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Opened 5 months ago
Closed 5 months ago
#17860 closed defect (can't reproduce)
Crash in compute_cap
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Surface | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.26100
ChimeraX Version: 1.11.dev202505140045 (2025-05-14 00:45:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Thread 0x0000d6b4 (most recent call first):
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\multiprocessing\pool.py", line 579 in _handle_results
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\threading.py", line 975 in run
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\threading.py", line 1038 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\threading.py", line 995 in _bootstrap
Thread 0x0000db5c (most recent call first):
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\multiprocessing\pool.py", line 531 in _handle_tasks
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\threading.py", line 975 in run
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\threading.py", line 1038 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\threading.py", line 995 in _bootstrap
Thread 0x0000b980 (most recent call first):
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\multiprocessing\connection.py", line 810 in _exhaustive_wait
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\multiprocessing\connection.py", line 878 in wait
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\multiprocessing\pool.py", line 502 in _wait_for_updates
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\multiprocessing\pool.py", line 522 in _handle_workers
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\threading.py", line 975 in run
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\threading.py", line 1038 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\threading.py", line 995 in _bootstrap
Thread 0x0000d694 (most recent call first):
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\threading.py", line 975 in run
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\threading.py", line 1038 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\threading.py", line 995 in _bootstrap
Thread 0x0000bf58 (most recent call first):
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\threading.py", line 975 in run
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\threading.py", line 1038 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\threading.py", line 995 in _bootstrap
Thread 0x00008f18 (most recent call first):
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\threading.py", line 975 in run
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\threading.py", line 1038 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\threading.py", line 995 in _bootstrap
Thread 0x0000dac0 (most recent call first):
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\threading.py", line 975 in run
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\threading.py", line 1038 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\threading.py", line 995 in _bootstrap
Thread 0x0000d238 (most recent call first):
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\threading.py", line 975 in run
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\threading.py", line 1038 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\threading.py", line 995 in _bootstrap
Thread 0x00007b0c (most recent call first):
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\threading.py", line 975 in run
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\threading.py", line 1038 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\threading.py", line 995 in _bootstrap
Thread 0x00000efc (most recent call first):
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\threading.py", line 975 in run
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\threading.py", line 1038 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\threading.py", line 995 in _bootstrap
Thread 0x0000da0c (most recent call first):
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\threading.py", line 975 in run
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\threading.py", line 1038 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\threading.py", line 995 in _bootstrap
Current thread 0x00008208 (most recent call first):
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\site-packages\chimerax\surface\cap.py", line 99 in compute_cap
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\site-packages\chimerax\surface\cap.py", line 41 in show_surface_clip_caps
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\site-packages\chimerax\surface\cap.py", line 28 in update_clip_caps
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\site-packages\chimerax\core\updateloop.py", line 73 in draw_new_frame
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\site-packages\chimerax\core\updateloop.py", line 150 in _redraw_timer_callback
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\site-packages\chimerax\core\__main__.py", line 1057 in init
File "C:\Program Files\ChimeraX 1.11.dev202505140045\bin\Lib\site-packages\chimerax\core\__main__.py", line 1220 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: _win32sysloader, win32api, win32com.shell.shell, chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, psutil._psutil_windows, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, 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, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lz4._version, lz4.frame._frame, msgpack._cmsgpack, PIL._imaging, chimerax.core._serialize, PIL._imagingmath (total: 55)
===== Log before crash start =====
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.11.dev202505140045 (2025-05-14)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 6ole
Summary of feedback from opening 6ole fetched from pdb
---
warnings | Atom OP1 has no neighbors to form bonds with according to residue template for U /w:13
Atom OP2 has no neighbors to form bonds with according to residue template for
U /w:13
6ole title:
Human ribosome nascent chain complex (CDH1-RNC) stalled by a drug-like
molecule with AP and PE tRNAs [more info...]
