Opened 5 months ago

Closed 5 months ago

#17865 closed defect (limitation)

Large number of structures → memory exhaustion

Reported by: alexandra.zahradnikova@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Platform Version:
Keywords: Cc: Tom Goddard
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: 1.10.dev202504240337 (2025-04-24 03:37:50 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
ChimeraX crashed when trying to open a very large file with one model containing 1000 submodels. This file (size 5 GB) was created by saving a ChimeraX session with 1000 frames (size of the CXS file 800 MB)  as a pdb file. It appears that the file was successfully opened since in the log there are all submodels listed.
Windows fatal exception: access violation

Current thread 0x00000f2c (most recent call first):
Windows fatal exception: access violation

===== Log before crash start =====
UCSF ChimeraX version: 1.10.dev202504240337 (2025-04-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> cd F:\Simulations_F\ProtLig_F\7tdg_WT_15

Current working directory is: F:\Simulations_F\ProtLig_F\7tdg_WT_15  

> open F:/Simulations_F/ProtLig_F/7tdg_WT_15/7tdg_WT15_ProtLig.pdb

Chain information for 7tdg_WT15_ProtLig.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 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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 1.1/B 1.2/B 1.3/B 1.4/B 1.5/B 1.6/B 1.7/B 1.8/B 1.9/B 1.10/B 1.11/B 1.12/B 1.13/B 1.14/B 1.15/B 1.16/B 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1.927/D 1.928/D 1.929/D 1.930/D 1.931/D 1.932/D 1.933/D 1.934/D 1.935/D 1.936/D 1.937/D 1.938/D 1.939/D 1.940/D 1.941/D 1.942/D 1.943/D 1.944/D 1.945/D 1.946/D 1.947/D 1.948/D 1.949/D 1.950/D 1.951/D 1.952/D 1.953/D 1.954/D 1.955/D 1.956/D 1.957/D 1.958/D 1.959/D 1.960/D 1.961/D 1.962/D 1.963/D 1.964/D 1.965/D 1.966/D 1.967/D 1.968/D 1.969/D 1.970/D 1.971/D 1.972/D 1.973/D 1.974/D 1.975/D 1.976/D 1.977/D 1.978/D 1.979/D 1.980/D 1.981/D 1.982/D 1.983/D 1.984/D 1.985/D 1.986/D 1.987/D 1.988/D 1.989/D 1.990/D 1.991/D 1.992/D 1.993/D 1.994/D 1.995/D 1.996/D 1.997/D 1.998/D 1.999/D 1.1000/D | No description available  
  


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.10.dev202504240337 (2025-04-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> help help:user




OpenGL version: 3.3.0 NVIDIA 572.76
OpenGL renderer: NVIDIA GeForce MX550/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: Dell Inc.
Model: Latitude 5431
OS: Microsoft Windows 11 Pro (Build 26100)
Memory: 67,904,073,728
MaxProcessMemory: 137,438,953,344
CPU: 16 12th Gen Intel(R) Core(TM) i5-1250P
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: 3.3.1
    build: 1.2.2.post1
    certifi: 2025.1.31
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.1
    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
    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: 1.60.5
    ChimeraX-AtomicLibrary: 14.1.15
    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: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    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: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.dev202504240337
    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: 1.6.1
    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: 2.7.9
    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: 1.1.1
    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: 1.1.4
    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
    DateTime: 5.5
    debugpy: 1.8.14
    decorator: 5.2.1
    docutils: 0.21.2
    et_xmlfile: 2.0.0
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.57.0
    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: 8.1.6
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.14
    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
    openpyxl: 3.1.5
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pathlib: 1.0.1
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.7
    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: 2.2.0
    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
    zope.interface: 7.2

Change History (5)

comment:1 by alexandra.zahradnikova@…, 5 months ago 

Dear All
I have re-run the script on another computer and it seems that the error was caused by ChimeraX using up all the memory (>40 GB)  while reading a 5-GB file.
Besta
Sasha Zahradnikova

-----Original Message-----
From: ChimeraX [mailto:ChimeraX-bugs-admin@cgl.ucsf.edu] 
Sent: Saturday, May 31, 2025 9:32 PM
To: alexandra.zahradnikova@savba.sk
Subject: Re: [ChimeraX] #17865: ChimeraX bug report submission

#17865: ChimeraX bug report submission
--------------------------------------+-----------------------------
 Reporter:  alexandra.zahradnikova@\u2026  |                Type:  defect
   Status:  new                       |            Priority:  normal
Component:  Unassigned                |          Blocked By:
 Blocking:                            |  Notify when closed:
--------------------------------------+-----------------------------

comment:2 by Eric Pettersen, 5 months ago

Cc: Tom Goddard added
Component: Unassigned → Platform
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Large number of structures → memory exhaustion

comment:3 by Eric Pettersen, 5 months ago

Status: accepted → feedback

Hi Sasha,

ChimeraX is going to be a lot less memory efficient opening 1000 structures representing trajectory frames than it is opening the corresponding trajectory. This is because for the individual-structure case it has to make 1000 copies of the non-coordinate structure/chain/residue/atom information (e.g. ribbon settings, secondary structure assignments, atomic radii, etc.) where the trajectory only needs one copy. I'm guessing if you had opened that PDB file with "coordsets true" (making it a trajectory) it would have worked.
Perhaps if you described what you were hoping to accomplish with the 1000 individual structures I could offer alternatives that might work.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:4 by alexandra.zahradnikova@…, 5 months ago 

Hi EricYes I understand. I was trying to calculate RMSF with pdbs because I could not figure out the structure of the objects for the RMSF calculation from a trajectory that you suggested to me a while ago. But now I saw that it is the only way so I have the script almost ready - I just have to finish the output to an Excel file. Thanks for the feedback and for the explanation, I haven't realized that so much info is stored with each structure on top of pdb data. Best regards SashaSent from my Galaxy
-------- Original message --------From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> Date: 02/06/2025  20:31  (GMT+01:00) To: pett@cgl.ucsf.edu, alexandra.zahradnikova@savba.sk Cc: goddard@cgl.ucsf.edu Subject: Re: [ChimeraX] #17865: Large number of structures → memory exhaustion #17865: Large number of structures → memory exhaustion-----------------------------------------------+----------------------          Reporter:  alexandra.zahradnikova@…  |      Owner:  pett              Type:  defect                    |     Status:  feedback          Priority:  normal                    |  Milestone:         Component:  Platform                  |    Version:        Resolution:                            |   Keywords:        Blocked By:                            |   Blocking:Notify when closed:                            |   Platform:  all           Project:  ChimeraX                  |-----------------------------------------------+----------------------Changes (by pett): * status:  accepted => feedbackComment: Hi Sasha,         ChimeraX is going to be a lot less memory efficient opening 1000 structures representing trajectory frames than it is opening the corresponding trajectory.  This is because for the individual-structure case it has to make 1000 copies of the non-coordinate structure/chain/residue/atom information (e.g. ribbon settings, secondary structure assignments, atomic radii, etc.) where the trajectory only needs one copy.  I'm guessing if you had opened that PDB file with "coordsets true" (making it a trajectory) it would have worked.         Perhaps if you described what you were hoping to accomplish with the 1000 individual structures I could offer alternatives that might work. --Eric         Eric Pettersen         UCSF Computer Graphics Lab-- Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/17865#comment:3>ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>ChimeraX Issue Tracker

comment:5 by Eric Pettersen, 5 months ago

Resolution: → limitation
Status: feedback → closed

Glad you've almost gotten the script working. I'll probably have built-in RMSF plotting/saving in a few months, but it could be several months, so finishing your script is definitely the way to go.

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