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#18474 closed defect (fixed)
Closing floating side view window crashes PySide ChimeraX
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | chimerax-programmers | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-15.6-arm64-arm-64bit
ChimeraX Version: 1.11.dev202508140657 (2025-08-14 06:57:21 UTC)
Description
Last time you used ChimeraX it crashed.
I had the Side View shown and it was floating and I clicked the side view close window button on the title bar and ChimeraX crashed. This is the PySide tech preview ChimeraX build.
Fatal Python error: Segmentation fault
Thread 0x000000046efef000 (most recent call first):
File "/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait
File "/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait
File "/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run
File "/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000464837000 (most recent call first):
File "/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 566 in select
File "/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/asyncio/base_events.py", line 1898 in _run_once
File "/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/asyncio/base_events.py", line 608 in run_forever
File "/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tornado/platform/asyncio.py", line 211 in start
File "/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/ipykernel/iostream.py", line 92 in _thread_main
File "/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000046382b000 (most recent call first):
File "/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 327 in wait
File "/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait
File "/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/IPython/core/history.py", line 1110 in run
File "/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/IPython/core/history.py", line 98 in only_when_enabled
File "/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/decorator.py", line 235 in fun
File "/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000428667000 (most recent call first):
File "/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait
File "/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait
File "/Users/goddard/Library/Application Support/ChimeraX/1.11/lib/python/site-packages/tqdm/_monitor.py", line 60 in run
File "/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Current thread 0x00000001f73b60c0 (most recent call first):
File "/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 368 in event_loop
File "/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1058 in init
File "/Users/goddard/Desktop/ChimeraX Aug 18 2025 pyside.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1223 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, shiboken6.Shiboken, PySide6.QtCore, PySide6.QtGui, PySide6.QtWidgets, PySide6.QtNetwork, PySide6.QtPrintSupport, PySide6.QtWebChannel, PySide6.QtWebEngineCore, PySide6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, psutil._psutil_osx, psutil._psutil_posix, chimerax.map._map, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, PIL._imaging, PIL._imagingmath, 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, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.mmcif.mmcif_write, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, sklearn.__check_build._check_build, lz4._version, lz4.frame._frame, scipy.integrate._odepack, scipy.integrate._quadpack, scipy.integrate._vode, scipy.integrate._dop, scipy.integrate._lsoda, scipy.interpolate._fitpack, scipy.interpolate._dfitpack, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, scipy.special.cython_special, scipy.stats._stats, scipy.stats._biasedurn, scipy.stats._levy_stable.levyst, scipy.stats._stats_pythran, scipy._lib._uarray._uarray, scipy.stats._ansari_swilk_statistics, scipy.stats._sobol, scipy.stats._qmc_cy, scipy.stats._mvn, scipy.stats._rcont.rcont, scipy.stats._unuran.unuran_wrapper, scipy.ndimage._nd_image, _ni_label, scipy.ndimage._ni_label, sklearn.utils._isfinite, sklearn.utils.sparsefuncs_fast, sklearn.utils.murmurhash, sklearn.utils._openmp_helpers, sklearn.metrics.cluster._expected_mutual_info_fast, sklearn.preprocessing._csr_polynomial_expansion, sklearn.preprocessing