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Opened 17 months ago
Closed 17 months ago
#15353 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.1-arm64-arm-64bit
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00000001de145ec0 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in __iter__
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/split.py", line 264 in atom_residues
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/split.py", line 206 in molecule_from_atoms
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/split.py", line 100 in
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/split.py", line 100 in split_molecule
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/split.py", line 63 in split
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, 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 (total: 52)
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===== Log before crash start =====
Startup Messages
---
warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr
bundle with that from OME-Zarr bundle
Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
that from NMRSTAR bundle
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/marla/Downloads/1vas.pdb
1vas.pdb title:
Atomic model of A pyrimidine dimer specific excision repair enzyme complexed
with A DNA substrate: structural basis for damaged DNA recognition [more
info...]
Chain information for 1vas.pdb #1
---
Chain | Description | UniProt
A | T4 endonuclease V (E.C.3.1.25.1) | END5_BPT4 2-138
B | DNA (5'-D(*ap*TP*CP*GP*CP*GP*TP*TP*GP*CP*GP*CP*T)-3') |
C | DNA (5'-D(*TP*ap*GP*CP*GP*CP*ap*ap*CP*GP*CP*GP*A)-3') |
> open /Users/marla/Downloads/3mr3.pdb
3mr3.pdb title:
Human DNA polymerase η - DNA ternary complex with the 3'T of A CPD In the
active site (TT1) [more info...]
Chain information for 3mr3.pdb #2
---
Chain | Description | UniProt
A | DNA polymerase η | POLH_HUMAN 1-432
P | DNA (5'-D(*CP*ap*GP*CP*GP*TP*CP*ap*T)-3') |
T | DNA (5'-D(*CP*ap*(TTD)P*ap*TP*GP*ap*CP*GP*CP*T)-3') |
Non-standard residues in 3mr3.pdb #2
---
DZ4 —
2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine
GOL — glycerol (glycerin; propane-1,2,3-triol)
MG — magnesium ion
TTD — cis-syn cyclobutane thymine dimer
([(3S,4S,9S,10R,12R,15AR,18BS,18CS)-3,7-dihydroxy-15A,15B-dimethyl-7-oxido-13,15,16,18-tetraoxohexadecahydro-1H-1,4-epox
Y-9,12-methano-6,8,11-trioxa-12A,14,17,18A-tetraaza-7-phosphacyclohexadeca[1,2,3,4-def]biphenylen-10-yl]methyl
dihydrogen phosphate)
> open /Users/marla/Downloads/3mr3.pdb
3mr3.pdb title:
Human DNA polymerase η - DNA ternary complex with the 3'T of A CPD In the
active site (TT1) [more info...]
Chain information for 3mr3.pdb #3
---
Chain | Description | UniProt
A | DNA polymerase η | POLH_HUMAN 1-432
P | DNA (5'-D(*CP*ap*GP*CP*GP*TP*CP*ap*T)-3') |
T | DNA (5'-D(*CP*ap*(TTD)P*ap*TP*GP*ap*CP*GP*CP*T)-3') |
Non-standard residues in 3mr3.pdb #3
---
DZ4 —
2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine
GOL — glycerol (glycerin; propane-1,2,3-triol)
MG — magnesium ion
TTD — cis-syn cyclobutane thymine dimer
([(3S,4S,9S,10R,12R,15AR,18BS,18CS)-3,7-dihydroxy-15A,15B-dimethyl-7-oxido-13,15,16,18-tetraoxohexadecahydro-1H-1,4-epox
Y-9,12-methano-6,8,11-trioxa-12A,14,17,18A-tetraaza-7-phosphacyclohexadeca[1,2,3,4-def]biphenylen-10-yl]methyl
dihydrogen phosphate)
> hide #1 models
> hide #!3 models
> show #!3 models
> select add #3
4250 atoms, 3920 bonds, 12 pseudobonds, 889 residues, 2 models selected
> select subtract #3
Nothing selected
> select add #3
4250 atoms, 3920 bonds, 12 pseudobonds, 889 residues, 2 models selected
> select subtract #3
Nothing selected
> hide #!3 models
> close session
> open /Users/marla/Downloads/1tez.pdb
1tez.pdb title:
Complex between DNA and the DNA photolyase from anacystis nidulans [more
info...]
