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#9279 closed defect (nonchimerax)

No space left on device

Reported by:	2173910144@…	Owned by:	Eric Pettersen
Priority:	normal	Milestone:
Component:	Input/Output	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open E:\实验\结构\6e9e.pdb format pdb

6e9e.pdb title:  
ESCAS13D-crRNA binary complex [more info...]  
  
Chain information for 6e9e.pdb #1  
---  
Chain | Description | UniProt  
A | ESCAS13D | B0MS50_9FIRM  
B | crRNA (52-mer) |  
  
Non-standard residues in 6e9e.pdb #1  
---  
MG — magnesium ion  
  

> Open 6E9F

Unknown command: Open 6E9F  

> open 6E9F

6e9f title:  
EsCas13d-crRNA-target RNA ternary complex [more info...]  
  
Chain information for 6e9f #2  
---  
Chain | Description | UniProt  
A | EsCas13d | B0MS50_9FIRM  
B | crRNA (52-MER) |  
C | RNA (27-mer) |  
  
Non-standard residues in 6e9f #2  
---  
MG — magnesium ion  
  

> delete #2/C

> morph #1 #2

Computed 51 frame morph #3  

> coordset #3 1,51

> show #3/A:
> 60-63,68,85,86,139,141-143,156,175,532,536,189,520,343,517,575,334,342,186,528,524,
> 346,373,376,377,379,381,386,406,409,435,443,447,581,582,627,630,631,639,641,642,645,676,679,680,720,723,
> 734,742,753,754,761,823,930,932,941,943 atoms

> open 6E9F

6e9f title:  
EsCas13d-crRNA-target RNA ternary complex [more info...]  
  
Chain information for 6e9f #4  
---  
Chain | Description | UniProt  
A | EsCas13d | B0MS50_9FIRM  
B | crRNA (52-MER) |  
C | RNA (27-mer) |  
  
Non-standard residues in 6e9f #4  
---  
MG — magnesium ion  
  

> delete #4/A-B

> crossfade

> hide ~#1,2,3 target ac

> view name p1

> movie record

> coordset #3

Traceback (most recent call last):  
File "F:\software\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "F:\software\ChimeraX 1.3\bin\lib\site-packages\chimerax\movie\movie.py",
line 172, in capture_image  
i.save(save_path, self.img_fmt)  
File "F:\software\ChimeraX 1.3\bin\lib\site-packages\PIL\Image.py", line 2235,
in save  
save_handler(self, fp, filename)  
File "F:\software\ChimeraX 1.3\bin\lib\site-packages\PIL\PpmImagePlugin.py",
line 149, in _save  
ImageFile._save(im, fp, [("raw", (0, 0) + im.size, 0, (rawmode, 0, 1))])  
File "F:\software\ChimeraX 1.3\bin\lib\site-packages\PIL\ImageFile.py", line
536, in _save  
s = e.encode_to_file(fh, bufsize)  
OSError: [Errno 28] No space left on device  
  
Error processing trigger "frame drawn":  
OSError: [Errno 28] No space left on device  
  
File "F:\software\ChimeraX 1.3\bin\lib\site-packages\PIL\ImageFile.py", line
536, in _save  
s = e.encode_to_file(fh, bufsize)  
  
See log for complete Python traceback.  
  

> crossfade

Traceback (most recent call last):  
File "F:\software\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File "F:\software\ChimeraX 1.3\bin\lib\json\\__init__.py", line 180, in dump  
fp.write(chunk)  
OSError: [Errno 28] No space left on device  
  
During handling of the above exception, another exception occurred:  
  
OSError: [Errno 28] No space left on device  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "F:\software\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "F:\software\ChimeraX 1.3\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 325, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "F:\software\ChimeraX 1.3\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 423, in add  
self._history.enqueue((item, typed))  
File "F:\software\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "F:\software\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "F:\software\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File "F:\software\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\safesave.py", line 85, in __exit__  
self._f.close()  
OSError: [Errno 28] No space left on device  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device  
  
File "F:\software\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\safesave.py", line 85, in __exit__  
self._f.close()  
  
See log for complete Python traceback.  
  

> show ~#1,2,3 target ac

Traceback (most recent call last):  
File "F:\software\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File "F:\software\ChimeraX 1.3\bin\lib\json\\__init__.py", line 180, in dump  
fp.write(chunk)  
OSError: [Errno 28] No space left on device  
  
During handling of the above exception, another exception occurred:  
  
OSError: [Errno 28] No space left on device  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "F:\software\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "F:\software\ChimeraX 1.3\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 325, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "F:\software\ChimeraX 1.3\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 423, in add  
self._history.enqueue((item, typed))  
File "F:\software\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "F:\software\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "F:\software\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File "F:\software\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\safesave.py", line 85, in __exit__  
self._f.close()  
OSError: [Errno 28] No space left on device  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device  
  
File "F:\software\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\safesave.py", line 85, in __exit__  
self._f.close()  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 442.50
OpenGL renderer: GeForce MX350/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: HUAWEI
Model: HBB-WX9
OS: Microsoft Windows 10 家庭中文版 (Build 19045)
Memory: 17,004,482,560
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-10210U CPU @ 1.60GHz
OSLanguage: zh-CN
Locale: ('zh_CN', 'cp936')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    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: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 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: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 2 years ago

Component:	Unassigned → Input/Output
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → No space left on device

comment:2 by Eric Pettersen, 2 years ago

Resolution:	→ nonchimerax
Status:	accepted → closed

Hi Faye,

You have run out of free space on your F: drive. You need to free up some space on that drive.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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