._target_encoder_fast, sklearn.metrics._dist_metrics, sklearn.metrics._pairwise_distances_reduction._datasets_pair, sklearn.utils._cython_blas, sklearn.metrics._pairwise_distances_reduction._base, sklearn.metrics._pairwise_distances_reduction._middle_term_computer, sklearn.utils._heap, sklearn.utils._sorting, sklearn.metrics._pairwise_distances_reduction._argkmin, sklearn.metrics._pairwise_distances_reduction._argkmin_classmode, sklearn.utils._vector_sentinel, sklearn.metrics._pairwise_distances_reduction._radius_neighbors, sklearn.metrics._pairwise_distances_reduction._radius_neighbors_classmode, sklearn.metrics._pairwise_fast, sklearn.neighbors._partition_nodes, sklearn.neighbors._ball_tree, sklearn.neighbors._kd_tree, sklearn.utils.arrayfuncs, sklearn.utils._random, sklearn.utils._seq_dataset, sklearn.linear_model._cd_fast, _loss, sklearn._loss._loss, sklearn.svm._liblinear, sklearn.svm._libsvm, sklearn.svm._libsvm_sparse, sklearn.linear_model._sag_fast, sklearn.utils._weight_vector, sklearn.linear_model._sgd_fast, sklearn.decomposition._online_lda_fast, sklearn.decomposition._cdnmf_fast, numba.core.typeconv._typeconv, numba._helperlib, numba._dynfunc, numba._dispatcher, numba.core.typing.builtins.itertools, numba.cpython.builtins.math, numba.core.runtime._nrt_python, numba.np.ufunc._internal, numba.experimental.jitclass._box, numba.core.typing.cmathdecl.cmath, numba.core.typing.mathdecl.math, numba.cpython.hashing.math, numba.cpython.hashing.sys, numba.cpython.numbers.math, numba.np.arraymath.math, numba.cpython.mathimpl.math, numba.cpython.mathimpl.sys, sklearn._isotonic, sklearn.tree._utils, sklearn.tree._tree, sklearn.tree._partitioner, sklearn.tree._splitter, sklearn.tree._criterion, sklearn.neighbors._quad_tree, sklearn.manifold._barnes_hut_tsne, sklearn.manifold._utils, scipy.cluster._vq, scipy.cluster._hierarchy, scipy.cluster._optimal_leaf_ordering, kiwisolver._cext, zmq.backend.cython._zmq, tornado.speedups, PySide6.QtDataVisualization, PySide6.QtOpenGL, PySide6.QtOpenGLWidgets, PySide6.QtSvg, openmm._openmm, openmm.app.internal.xtc_utils, openmm.app.internal.compiled (total: 220)
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"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
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"vmSummary" : "ReadOnly portion of Libraries: Total=2.1G resident=0K(0%) swapped_out_or_unallocated=2.1G(100%)\nWritable regions: Total=6.9G written=2731K(0%) resident=2731K(0%) swapped_out=0K(0%) unallocated=6.9G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG image 1584K 46 \nColorSync 688K 37 \nCoreAnimation 2448K 127 \nCoreGraphics 128K 7 \nCoreUI image data 5376K 42 \nFoundation 32K 2 \nKernel Alloc Once 48K 2 \nMALLOC 4.6G 203 \nMALLOC guard page 288K 18 \nMach message 96K 4 \nOpenGL GLSL 256K 3 \nPROTECTED_MEMORY 16K 1 \nSTACK GUARD 57.4M 89 \nStack 288.9M 89 \nVM_ALLOCATE 664.0M 807 \nVM_ALLOCATE (reserved) 1.4G 6 reserved VM address space (unallocated)\n__AUTH 5520K 696 \n__AUTH_CONST 77.4M 943 \n__CTF 824 1 \n__DATA 40.2M 1306 \n__DATA_CONST 63.3M 1296 \n__DATA_DIRTY 2777K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 684.0M 349 \n__OBJC_RO 61.4M 1 \n__OBJC_RW 2396K 1 \n__TEXT 1.5G 1317 \n__TEXT (graphics) 352K 1 \n__TPRO_CONST 128K 2 \ndyld private memory 28.1M 188 \nmapped file 629.5M 87 \npage table in kernel 2731K 1 \nshared memory 3296K 26 \n=========== ======= ======= \nTOTAL 10.0G 8046 \nTOTAL, minus reserved VM space 8.6G 8046 \n",
"legacyInfo" : {
"threadTriggered" : {
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"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "28f42922aa61bf67b7398c44b1a0240cfab7923f",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "61675b89201f677a9a4cbd65",
"factorPackIds" : {
"HEALTH_FEATURE_AVAILABILITY" : "65a855f5f087695cfac03d1f"
},
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},
{
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],
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]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.11.dev202508140657 (2025-08-14)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 1tw7 format mmcif fromDatabase pdb
1tw7 title:
Wide Open 1.3A Structure of a Multi-drug Resistant HIV-1 Protease Represents a
Novel Drug Target [more info...]
