![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Closed 2 years ago
#9680 closed defect (can't reproduce)
Crash in structure_chain_trace_atoms
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | pett | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-6.2.0-31-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 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 0x00007f526e9f6b80 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/atomic/molobject.py", line 1628 in chain_trace_atoms
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/atomic/structure.py", line 469 in _update_chain_trace_graphics
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/atomic/structure.py", line 375 in _update_graphics
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/atomic/structure.py", line 359 in update_graphics_if_needed
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/atomic/structure.py", line 1809 in _update_graphics_if_needed
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 138 in invoke
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 237 in _activate
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 206 in activate
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 382 in activate_trigger
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/graphics/view.py", line 283 in check_for_drawing_change
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/graphics/view.py", line 635 in drawing_bounds
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/models.py", line 733 in add
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 249 in provider_open
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 119 in cmd_open
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 38 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/open_command/dialog.py", line 162 in _qt_safe
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 87 in _run_code
File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /home/todd/code/nobias/scratch/cache/2023-08-31_07-58-05-776814/trajectory.pdb
Chain information for trajectory.pdb
---
Chain | Description
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A
1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A 1.21/A 1.22/A 1.23/A
1.24/A 1.25/A 1.26/A 1.27/A 1.28/A 1.29/A 1.30/A 1.31/A 1.32/A 1.33/A 1.34/A
1.35/A 1.36/A 1.37/A 1.38/A 1.39/A 1.40/A 1.41/A 1.42/A 1.43/A 1.44/A 1.45/A
1.46/A 1.47/A 1.48/A 1.49/A 1.50/A 1.51/A 1.52/A 1.53/A 1.54/A 1.55/A 1.56/A
1.57/A 1.58/A 1.59/A 1.60/A 1.61/A 1.62/A 1.63/A 1.64/A 1.65/A 1.66/A 1.67/A
1.68/A 1.69/A 1.70/A 1.71/A 1.72/A 1.73/A 1.74/A 1.75/A 1.76/A 1.77/A 1.78/A
1.79/A 1.80/A 1.81/A 1.82/A 1.83/A 1.84/A 1.85/A 1.86/A 1.87/A 1.88/A 1.89/A
1.90/A 1.91/A 1.92/A 1.93/A 1.94/A 1.95/A 1.96/A 1.97/A 1.98/A 1.99/A 1.100/A
1.101/A 1.102/A 1.103/A 1.104/A 1.105/A 1.106/A 1.107/A 1.108/A 1.109/A
1.110/A 1.111/A 1.112/A 1.113/A 1.114/A 1.115/A 1.116/A 1.117/A 1.118/A
1.119/A 1.120/A 1.121/A 1.122/A 1.123/A 1.124/A 1.125/A 1.126/A 1.127/A
1.128/A 1.129/A 1.130/A 1.131/A 1.132/A 1.133/A 1.134/A 1.135/A 1.136/A
1.137/A 1.138/A 1.139/A 1.140/A 1.141/A 1.142/A 1.143/A 1.144/A 1.145/A
