![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 months ago
Last modified 2 months ago
#18474 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | chimerax-programmers | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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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{
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"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
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"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
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"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
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"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 3174368,
"uuid" : "1a037942-11e0-3fc8-aad2-20b11e7ae1a4",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
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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" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "28f42922aa61bf67b7398c44b1a0240cfab7923f",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "61675b89201f677a9a4cbd65",
"factorPackIds" : {
"HEALTH_FEATURE_AVAILABILITY" : "65a855f5f087695cfac03d1f"
},
"deploymentId" : 240000218
},
{
"rolloutId" : "60f8ddccefea4203d95cbeef",
"factorPackIds" : {
},
"deploymentId" : 240000025
}
],
"experiments" : [
]
}
}
===== 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
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