Chain information for 1tw7 #1
---
Chain | Description
A B | protease
Non-standard residues in 1tw7 #1
---
NA — sodium ion
54 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
1890 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> ui tool show Boltz
> boltz predict protein /A protein /B ligandCcd NA(2) name 1tw7
Running Boltz prediction of protein with 198 residues, 2 ligands NA (2) on gpu
Using cached multiple sequence alignment
/Users/goddard/Downloads/ChimeraX/BoltzMSA/1tw7_msa
Confidence score 0.96, pTM 0.97, ipTM 0.96 (ligand 0.94, protein 0.96), pLDDT
0.96
Boltz prediction completed in 47 seconds (start boltz 4 sec, sequence search 0
sec, load weights 11 sec, structure inference 33 sec)
Please cite Boltz-1 Democratizing Biomolecular Interaction Modeling. BioRxiv
https://doi.org/10.1101/2024.11.19.624167 if you use these predictions.
> open /Users/goddard/Desktop/boltz/boltz_1tw7_6/1tw7_model_0.cif logInfo
> false
Matchmaker 1tw7, chain A (#1) with 1tw7_model_0.cif, chain A (#2), sequence
alignment score = 496.9
RMSD between 99 pruned atom pairs is 0.382 angstroms; (across all 99 pairs:
0.382)
> boltz predict protein #1/A protein #1/B ligandSmiles
> CC(C)CN(C[C@H]([C@H](CC1=CC=CC=C1)NC(=O)O[C@H]2CO[C@@H]3[C@H]2CCO3)O)S(=O)(=O)C4=CC=C(C=C4)N
> name 1tw7 affinity
> CC(C)CN(C[C@H]([C@H](CC1=CC=CC=C1)NC(=O)O[C@H]2CO[C@@H]3[C@H]2CCO3)O)S(=O)(=O)C4=CC=C(C=C4)N
Running Boltz prediction of protein with 198 residues, 1 ligands
CC(C)CN(C[C@H]([C@H](CC1=CC=CC=C1)NC(=O)O[C@H]2CO[C@@H]3[C@H]2CCO3)O)S(=O)(=O)C4=CC=C(C=C4)N
on gpu
Using cached multiple sequence alignment
/Users/goddard/Downloads/ChimeraX/BoltzMSA/1tw7_msa
> ui tool show "Similar Structures"
> foldseek #1/A
Found 409 similar structures to 1tw7 #1/A in pdb database using foldseek, name
fs1
> open 3omh
Summary of feedback from opening 3omh fetched from pdb
---
note | Fetching compressed mmCIF 3omh from http://files.rcsb.org/download/3omh.cif
3omh title:
Crystal structure of PTPN22 in complex with SKAP-HOM pTyr75 peptide [more
info...]
Chain information for 3omh #3
---
Chain | Description | UniProt
A B C D | Tyrosine-protein phosphatase non-receptor type 22 | PTN22_HUMAN 1-294
E F G H | Src kinase-associated phosphoprotein 2 | SKAP2_HUMAN 390-398
3omh mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
4| author_and_software_defined_assembly
Deleted 7 extra chains, 102 C-terminal residues, 169 N-terminal residues, 139
non-polymer residues more than 3.0 Angstroms away.
Alignment of 3omh chain C to query has RMSD 0.852 using 9 of 23 paired
residues within cutoff distance 2.0
> open 6nir
Summary of feedback from opening 6nir fetched from pdb
---
note | Fetching compressed mmCIF 6nir from http://files.rcsb.org/download/6nir.cif
6nir title:
Crystal structure of a GII.4 norovirus HOV protease [more info...]