1.146/A 1.147/A 1.148/A 1.149/A 1.150/A 1.151/A 1.152/A 1.153/A 1.154/A
1.155/A 1.156/A 1.157/A 1.158/A 1.159/A 1.160/A 1.161/A 1.162/A 1.163/A
1.164/A 1.165/A 1.166/A 1.167/A 1.168/A 1.169/A 1.170/A 1.171/A 1.172/A
1.173/A 1.174/A 1.175/A 1.176/A 1.177/A 1.178/A 1.179/A 1.180/A 1.181/A
1.182/A 1.183/A 1.184/A 1.185/A 1.186/A 1.187/A 1.188/A 1.189/A 1.190/A
1.191/A 1.192/A 1.193/A 1.194/A 1.195/A 1.196/A 1.197/A 1.198/A 1.199/A
1.200/A 1.201/A 1.202/A 1.203/A 1.204/A 1.205/A 1.206/A 1.207/A 1.208/A
1.209/A 1.210/A 1.211/A 1.212/A 1.213/A 1.214/A 1.215/A 1.216/A 1.217/A
1.218/A 1.219/A 1.220/A 1.221/A 1.222/A 1.223/A 1.224/A 1.225/A 1.226/A
1.227/A 1.228/A 1.229/A 1.230/A 1.231/A 1.232/A 1.233/A 1.234/A 1.235/A
1.236/A 1.237/A 1.238/A 1.239/A 1.240/A 1.241/A 1.242/A 1.243/A 1.244/A
1.245/A 1.246/A 1.247/A 1.248/A 1.249/A 1.250/A 1.251/A 1.252/A 1.253/A
1.254/A 1.255/A 1.256/A 1.257/A 1.258/A 1.259/A 1.260/A 1.261/A 1.262/A
1.263/A 1.264/A 1.265/A 1.266/A 1.267/A 1.268/A 1.269/A 1.270/A 1.271/A
1.272/A 1.273/A 1.274/A 1.275/A 1.276/A 1.277/A 1.278/A 1.279/A 1.280/A
1.281/A 1.282/A 1.283/A 1.284/A 1.285/A 1.286/A 1.287/A 1.288/A 1.289/A
1.290/A 1.291/A 1.292/A 1.293/A 1.294/A 1.295/A 1.296/A 1.297/A 1.298/A
1.299/A 1.300/A 1.301/A 1.302/A 1.303/A 1.304/A 1.305/A 1.306/A 1.307/A
1.308/A 1.309/A 1.310/A 1.311/A 1.312/A 1.313/A 1.314/A 1.315/A 1.316/A
1.317/A 1.318/A 1.319/A 1.320/A 1.321/A 1.322/A 1.323/A 1.324/A 1.325/A
1.326/A 1.327/A 1.328/A 1.329/A 1.330/A 1.331/A 1.332/A 1.333/A 1.334/A
1.335/A 1.336/A 1.337/A 1.338/A 1.339/A 1.340/A 1.341/A 1.342/A 1.343/A
1.344/A 1.345/A 1.346/A 1.347/A 1.348/A 1.349/A 1.350/A 1.351/A 1.352/A
1.353/A 1.354/A 1.355/A 1.356/A 1.357/A 1.358/A 1.359/A 1.360/A 1.361/A
1.362/A 1.363/A 1.364/A 1.365/A 1.366/A 1.367/A 1.368/A 1.369/A 1.370/A
1.371/A 1.372/A 1.373/A 1.374/A 1.375/A 1.376/A 1.377/A 1.378/A 1.379/A
1.380/A 1.381/A 1.382/A 1.383/A 1.384/A 1.385/A 1.386/A 1.387/A 1.388/A
1.389/A 1.390/A 1.391/A 1.392/A 1.393/A 1.394/A 1.395/A 1.396/A 1.397/A
1.398/A 1.399/A 1.400/A 1.401/A 1.402/A 1.403/A 1.404/A 1.405/A 1.406/A
1.407/A 1.408/A 1.409/A 1.410/A 1.411/A 1.412/A 1.413/A 1.414/A 1.415/A
1.416/A 1.417/A 1.418/A 1.419/A 1.420/A 1.421/A 1.422/A 1.423/A 1.424/A
1.425/A 1.426/A 1.427/A 1.428/A 1.429/A 1.430/A 1.431/A 1.432/A 1.433/A
1.434/A 1.435/A 1.436/A 1.437/A 1.438/A 1.439/A 1.440/A 1.441/A 1.442/A
1.443/A 1.444/A 1.445/A 1.446/A 1.447/A 1.448/A 1.449/A 1.450/A 1.451/A
1.452/A 1.453/A 1.454/A 1.455/A 1.456/A 1.457/A 1.458/A 1.459/A 1.460/A
1.461/A 1.462/A 1.463/A 1.464/A 1.465/A 1.466/A 1.467/A 1.468/A 1.469/A
1.470/A 1.471/A 1.472/A 1.473/A 1.474/A 1.475/A 1.476/A 1.477/A 1.478/A
1.479/A 1.480/A 1.481/A 1.482/A 1.483/A 1.484/A 1.485/A 1.486/A 1.487/A
1.488/A 1.489/A 1.490/A 1.491/A 1.492/A 1.493/A 1.494/A 1.495/A 1.496/A
1.497/A 1.498/A 1.499/A 1.500/A 1.501/A 1.502/A 1.503/A 1.504/A 1.505/A
1.506/A 1.507/A 1.508/A 1.509/A 1.510/A 1.511/A 1.512/A 1.513/A 1.514/A
1.515/A 1.516/A 1.517/A 1.518/A 1.519/A 1.520/A 1.521/A 1.522/A 1.523/A
1.524/A 1.525/A 1.526/A 1.527/A 1.528/A 1.529/A 1.530/A 1.531/A 1.532/A
