Opened 5 years ago

Closed 5 years ago

Last modified 5 years ago

#4212 closed defect (can't reproduce)

Timeout writing session file

Reported by: weberm@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Sessions Version:
Keywords: Cc: Greg Couch
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
Upon saving of sessions after writing of image snapshots (on white background)to disk, ChimeraX ends in an endless loop in attempting to write the file to SSD when using PDB code 3q1r or 3zd5 (relatively small; 16 GB of RAM).
Error message: SHGetFileInfo() timed out for C:\Users\weber\Desktop\AG Falcone_work\Parasitologie-Seminar 2021-02-05\PDB

Log:
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Users/weber/Desktop/AG Falcone_work/Parasitologie-Seminar
> 2021-02-05/PDB/3q1r_holoRNaseP_THEMA.cif"

3q1r_holoRNaseP_THEMA.cif title:  
Crystal structure of a bacterial RNase P holoenzyme in complex with TRNA and
in the presence of 5' leader [more info...]  
  
Chain information for 3q1r_holoRNaseP_THEMA.cif #1  
---  
Chain | Description  
A | Ribonuclease P protein component  
B | RNase P RNA  
C | TRNA (phe)  
D | TRNA 5' leader  
  
Non-standard residues in 3q1r_holoRNaseP_THEMA.cif #1  
---  
MG — magnesium ion  
  

> lighting full

> nucleotides tube/slab shape box

> color bychain

> show surfaces

> transparency 70

> hide surfaces

> show surfaces

> hide surfaces

> show surfaces

> save C:\Users\weber\Desktop\image1.png supersample 3

> set bgColor white

> save C:\Users\weber\Desktop\image2.png supersample 3

> set bgColor black

SHGetFileInfo() timed out for C:\Users\weber\Desktop\AG
Falcone_work\Parasitologie-Seminar 2021-02-05\PDB  

SHGetFileInfo() timed out for C:\Users\weber\Desktop\AG
Falcone_work\Parasitologie-Seminar 2021-02-05\PDB\3zd5_Hammerhead_SCHMA.cxs  

SHGetFileInfo() timed out for C:\Users\weber\Desktop\AG
Falcone_work\Parasitologie-Seminar 2021-02-05\PDB\3zd5_Hammerhead_SCHMA.cxs  

SHGetFileInfo() timed out for C:\Users\weber\Desktop\AG
Falcone_work\Parasitologie-Seminar 2021-02-05\PDB  

SHGetFileInfo() timed out for C:\Users\weber\Desktop\AG
Falcone_work\Parasitologie-Seminar 2021-02-05\PDB  

SHGetFileInfo() timed out for C:\Users\weber\Desktop\AG
Falcone_work\Parasitologie-Seminar 2021-02-05\PDB  

SHGetFileInfo() timed out for C:\Users\weber\Desktop\AG
Falcone_work\Parasitologie-Seminar 2021-02-05\PDB\3zd5_Hammerhead_SCHMA.cxs  

SHGetFileInfo() timed out for C:\Users\weber\Desktop\AG
Falcone_work\Parasitologie-Seminar 2021-02-05\PDB  

SHGetFileInfo() timed out for C:\Users\weber\Desktop\AG
Falcone_work\Parasitologie-Seminar 2021-02-05\PDB  

SHGetFileInfo() timed out for C:\Users\weber\Desktop\AG
Falcone_work\Parasitologie-Seminar 2021-02-05\PDB\3zd5_Hammerhead_SCHMA.cxs  

SHGetFileInfo() timed out for C:\Users\weber\Desktop\AG
Falcone_work\Parasitologie-Seminar 2021-02-05\PDB  

SHGetFileInfo() timed out for C:\Users\weber\Desktop\AG
Falcone_work\Parasitologie-Seminar 2021-02-05\PDB  

SHGetFileInfo() timed out for C:\Users\weber\Desktop\AG
Falcone_work\Parasitologie-Seminar 2021-02-05\PDB\3zd5_Hammerhead_SCHMA.cxs  

SHGetFileInfo() timed out for C:\Users\weber\Desktop\AG
Falcone_work\Parasitologie-Seminar 2021-02-05\PDB  

SHGetFileInfo() timed out for C:\Users\weber\Desktop\AG
Falcone_work\Parasitologie-Seminar 2021-02-05\PDB  

SHGetFileInfo() timed out for C:\Users\weber\Desktop\AG
Falcone_work\Parasitologie-Seminar 2021-02-05\PDB\3zd5_Hammerhead_SCHMA.cxs  

SHGetFileInfo() timed out for C:\Users\weber\Desktop\AG
Falcone_work\Parasitologie-Seminar 2021-02-05\PDB  

SHGetFileInfo() timed out for C:\Users\weber\Desktop\AG
Falcone_work\Parasitologie-Seminar 2021-02-05\PDB\3zd5_Hammerhead_SCHMA.cxs  

SHGetFileInfo() timed out for C:\Users\weber\Desktop\AG
Falcone_work\Parasitologie-Seminar 2021-02-05\PDB  

SHGetFileInfo() timed out for C:\Users\weber\Desktop\AG
Falcone_work\Parasitologie-Seminar 2021-02-05\PDB\3zd5_Hammerhead_SCHMA.cxs  