Chain information for 6nir #4
---
Chain | Description
A B C D | HOV protease
X | HOV protease fragment
6nir mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
5209 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Deleted 4 extra chains, 34 C-terminal residues, 47 N-terminal residues.
Alignment of 6nir chain D to query has RMSD 1.27 using 8 of 70 paired residues
within cutoff distance 2.0
> similarstructures traces
409 backbone traces
> similarstructures cluster #1/A:27,86,26,52,66 clusterDistance 1.5
Clustered 320 of 409 hits that have the specified 5 residues into 5 groups
Confidence score 0.92, pTM 0.98, ipTM 0.97 (ligand 0.97, protein 0.98), pLDDT
0.91
Ligand
CC(C)CN(C[C@H]([C@H](CC1=CC=CC=C1)NC(=O)O[C@H]2CO[C@@H]3[C@H]2CCO3)O)S(=O)(=O)C4=CC=C(C=C4)N
predicted binding affinity 0.091 uM, predicted binding probability 0.82
Boltz prediction completed in 122 seconds (start boltz 3 sec, sequence search
0 sec, load weights 11 sec, structure inference 36 sec, load affinity weights
11 sec, affinity inference 61 sec)
> open /Users/goddard/Desktop/boltz/boltz_1tw7_7/1tw7_model_0.cif logInfo
> false
Matchmaker 1tw7, chain A (#1) with 1tw7_model_0.cif, chain A (#6), sequence
alignment score = 504.1
RMSD between 99 pruned atom pairs is 0.404 angstroms; (across all 99 pairs:
0.404)
> hide #!3 models
> hide #6 models
> hide #!5 models
> hide #4 models
> hide #2 models
> open 3bxr
Summary of feedback from opening 3bxr fetched from pdb
---
notes | Fetching compressed mmCIF 3bxr from http://files.rcsb.org/download/3bxr.cif
Fetching CCD DRR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/DRR/DRR.cif
3bxr title:
Crystal Structures Of Highly Constrained Substrate And Hydrolysis Products
Bound To HIV-1 Protease. Implications For Catalytic Mechanism [more info...]
Chain information for 3bxr #7
---
Chain | Description | UniProt
A B | Protease | POL_HV1A2 1-99 101-199
Non-standard residues in 3bxr #7
---
DRR —
(9S,12S)-9-(1-methylethyl)-N-[(8S,11S)-8-[(1S)-1-methylpropyl]-7,10-dioxo-2-oxa-6,9-diazabicyclo[11.2.2]heptadeca-1(15),13,16-trien-11-yl]-7,10-dioxo-2-oxa-8,11-diazabicyclo[12.2.2]octadeca-1(16),14,17-triene-12-carboxamide
SO4 — sulfate ion
58 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Hit structure sequence 3bxr_B amino acid A at sequence position 66 does not
match sequence alignment G at position 66. Structure sequence
PQITLWKRPLVTIRIGGQLKEALLNTGADDTVIEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPVEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF.
Alignment sequence
PQITLWKRPLVTIRIGGQLKEALLNTGADDTVIEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPVEIGHKAIGTVLVGPTPVNIIGRNLLTQIGTLNF.
Deleted 1 extra chains, 2 C-terminal residues, 140 non-polymer residues more
than 3.0 Angstroms away.
Alignment of 3bxr chain B to query has RMSD 0.796 using 56 of 97 paired
residues within cutoff distance 2.0
> show #!3 models
> show #6 models
> hide #!3 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> select subtract #3.1
Nothing selected
> select add #3.1
Nothing selected
> show #1,6-7#!3 atoms
> select subtract #3.1
Nothing selected
> select add #3.1
Nothing selected
> select #3
206 atoms, 209 bonds, 24 residues, 1 model selected
> open 1080 format ccp4 fromDatabase emdb
Opened emdb 1080 as #8, grid size 100,100,100, pixel 2.7, shown at level
0.852, step 1, values float32
> volume #8 level 1.657
> volume #8 style image
> volume #8 level -0.0001241,0 level 1.675,0.8 level 2.365,1
> volume #8 step 2
> volume #8 step 1
> ui tool show "Fit Loops"
Populating font family aliases took 163 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.