1.533/A 1.534/A 1.535/A 1.536/A 1.537/A 1.538/A 1.539/A 1.540/A 1.541/A
1.542/A 1.543/A 1.544/A 1.545/A 1.546/A 1.547/A 1.548/A 1.549/A 1.550/A
1.551/A 1.552/A 1.553/A 1.554/A 1.555/A 1.556/A 1.557/A 1.558/A 1.559/A
1.560/A 1.561/A 1.562/A 1.563/A 1.564/A 1.565/A 1.566/A 1.567/A 1.568/A
1.569/A 1.570/A 1.571/A 1.572/A 1.573/A 1.574/A 1.575/A 1.576/A 1.577/A
1.578/A 1.579/A 1.580/A 1.581/A 1.582/A 1.583/A 1.584/A 1.585/A 1.586/A
1.587/A 1.588/A 1.589/A 1.590/A 1.591/A 1.592/A 1.593/A 1.594/A 1.595/A
1.596/A 1.597/A 1.598/A 1.599/A 1.600/A 1.601/A 1.602/A 1.603/A 1.604/A
1.605/A 1.606/A 1.607/A 1.608/A 1.609/A 1.610/A 1.611/A 1.612/A 1.613/A
1.614/A 1.615/A 1.616/A 1.617/A 1.618/A 1.619/A 1.620/A 1.621/A 1.622/A
1.623/A 1.624/A 1.625/A 1.626/A 1.627/A 1.628/A 1.629/A 1.630/A 1.631/A
1.632/A 1.633/A 1.634/A 1.635/A 1.636/A 1.637/A 1.638/A 1.639/A 1.640/A
1.641/A 1.642/A 1.643/A 1.644/A 1.645/A 1.646/A 1.647/A 1.648/A 1.649/A
1.650/A 1.651/A 1.652/A 1.653/A 1.654/A 1.655/A 1.656/A 1.657/A 1.658/A
1.659/A 1.660/A 1.661/A 1.662/A 1.663/A 1.664/A 1.665/A 1.666/A 1.667/A
1.668/A 1.669/A 1.670/A 1.671/A 1.672/A 1.673/A 1.674/A 1.675/A 1.676/A
1.677/A 1.678/A 1.679/A 1.680/A 1.681/A 1.682/A 1.683/A 1.684/A 1.685/A
1.686/A 1.687/A 1.688/A 1.689/A 1.690/A 1.691/A 1.692/A 1.693/A 1.694/A
1.695/A 1.696/A 1.697/A 1.698/A 1.699/A 1.700/A 1.701/A 1.702/A 1.703/A
1.704/A 1.705/A 1.706/A 1.707/A 1.708/A 1.709/A 1.710/A 1.711/A 1.712/A
1.713/A 1.714/A 1.715/A 1.716/A 1.717/A 1.718/A 1.719/A 1.720/A 1.721/A
1.722/A 1.723/A 1.724/A 1.725/A 1.726/A 1.727/A 1.728/A 1.729/A 1.730/A
1.731/A 1.732/A 1.733/A 1.734/A 1.735/A 1.736/A 1.737/A 1.738/A 1.739/A
1.740/A 1.741/A 1.742/A 1.743/A 1.744/A 1.745/A 1.746/A 1.747/A 1.748/A
1.749/A 1.750/A 1.751/A 1.752/A 1.753/A 1.754/A 1.755/A 1.756/A 1.757/A
1.758/A 1.759/A 1.760/A 1.761/A 1.762/A 1.763/A 1.764/A 1.765/A 1.766/A
1.767/A 1.768/A 1.769/A 1.770/A 1.771/A 1.772/A 1.773/A 1.774/A 1.775/A
1.776/A 1.777/A 1.778/A 1.779/A 1.780/A 1.781/A 1.782/A 1.783/A 1.784/A
1.785/A 1.786/A 1.787/A 1.788/A 1.789/A 1.790/A 1.791/A 1.792/A 1.793/A
1.794/A 1.795/A 1.796/A 1.797/A 1.798/A 1.799/A 1.800/A 1.801/A 1.802/A
1.803/A 1.804/A 1.805/A 1.806/A 1.807/A 1.808/A 1.809/A 1.810/A 1.811/A
1.812/A 1.813/A 1.814/A 1.815/A 1.816/A 1.817/A 1.818/A 1.819/A 1.820/A
1.821/A 1.822/A 1.823/A 1.824/A 1.825/A 1.826/A 1.827/A 1.828/A 1.829/A
1.830/A 1.831/A 1.832/A 1.833/A 1.834/A 1.835/A 1.836/A 1.837/A 1.838/A
1.839/A 1.840/A 1.841/A 1.842/A 1.843/A 1.844/A 1.845/A 1.846/A 1.847/A
1.848/A 1.849/A 1.850/A 1.851/A 1.852/A 1.853/A 1.854/A 1.855/A 1.856/A
1.857/A 1.858/A 1.859/A 1.860/A 1.861/A 1.862/A 1.863/A 1.864/A 1.865/A
1.866/A 1.867/A 1.868/A 1.869/A 1.870/A 1.871/A 1.872/A 1.873/A 1.874/A
1.875/A 1.876/A 1.877/A 1.878/A 1.879/A 1.880/A 1.881/A 1.882/A 1.883/A
1.884/A 1.885/A 1.886/A 1.887/A 1.888/A 1.889/A 1.890/A 1.891/A 1.892/A
1.893/A 1.894/A 1.895/A 1.896/A 1.897/A 1.898/A 1.899/A 1.900/A 1.901/A
1.902/A 1.903/A 1.904/A 1.905/A 1.906/A 1.907/A 1.908/A 1.909/A 1.910/A
1.911/A 1.912/A 1.913/A 1.914/A 1.915/A 1.916/A 1.917/A 1.918/A 1.919/A