Chain information for 6ole #1
---
Chain | Description | UniProt
A | 60S ribosomal protein L8 | RL8_HUMAN 2-253
B | 60S ribosomal protein L3 | RL3_HUMAN 2-398
C | 60S ribosomal protein L4 | RL4_HUMAN 3-365
D | 5.8S ribosomal RNA |
E | 5S ribosomal RNA |
F | 60S ribosomal protein L5 | RL5_HUMAN 4-297
G | 60S ribosomal protein L6 | RL6_HUMAN 42-288
H | 60S ribosomal protein L7 | RL7_HUMAN 24-248
I | 60S ribosomal protein L7a | RL7A_HUMAN 29-262
J | 60S ribosomal protein L9 | RL9_HUMAN 1-191
K | 60S ribosomal protein L10 | RL10_HUMAN 3-213
L | 60S ribosomal protein L11 | RL11_HUMAN 9-177
M | 60S ribosomal protein L13 | RL13_HUMAN 2-206
N | 60S ribosomal protein L14 | RL14_HUMAN 2-140
O | 60S ribosomal protein L15 | RL15_HUMAN 2-204
P | 60S ribosomal protein L13a | RL13A_HUMAN 5-199
Q | 60S ribosomal protein L17 | RL17_HUMAN 2-154
R | 60S ribosomal protein L18 | RL18_HUMAN 2-188
S | 60S ribosomal protein L19 | RL19_HUMAN 2-182
S2 | 18S ribosomal RNA |
SA | 40S ribosomal protein SA | RSSA_HUMAN 3-223
SB | 40S ribosomal protein S3a | RS3A_HUMAN 21-234
SC | 40S ribosomal protein S2 | RS2_HUMAN 59-278
SD | 40S ribosomal protein S3 | RS3_HUMAN 2-227
SE | 40S ribosomal protein S4, X isoform | RS4X_HUMAN 2-260
SF | 40S ribosomal protein S5 | RS5_HUMAN 16-204
SG | 40S ribosomal protein S6 | RS6_HUMAN 1-237
SH | 40S ribosomal protein S7 | RS7_HUMAN 5-193
SI | 40S ribosomal protein S8 | RS8_HUMAN 2-205
SJ | 40S ribosomal protein S9 | RS9_HUMAN 2-186
SK | 40S ribosomal protein S10 | RS10_HUMAN 1-98
SL | 40S ribosomal protein S11 | RS11_HUMAN 2-154
SM | 40S ribosomal protein S12 | RS12_HUMAN 15-132
SN | 40S ribosomal protein S13 | RS13_HUMAN 2-151
SO | 40S ribosomal protein S14 | RS14_HUMAN 15-151
SP | 40S ribosomal protein S15 | RS15_HUMAN 10-136
SQ | 40S ribosomal protein S16 | RS16_HUMAN 1-146
SR | 40S ribosomal protein S17 | RS17_HUMAN 2-135
SS | 40S ribosomal protein S18 | RS18_HUMAN 1-145
ST | 40S ribosomal protein S19 | RS19_HUMAN 2-144
SU | 40S ribosomal protein S20 | RS20_HUMAN 16-119
SV | 40S ribosomal protein S21 | RS21_HUMAN 1-82
SW | 40S ribosomal protein S15a | RS15A_HUMAN 2-130
SX | 40S ribosomal protein S23 | RS23_HUMAN 2-142
SY | 40S ribosomal protein S24 | RS24_HUMAN 2-132
SZ | 40S ribosomal protein S25 | RS25_HUMAN 43-115
Sa | 40S ribosomal protein S26 | RS26_HUMAN 2-103
Sb | 40S ribosomal protein S27 | RS27_HUMAN 2-83
Sc | 40S ribosomal protein S28 | RS28_HUMAN 5-68
Sd | 40S ribosomal protein S29 | RS29_HUMAN 2-56
Se | 40S ribosomal protein S30 | E9PR30_HUMAN 2-58
Sf | 40S ribosomal protein S27a | RS27A_HUMAN 85-151
Sg | Receptor of activated protein C kinase 1 | RACK1_HUMAN 3-314
T | 60S ribosomal protein L18a | RL18A_HUMAN 1-175
U | 60S ribosomal protein L21 | RL21_HUMAN 2-158
V | 60S ribosomal protein L22 | RL22_HUMAN 18-116
W | 60S ribosomal protein L23 | Q9BTQ7_HUMAN 12-140
X | 60S ribosomal protein L24 | RL24_HUMAN 2-62
Y | 60S ribosomal protein L23a | RL23A_HUMAN 39-155
Z | 60S ribosomal protein L26 | RL26_HUMAN 1-134
a | 60S ribosomal protein L27 | RL27_HUMAN 3-136
b | 60S ribosomal protein L27a | RL27A_HUMAN 2-148
c | 60S ribosomal protein L29 | RL29_HUMAN 2-122
d | 60S ribosomal protein L30 | RL30_HUMAN 7-109
e | 60S ribosomal protein L31 | RL31_HUMAN 18-123
f | 60S ribosomal protein L32 | RL32_HUMAN 2-130
g | 60S ribosomal protein L35a | RL35A_HUMAN 2-110
h | 60S ribosomal protein L34 | RL34_HUMAN 2-115
i | 60S ribosomal protein L35 | RL35_HUMAN 2-123
j | 60S ribosomal protein L36 | RL36_HUMAN 5-101
k | 60S ribosomal protein L37 | RL37_HUMAN 2-85
l | 60S ribosomal protein L38 | RL38_HUMAN 2-70
m | 60S ribosomal protein L39 | RL39_HUMAN 2-51
n | 60S ribosomal protein L40 | RL40_HUMAN 78-127
o | 60S ribosomal protein L41 | RL41_HUMAN 1-25
p | 60S ribosomal protein L36a | RL36A_HUMAN 2-106
q | 60S ribosomal protein L37a | RL37A_HUMAN 2-92
r | 60S ribosomal protein L28 | RL28_HUMAN 2-123
t | 28S ribosomal RNA |
u | AP RNA |
v | PE RNA |
w | mRNA |
y | Cadherin-1 | CADH1_HUMAN 1-39
Non-standard residues in 6ole #1
---
B8N —
(2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic
acid
MG — magnesium ion
MVM —
N-(3-chloropyridin-2-yl)-N-[(3R)-piperidin-3-yl]-4-(3H-[1,2,3]triazolo[4,5-b]pyridin-3-yl)benzamide
ZN — zinc ion
24 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> cartoon
> style stick
Changed 214927 atom styles
> select /y /w /t
77844 atoms, 87051 bonds, 3212 pseudobonds, 3663 residues, 3 models selected
> select add protein
169272 atoms, 180111 bonds, 3216 pseudobonds, 15015 residues, 4 models
selected
> select ~sel
45655 atoms, 50978 bonds, 1763 pseudobonds, 2187 residues, 3 models selected
> hide sel
> hide sel target c
> hide
> select :MVM