Chain information for 1tez.pdb #1
---
Chain | Description | UniProt
A B C D | DNA photolyase; photoreactivating enzyme | PHR_SYNLE 2-475
I K | 5'-D(*ap*TP*CP*GP*GP*CP*T*(TCP)P*CP*GP*C)-3' |
J L | 5'-D(P*CP*GP*ap*ap*GP*CP*CP*GP*A)-3' |
M O | 5'-D(*TP*CP*GP*C)-3' |
N P | 5'-D(P*GP*CP*CP*GP*A)-3' |
Non-standard residues in 1tez.pdb #1
---
C — cytidine-5'-monophosphate
FAD — flavin-adenine dinucleotide
G — guanosine-5'-monophosphate
HDF — 8-hydroxy-10-(D-ribo-2,3,4,5-tetrahydroxypentyl)-5-deazaisoalloxazine
MG — magnesium ion
TCP — 5'-methylthymidine
> open /Users/marla/Downloads/7yc7.pdb
7yc7.pdb title:
Dark, fully reduced structure of the mmcpdii-DNA complex As produced At
swissfel [more info...]
Chain information for 7yc7.pdb #2
---
Chain | Description
A B | DNA photolyase
C E | CPD photolesion containing DNA
D F | complementary oligonucleotide to the CPD containing DNA
Non-standard residues in 7yc7.pdb #2
---
FAD — flavin-adenine dinucleotide
SO4 — sulfate ion
TTD — cis-syn cyclobutane thymine dimer
([(3S,4S,9S,10R,12R,15AR,18BS,18CS)-3,7-dihydroxy-15A,15B-dimethyl-7-oxido-13,15,16,18-tetraoxohexadecahydro-1H-1,4-epox
Y-9,12-methano-6,8,11-trioxa-12A,14,17,18A-tetraaza-7-phosphacyclohexadeca[1,2,3,4-def]biphenylen-10-yl]methyl
dihydrogen phosphate)
> hide #!1 models
> select add #2
8468 atoms, 8510 bonds, 1233 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> show sel cartoons
> split #2
Split 7yc7.pdb (#2) into 6 models
Chain information for 7yc7.pdb A #2.1
---
Chain | Description
A | No description available
Chain information for 7yc7.pdb B #2.2
---
Chain | Description
B | No description available
Chain information for 7yc7.pdb C #2.3
---
Chain | Description
C | No description available
Chain information for 7yc7.pdb D #2.4
---
Chain | Description
D | No description available
Chain information for 7yc7.pdb E #2.5
---
Chain | Description
E | No description available
Chain information for 7yc7.pdb F #2.6
---
Chain | Description
F | No description available
> hide #2.1 models
> hide #2.3 models
> hide #2.4 models
> ui tool show "Blast Protein"
> ui tool show "Show Sequence Viewer"
> sequence chain #2.2/B
Alignment identifier is 2.2/B
> select #2.2/B:-4--3
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #2.2/B:-4-10
114 atoms, 115 bonds, 15 residues, 1 model selected
> select #2.2/B:462
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2.2/B:462
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2.2/B:-4
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2.2/B:-4
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2.2/B:234
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2.2/B:234-235
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #2.2/B:239
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2.2/B:239-241
20 atoms, 19 bonds, 3 residues, 1 model selected
> select #2.2/B:336-337
21 atoms, 21 bonds, 2 residues, 1 model selected
> select #2.2/B:336-339
37 atoms, 37 bonds, 4 residues, 1 model selected
> select #2.2/B:300
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2.2/B:300-303
33 atoms, 32 bonds, 4 residues, 1 model selected
> select #2.2/B:350-351
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #2.2/B:350-352
25 atoms, 25 bonds, 3 residues, 1 model selected
> select #2.2/B:446-447
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #2.2/B:446-451
47 atoms, 46 bonds, 6 residues, 1 model selected
> select
> #2.2/B:4-6,34-48,60-86,96-108,120-134,148-153,159-175,226-230,233-256,267-273,277-288,291-316,321-336,346-352,357-371,374-388,391-407,412-425,444-450,453-461
2149 atoms, 2193 bonds, 270 residues, 1 model selected
> select #2.2/B:263
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2.2/B:263-264
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #2.2/B:252-253
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #2.2/B:252-253
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #2.2/B:246
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2.2/B:246-247
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #2.2/B:249
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2.2/B:249-251
19 atoms, 18 bonds, 3 residues, 1 model selected
> select #2.2/B:254
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2.2/B:254-256
24 atoms, 23 bonds, 3 residues, 1 model selected
> select #2.2/B:260
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2.2/B:260-262
17 atoms, 16 bonds, 3 residues, 1 model selected
> select #2.2/B:238
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2.2/B:238-239
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #2.2/B:234
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2.2/B:234-236
19 atoms, 18 bonds, 3 residues, 1 model selected
> select #2.2/B:240-241