> ui tool show "Side View"
> ui tool show Shell
> ui windowfill toggle
> ui tool show "Color Actions"
> color sel #ff666dff
> color sel #ff666dfc
> color sel #ff666ded
> color sel #ff666de0
> color sel #ff666dd7
> color sel #ff666dcd
> color sel #ff666dc7
> color sel #ff666dbd
> color sel #ff666db5
> color sel #ff666db0
> color sel #ff666dac
> color sel #ff666da7
> color sel #ff666da5
> color sel #ff666da3
> color sel #ff666da1
> color sel #ff666d9b
> color sel #ff666d97
> color sel #ff666d91
> color sel #ff666d8e
> color sel #ff666d8a
> color sel #ff666d88
> color sel #ff666d85
> color sel #ff666d82
> color sel #ff666d81
> color sel #ff666d80
> color sel #ff666d73
> color sel #ff666d60
> color sel #ff666d56
> color sel #ff666d42
> color sel #ff666d37
> color sel #ff666d27
> color sel #ff666d1f
> color sel #ff666d15
> color sel #ff666d11
> color sel #ff666d10
> color sel #ff666d0e
> color sel #ff666d0d
> color sel #ff666d0c
> color sel #ff666d0b
> color sel #ff666d0c
> color sel #ff666d0d
> color sel #ff666d0e
> color sel #ff666d0f
> color sel #ff666d10
> color sel #ff666d16
> color sel #ff666d1a
> color sel #ff666d20
> color sel #ff666d30
> color sel #ff666d40
> color sel #ff666d4a
> color sel #ff666d51
> color sel #ff666d54
> color sel #ff666d59
> color sel #ff666d5b
> color sel #ff666d5f
> color sel #ff666d64
> color sel #ff666d66
> color sel #ff666d67
> color sel #ff666d68
> color sel #ff666d67
> color sel #ff666d61
> color sel #ff666d5d
> color sel #ff666d57
> color sel #ff666d54
> color sel #ff666d4a
> color sel #ff666d43
> color sel #ff666d35
> color sel #ff666d2e
> color sel #ff666d22
> color sel #ff666d1d
> color sel #ff666d15
> color sel #ff666d12
> color sel #ff666d11
> color sel #ff666d14
> color sel #ff666d1a
> color sel #ff666d24
> color sel #ff666d2b
> color sel #ff666d3f
> color sel #ff666d54
> color sel #ff666d61
> color sel #ff666d77
> color sel #ff666d87
> color sel #ff666d8f
> color sel #ff666d96
> color sel #ff666d9a
> color sel #ff666d9c
> color sel #ff666d9f
> color sel #ff666da1
> color sel #ff666da6
> color sel #ff666da9
> color sel #ff666daf
> color sel #ff666db4
> color sel #ff666dbd
> color sel #ff666dc6
> color sel #ff666dcc
> color sel #ff666dd4
> color sel #ff666dde
> color sel #ff666de1
> color sel #ff666dea
> color sel #ff666df1
> color sel #ff666df6
> color sel #ff666df9
> color sel #ff666dff
> color sel #ff666dee
> color sel #ff666de1
> color sel #ff666dcd
> color sel #ff666dbd
> color sel #ff666db7
> color sel #ff666dae
> color sel #ff666da9
> color sel #ff666da6
> color sel #ff666da5
> color sel #ff666da6
> color sel #ff666da7
> color sel #ff666da8
> color sel #ff666dad
> color sel #ff666db9
> color sel #ff666dc5
> color sel #ff666ddf
> color sel #ff666df2
> color sel #ff666dff
> ui mousemode right tug
Missing atoms or parameterization needed by force field.