1.920/A 1.921/A 1.922/A 1.923/A 1.924/A 1.925/A 1.926/A 1.927/A 1.928/A
1.929/A 1.930/A 1.931/A 1.932/A 1.933/A 1.934/A 1.935/A 1.936/A 1.937/A
1.938/A 1.939/A 1.940/A 1.941/A 1.942/A 1.943/A 1.944/A 1.945/A 1.946/A
1.947/A 1.948/A 1.949/A 1.950/A 1.951/A 1.952/A 1.953/A 1.954/A 1.955/A
1.956/A 1.957/A 1.958/A 1.959/A 1.960/A 1.961/A 1.962/A 1.963/A 1.964/A
1.965/A 1.966/A 1.967/A 1.968/A 1.969/A 1.970/A 1.971/A 1.972/A 1.973/A
1.974/A 1.975/A 1.976/A 1.977/A 1.978/A 1.979/A 1.980/A 1.981/A 1.982/A
1.983/A 1.984/A 1.985/A 1.986/A 1.987/A 1.988/A 1.989/A 1.990/A 1.991/A
1.992/A 1.993/A 1.994/A 1.995/A 1.996/A 1.997/A 1.998/A 1.999/A 1.1000/A | No
description available
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 3.3.0 NVIDIA 530.30.02
OpenGL renderer: NVIDIA GeForce RTX 4090/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: ASUS
Model: System Product Name
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 24 AMD Ryzen 9 5900X 12-Core Processor
Cache Size: 512 KB
Memory:
total used free shared buff/cache available
Mem: 125Gi 34Gi 60Gi 132Mi 31Gi 90Gi
Swap: 2.0Gi 0B 2.0Gi
Graphics:
07:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:2684] (rev a1)
Subsystem: PNY Device [196e:13ad]
Kernel driver in use: nvidia
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2023.5.7
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
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: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
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: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.21.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
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: 1.1.1
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: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.6.0
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
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: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
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: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
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: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
distro: 1.7.0
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
MolecularDynamicsViewer: 1.4
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 23.1
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.2.1
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
Send2Trash: 1.8.2
SEQCROW: 1.7.3
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (2)
comment:1 by , 2 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Graphics |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash in structure_chain_trace_atoms |
comment:2 by , 2 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
Crashed in structure_chain_trace_atoms(void *mol) C++ code in molc.cpp after opening 1000 models from a PDB file.
Would need a C++ stack trace or the input file to debug further.
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Routine was largely written by you, with tweaks by me. Don't know that anything can really be done without a test case.