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #2.2/B:240-243
30 atoms, 29 bonds, 4 residues, 1 model selected
> select #2.2/B:164
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2.2/B:164-165
18 atoms, 18 bonds, 2 residues, 1 model selected
> select #2.2/B:167
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2.2/B:167-169
25 atoms, 25 bonds, 3 residues, 1 model selected
> select #2.2/B:160
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2.2/B:160-161
15 atoms, 15 bonds, 2 residues, 1 model selected
> select #2.2/B:155
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2.2/B:155-158
40 atoms, 41 bonds, 4 residues, 1 model selected
> select #2.2/B:233
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2.2/B:233-237
28 atoms, 27 bonds, 5 residues, 1 model selected
> select #2.2/B:241
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2.2/B:163-241
369 atoms, 384 bonds, 46 residues, 1 model selected
> select
> #2.2/B:4-6,34-48,60-86,96-108,120-134,148-153,159-175,226-230,233-256,267-273,277-288,291-316,321-336,346-352,357-371,374-388,391-407,412-425,444-450,453-461
2149 atoms, 2193 bonds, 270 residues, 1 model selected
> select #2.2/B:229-230
21 atoms, 22 bonds, 2 residues, 1 model selected
> select #2.2/B:229-232
33 atoms, 35 bonds, 4 residues, 1 model selected
> select #2.2/B:235
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2.2/B:235-236
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #2.2/B:238-239
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #2.2/B:238-240
18 atoms, 17 bonds, 3 residues, 1 model selected
> select #2.2/B:245
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2.2/B:245-247
21 atoms, 20 bonds, 3 residues, 1 model selected
> select
> #2.2/B:4-6,34-48,60-86,96-108,120-134,148-153,159-175,226-230,233-256,267-273,277-288,291-316,321-336,346-352,357-371,374-388,391-407,412-425,444-450,453-461
2149 atoms, 2193 bonds, 270 residues, 1 model selected
> select #2.2/B:185-186
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #2.2/B:185-224
50 atoms, 50 bonds, 7 residues, 1 model selected
> select #2.2/B:-4
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2.2/B:-4--2
22 atoms, 22 bonds, 3 residues, 1 model selected
> select #2.2/B:0
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2.2/B:0-70
534 atoms, 544 bonds, 71 residues, 1 model selected
> select #2.2/B:435-436
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #2.2/B:435-449
120 atoms, 121 bonds, 15 residues, 1 model selected
> select add #2.2
3597 atoms, 3587 bonds, 548 residues, 1 model selected
> select subtract #2.2
Nothing selected
> close session
> open /Users/marla/Downloads/3tbl.pdb
3tbl.pdb title:
Structure of mono-ubiquitinated PCNA: implications for DNA polymerase
switching and okazaki fragment maturation [more info...]
Chain information for 3tbl.pdb #1
---
Chain | Description | UniProt
A B C | proliferating cell nuclear antigen | PCNA_HUMAN 1-261
D E | ubiquitin | RS27A_HUMAN 1-76
> hide cartoons
> hide atoms
> show cartoons
> split #1
===== Log before crash end =====
Log:
Startup Messages
---
warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr
bundle with that from OME-Zarr bundle
Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
that from NMRSTAR bundle
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,7
Model Number: MRW13D/A
Chip: Apple M3 Pro
Total Number of Cores: 12 (6 performance and 6 efficiency)
Memory: 18 GB
System Firmware Version: 10151.41.12
OS Loader Version: 10151.41.12
Software:
System Software Overview:
System Version: macOS 14.1 (23B2073)
Kernel Version: Darwin 23.1.0
Time since boot: 7 Tage, 5 Stunden und 14 Minuten
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 18
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.1
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
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: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.13
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.3
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.2
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
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: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.0
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.0
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.5.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.8
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
Pillow: 10.0.1
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.3
urllib3: 2.1.0
wcwidth: 0.2.12
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 17 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 17 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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