SHGetFileInfo() timed out for C:\Users\weber\Desktop\AG
Falcone_work\Parasitologie-Seminar 2021-02-05\PDB  

SHGetFileInfo() timed out for C:\Users\weber\Desktop\AG
Falcone_work\Parasitologie-Seminar 2021-02-05\PDB  

SHGetFileInfo() timed out for C:\Users\weber\Desktop\AG
Falcone_work\Parasitologie-Seminar 2021-02-05\PDB\3zd5_Hammerhead_SCHMA.cxs  

SHGetFileInfo() timed out for C:\Users\weber\Desktop\AG
Falcone_work\Parasitologie-Seminar 2021-02-05\PDB  

SHGetFileInfo() timed out for C:\Users\weber\Desktop\AG
Falcone_work\Parasitologie-Seminar 2021-02-05\PDB  

SHGetFileInfo() timed out for C:\Users\weber\Desktop\AG
Falcone_work\Parasitologie-Seminar 2021-02-05\PDB\3zd5_Hammerhead_SCHMA.cxs  

SHGetFileInfo() timed out for C:\Users\weber\Desktop\AG
Falcone_work\Parasitologie-Seminar 2021-02-05\PDB  

SHGetFileInfo() timed out for C:\Users\weber\Desktop\AG
Falcone_work\Parasitologie-Seminar 2021-02-05\PDB  

SHGetFileInfo() timed out for C:\Users\weber\Desktop\AG
Falcone_work\Parasitologie-Seminar 2021-02-05\PDB\3zd5_Hammerhead_SCHMA.cxs  

SHGetFileInfo() timed out for C:\Users\weber\Desktop\AG
Falcone_work\Parasitologie-Seminar 2021-02-05\PDB  

SHGetFileInfo() timed out for C:\Users\weber\Desktop\AG
Falcone_work\Parasitologie-Seminar 2021-02-05\PDB  

SHGetFileInfo() timed out for C:\Users\weber\Desktop\AG
Falcone_work\Parasitologie-Seminar 2021-02-05\PDB\3zd5_Hammerhead_SCHMA.cxs  

SHGetFileInfo() timed out for C:\Users\weber\Desktop\AG
Falcone_work\Parasitologie-Seminar 2021-02-05\PDB  

SHGetFileInfo() timed out for C:\Users\weber\Desktop\AG
Falcone_work\Parasitologie-Seminar 2021-02-05\PDB  

SHGetFileInfo() timed out for C:\Users\weber\Desktop\AG
Falcone_work\Parasitologie-Seminar 2021-02-05\PDB\3zd5_Hammerhead_SCHMA.cxs  

SHGetFileInfo() timed out for C:\Users\weber\Desktop\AG
Falcone_work\Parasitologie-Seminar 2021-02-05\PDB  




OpenGL version: 3.3.0 NVIDIA 431.53
OpenGL renderer: GeForce GTX 1060/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Alienware
Model: Alienware 13 R3
OS: Microsoft Windows 10 Pro (Build 19041)
Memory: 17,046,663,168
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    gdcm: 2.8.8
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5+mkl
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pywin32: 228
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2
    WMI: 1.5.1

Change History (3)

comment:1 by Eric Pettersen, 5 years ago

Cc: Greg Couch added
Component: Unassigned → Sessions
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Timeout writing session file

Reported by Michael Weber

possibly relevant: ​https://github.com/Slicer/Slicer/issues/4926

comment:2 by Tom Goddard, 5 years ago

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

The error message is from the Qt window toolkit and means it was asking Windows for file system information and it timed out -- maybe that means some disk did not respond. I could not find out online much about SHGetFileInfo() timing out.

Are you trying to save the session using the Save dialog (menu File / Save, or the toolbar Save button)? That would try to show a Save File dialog and that dialog may ask for info about all your disks to show them in the file browser. Even a different disk from the one you are writing to not responding could cause these errors. Possibly if you instead save your session with a typed command

save ~/Desktop/mysession.cxs

it will work without these errors because it won't use the Qt save dialog.

I don't have other ideas. It seems to be a problem with your Windows computer, not with ChimeraX.

in reply to:  3 ; comment:3 by weberm@…, 5 years ago 

Hi,
I tried to reproduce the error myself, but it did not work. Very 
strange, because the entire day I had that problem.
Maybe it was indeed due to a network drive not connecting properly - I 
had several linked on that day (which I did not connect to today).
Thanks anyway for your kind and fast attempt to help and all the 
explanations.
Best regards,
Michael.

P.S.: Maybe one question: I use SwissDock for molecular docking 
experiments and there is an explanation on how to examine the output 
results in Chimera. Unfortunately all those workflows appear not to work 
in ChimeraX - are there any plans (or even already existing 
documentation which very well might have escaped my attention) to get 
these working in ChimeraX as well? Invoking ViewDockX from either the 
menu >tools>general>ViewDockX or by typing the command after having 
loaded a PDB structure plus the docked ligands just results in the 
message "No suitable models found for ViewDockX".

Am 05.02.2021 01:45 schrieb ChimeraX:
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