #1
> select ::name="ADP"
27 atoms, 29 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select ::name="MG"
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select ::name="WTN"
30 atoms, 34 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> ui tool show "Dock Prep"
Starting dock prep
Deleting solvent
Deleting non-metal-complex ions
Deleting non-current alt locs
Filling out missing side chains
/A HIS 177: phi -56.2, psi none trans
/A LYS 496: phi 58.0, psi 10.9 trans
/A PHE 502: phi -71.4, psi -64.6 trans
/A VAL 676: phi 54.0, psi none trans
Applying HIS rotamer (chi angles: -172.6 -83.8) to /A HIS 177
Applying LYS rotamer (chi angles: -64.6 -175.4 -71.6 -67.6) to /A LYS 496
Applying PHE rotamer (chi angles: -73.3 103.4) to /A PHE 502
Applying VAL rotamer (chi angles: 175.9) to /A VAL 676
Summary of feedback from adding hydrogens to 8etr.pdb #2
---
notes | Termini for 8etr.pdb (#2) chain A determined from SEQRES records
Chain-initial residues that are actual N termini: /A LYS 134
Chain-initial residues that are not actual N termini: /A LEU 164, /A ILE 203,
/A GLU 217, /A CYS 463, /A LYS 516, /A SER 555, /A SER 590
Chain-final residues that are actual C termini: /A VAL 676
Chain-final residues that are not actual C termini: /A ILE 151, /A HIS 177, /A
ASP 212, /A LEU 451, /A VAL 512, /A GLU 538, /A ARG 588
293 hydrogen bonds
40 hydrogens added
Closest equivalent command: addcharge standardizeResidues none
Using Amber 20 recommended default charges and atom types for standard
residues
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9-rc2024.11.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/add_charge/charge.py", line 129, in add_standard_charges
h.charge, h.gaff_type = hyd_charge_type_data[(h.residue.amber_name,
heavy.name.lower())]
~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
KeyError: ('VAL', 'c')
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9-rc2024.11.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/add_charge/tool.py", line 120, in add_charges
self._finish_add_charge(residues)
File
"/Applications/ChimeraX-1.9-rc2024.11.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/add_charge/tool.py", line 146, in _finish_add_charge
non_std = add_standard_charges(self.session, residues=residues, **params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9-rc2024.11.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/add_charge/charge.py", line 131, in add_standard_charges
raise ChargeError("Hydrogen %s bonded to atom that should not have hydrogens
(%s)"
chimerax.add_charge.charge.ChargeError: Hydrogen /A VAL 676 HC bonded to atom
that should not have hydrogens (/A VAL 676 C)
chimerax.add_charge.charge.ChargeError: Hydrogen /A VAL 676 HC bonded to atom
that should not have hydrogens (/A VAL 676 C)
File
"/Applications/ChimeraX-1.9-rc2024.11.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/add_charge/charge.py", line 131, in add_standard_charges
raise ChargeError("Hydrogen %s bonded to atom that should not have hydrogens
(%s)"
See log for complete Python traceback.
> save
> /Users/elizabethkwon/Documents/TFM_Internship/MS_Project/drugs:ligands/8etr_cleaned.mol2
> save
> /Users/elizabethkwon/Documents/TFM_Internship/MS_Project/drugs:ligands/8etr_cleaned.pdb
> open /Users/elizabethkwon/Downloads/8zem.cif
Summary of feedback from opening /Users/elizabethkwon/Downloads/8zem.cif
---
notes | Fetching CCD A1D79 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/9/A1D79/A1D79.cif
Fetching CCD ADP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/ADP/ADP.cif
8zem.cif title:
Crystal Structure of NLRP3 NACHT domain in complex with NP3-1 [more info...]
Chain information for 8zem.cif #1
---
Chain | Description | UniProt
A | NACHT, LRR and PYD domains-containing protein 3 | NLRP3_HUMAN 131-679
Non-standard residues in 8zem.cif #1
---
A1D79 —
1-[5-[2,3-bis(chloranyl)phenyl]-2,3-dihydro-1~{H}-inden-4-yl]-3-[4-(2-oxidanylpropan-2-yl)thiophen-2-yl]sulfonyl-
urea
ADP — adenosine-5'-diphosphate
> select add #2
7846 atoms, 7929 bonds, 7 pseudobonds, 471 residues, 3 models selected
> close #2
> select ::name="A1D79"::name="ADP"
60 atoms, 65 bonds, 2 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> ui tool show "Dock Prep"
Starting dock prep
Deleting solvent
Deleting non-metal-complex ions
Deleting non-current alt locs
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9rc202411061937 (2024-11-06)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show Registration
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.4
Locale: 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: MacBookAir10,1
Model Number: MGNA3LL/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 10151.121.1
OS Loader Version: 10151.121.1
Software:
System Software Overview:
System Version: macOS 14.5 (23F79)
Kernel Version: Darwin 23.5.0
Time since boot: 16 days, 12 hours, 2 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.7.1
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
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: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.7
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: 2.4.7
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13
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: 1.9rc202411061937
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: 1.2.5
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: 1.1.11
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: 1.5.17
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-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: 1.6.1
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: 3.2.6
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: 1.3.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.7
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.54.1
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.12.1
html2text: 2024.2.26
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: 2.10.1
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
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: 6.4.1
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 , 7 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in QListWidgetitem.text() |
comment:2 by , 7 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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...or possibly in QListWidget.selectedItems()