31 atoms, 35 bonds, 1 residue, 1 model selected
> show sel
> view sel
> ui tool show "Side View"
> select /t
77338 atoms, 86518 bonds, 3212 pseudobonds, 3613 residues, 3 models selected
> surface sel
> view sel
> select :MVM
31 atoms, 35 bonds, 1 residue, 1 model selected
> view sel
> hide surfaces
> select /w
213 atoms, 235 bonds, 10 residues, 1 model selected
> view sel
> select /y
293 atoms, 298 bonds, 40 residues, 1 model selected
> view sel
> show /w
> select add /w
506 atoms, 533 bonds, 50 residues, 1 model selected
> view sel
> vr true
> lighting simple
started SteamVR rendering
> view :MVM
> show :MVM
> select /t /y :MVM
77369 atoms, 86553 bonds, 3212 pseudobonds, 3614 residues, 3 models selected
> select ~sel
137558 atoms, 144536 bonds, 1805 pseudobonds, 13588 residues, 8 models
selected
> hide sel
> hide sel target c
> show /y
> cartoon
> hide cartoons
> cartoon sel
> show
> cartoon
> hide
> select :MVM
31 atoms, 35 bonds, 1 residue, 1 model selected
> show sel
> select /t /y
77631 atoms, 86816 bonds, 3212 pseudobonds, 3653 residues, 3 models selected
> sel~sel
Unknown command: sel~sel
> select ~ sel
137296 atoms, 144273 bonds, 1805 pseudobonds, 13549 residues, 8 models
selected
> hide sel target c
> surface /t
> view :MVM
> transparency 40
> select /w
213 atoms, 235 bonds, 10 residues, 1 model selected
> show sel
> select /w
213 atoms, 235 bonds, 10 residues, 1 model selected
> view sel
> cartoon sel
> select /y
293 atoms, 298 bonds, 40 residues, 1 model selected
> select :40
692 atoms, 645 bonds, 75 residues, 1 model selected
> select /y :40
Nothing selected
> view sel
No objects specified.
> show /y
> hide surfaces
> select /u /v
3233 atoms, 3606 bonds, 130 pseudobonds, 154 residues, 2 models selected
> show sel
> cartoon sel
> surface /t
> ~select
Nothing selected
> transparency 10
> save E:/exit-funnel-session.cxs
> select /Q
1242 atoms, 1268 bonds, 153 residues, 1 model selected
> show sel
> cartoon sel
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.11.dev202505140045 (2025-05-14)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 3.3.0 NVIDIA 572.16
OpenGL renderer: NVIDIA GeForce RTX 2070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows
Manufacturer: HP
Model: OMEN by HP Obelisk Desktop 875-0xxx
OS: Microsoft Windows 11 Home (Build 26100)
Memory: 34,206,519,296
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-9700 CPU @ 3.00GHz
OSLanguage: en-US
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.3.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.3.2
build: 1.2.2.post1
certifi: 2025.4.26
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.3
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.18
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: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
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: 1.2.6
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.dev202505140045
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: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.1
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
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
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
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-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
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: 1.45.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.10
contourpy: 1.3.2
coverage: 7.8.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.58.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.13.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.5.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pynmrstar: 3.3.5
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
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.3.5
pytest-cov: 6.1.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pywin32: 310
pyzmq: 26.4.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
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: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.13.2
tzdata: 2025.2
urllib3: 2.4.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
WMI: 1.5.1
Change History (2)
comment:1 by , 5 months ago
| Component: | Unassigned → Surface |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash in compute_cap |
comment:2 by , 5 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
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Crashed in the C++ cap computation. Haven't seen this crash in the last 4 years and saw it a few times before that. Could be crashing in gluTess*() libGLU routine which is used to triangulate the crash.