All heavy atoms and hydrogens with standard names are required.
Error with ignoreExternalBonds=False was
No template found for residue 1 (ILE). The set of atoms is similar to HID, but
it is missing 9 atoms. For more information, see
https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#template
Error with ignoreExternalBonds=True was
No template found for residue 1 (ILE). The set of atoms is similar to HID, but
it is missing 9 atoms. For more information, see
https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#template
> ui mousemode right label
> label #3/C:192
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.11.dev202508140657 (2025-08-14)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2 Ultra
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PySide6 6.9.1, Qt 6.9.1
Qt runtime version: 6.9.1
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac Studio
Model Identifier: Mac14,14
Model Number: Z1800003VLL/A
Chip: Apple M2 Ultra
Total Number of Cores: 24 (16 performance and 8 efficiency)
Memory: 64 GB
System Firmware Version: 11881.140.96
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.6 (24G84)
Kernel Version: Darwin 24.6.0
Time since boot: 10 days, 21 hours, 54 minutes
Graphics/Displays:
Apple M2 Ultra:
Chipset Model: Apple M2 Ultra
Type: GPU
Bus: Built-In
Total Number of Cores: 60
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
PHL 278B1:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.4
blockdiag: 3.0.0
blosc2: 3.7.1
build: 1.2.2.post1
certifi: 2025.7.14
cftime: 1.6.4.post1
charset-normalizer: 3.4.3
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.0.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.12
ChimeraX-AtomicLibrary: 14.1.22
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.dev202508140657
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.17
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.5.1
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: 1.0.1
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: 1.15.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.3.8
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.4
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.4
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: 1.5.2
ChimeraX-Scenes: 0.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.2
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
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: 1.19.1
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: 2.5.2
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: 1.48.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.3
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: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.10.4
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.2
debugpy: 1.8.16
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.59.1
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.30.1
ipython: 9.4.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.7
jedi: 0.19.2
Jinja2: 3.1.6
joblib: 1.5.0
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.9
line_profiler: 5.0.0
llvmlite: 0.44.0
lxml: 5.3.1
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.2
matplotlib: 3.10.3
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numba: 0.61.2
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.5
pynndescent: 0.5.13
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PySide6: 6.9.1
PySide6_Addons: 6.9.1
PySide6_Essentials: 6.9.1
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.1
qtconsole: 5.6.1
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
requests: 2.32.4
roman-numerals-py: 3.1.0
scikit-learn: 1.6.1
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
shiboken6: 6.9.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
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: 0.7.5
tables: 3.10.2
tcia_utils: 1.5.1
threadpoolctl: 3.6.0
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.2
tqdm: 4.67.1
traitlets: 5.14.3
typing_extensions: 4.14.1
tzdata: 2025.2
umap-learn: 0.5.7
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Change History (5)
comment:1 by , 2 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Closing floating side view window crashes PySide ChimeraX |
comment:2 by , 2 months ago
I was able to reproduce this with a docked side view. I can see that the error is in ~QDockWidget and the fact that the parentWasChanged event was in the stack trace led me to believe the line causing the crash was self.setParent(None) in the close method of the side view's graphics QWindow. I commented that call out and the crash went away.
Is that call actually necessary? Do we need to set the parent of a widget that's about to be deleted to None?
comment:4 by , 8 weeks ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
I was able to reproduce this on PyQt6 actually. It appears that on Qt6, this causes the already-deleted widget to get a parentChanged event which crashes ChimeraX. I took the line out and noted that information in the commit message.
comment:5 by , 8 weeks ago
Interesting. Fortunately closing floating side view in ChimeraX 1.10 / Qt 6.8 does not cause a crash (test on Mac). But closing it in Qt 6.9 in the ChimeraX daily build on Mac does cause a crash as Zach found.
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Got the same crash when I repeated, show side view, drag it out so it is floating, close it.