Context Navigation

← Previous Ticket
Next Ticket →

#17860 closed defect (can't reproduce)

Crash in compute_cap

Reported by:	chimerax-bug-report@…	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 pett, 5 months ago

Component:	Unassigned → Surface
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Crash in compute_cap

comment:2 by Tom Goddard, 5 months ago

Resolution:	→ can't reproduce
Status:	assigned → closed

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.

Note: See TracTickets for help on using tickets.

Download in other formats: