The following bug report has been submitted:
Platform: Windows-10-10.0.17763
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
While running a script tested on my Mac on the same data (but binned 4 times), I get this following error from the Windows installation.
fly p2 p1 100
wait
display #1
volume #2-6 transparency 0.8
2dlabels text Nuclei color #5555ff size 18 xpos .03 ypos .92 bold true bgColor black margin 5
2dlabels text Mitochondria color #aa557f size 18 xpos .03 ypos .87 bold true bgColor black margin 5
2dlabels text "Actin bundles" color #f514fd size 18 xpos .03 ypos .82 bold true bgColor black margin 5
2dlabels text "Cell junctions" color #11ffcc size 18 xpos .03 ypos .77 bold true bgColor black margin 5
2dlabels text "Entotic cell" color #ff9429 size 18 xpos .03 ypos .72 bold true bgColor black margin 5
volume all planes z,1344,60
wait 1284
~display #1
OSError: [Errno 28] No space left on device During handling of the above exception, another exception occurred: Traceback (most recent call last): File "C:\Users\imprima\ChimeraX 1.4\bin\lib\site-packages\chimerax\core\triggerset.py", line 134, in invoke return self._func(self._name, data) File "C:\Users\imprima\ChimeraX 1.4\bin\lib\site-packages\chimerax\cmd_line\tool.py", line 350, in _command_started_cb self.history_dialog.add(self._just_typed_command or cmd_text, File "C:\Users\imprima\ChimeraX 1.4\bin\lib\site-packages\chimerax\cmd_line\tool.py", line 452, in add self._history.enqueue((item, typed)) File "C:\Users\imprima\ChimeraX 1.4\bin\lib\site-packages\chimerax\core\history.py", line 171, in enqueue self.save() File "C:\Users\imprima\ChimeraX 1.4\bin\lib\site-packages\chimerax\core\history.py", line 201, in save self._history.save(self._queue) File "C:\Users\imprima\ChimeraX 1.4\bin\lib\site-packages\chimerax\core\history.py", line 109, in save json.dump(obj, f, ensure_ascii=False) File "C:\Users\imprima\ChimeraX 1.4\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 "C:\Users\imprima\ChimeraX 1.4\bin\lib\site-packages\chimerax\core\safesave.py", line 85, in __exit__ self._f.close()
Log:
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open C:\Users\imprima\Desktop\F107A_binaries_bin2\F107_A1_bin1_session.cxs
> format session
Opened f107a_flipz.mrc as #1, grid size 1647,1506,1350, pixel 300, shown at
step 1, values int8
Opened nuclei_f107a_flipz.mrc as #2, grid size 1647,1506,1350, pixel 300,
shown at level 0.8,100, step 2, values int8
Opened mitos_f107a_flipz.mrc as #3, grid size 1647,1506,1350, pixel 300, shown
at level 0.8,100, step 2, values int8
Opened actin_f107a_flipz.mrc as #4, grid size 1647,1506,1350, pixel 300, shown
at level 0.8,100, step 2, values int8
Opened junctions_f107a_flipz.mrc as #5, grid size 1647,1506,1350, pixel 300,
shown at level 0.8,100, step 2, values int8
Opened phantom_f107a_flipz.mrc as #6, grid size 1647,1506,1350, pixel 300,
shown at level 0.8,100, step 2, values int8
Log from Mon Jun 27 14:15:40 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open C:/Users/imprima/Desktop/F107A_binaries_bin2/F107_A1_bin1_session.cxs
Opened f107a_flipz.mrc as #1, grid size 1647,1506,1350, pixel 300, shown at
step 1, values int8
Log from Mon Jun 27 13:14:10 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open Y:/Edoardo/ChimeraX_processing/F107A_binaries_bin2/data/f107a_flipz.mrc
Opened f107a_flipz.mrc as #1, grid size 1647,1506,1350, pixel 300, shown at
step 1, values int8
> volume showOutlineBox true
> save
> Y:/Edoardo/ChimeraX_processing/F107A_binaries_bin2/F107_A1_bin1_session.cxs
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume #1 region 0,0,0,1646,1505,1349 step 1 colorMode opaque8 imageMode
> "box faces"
> ui mousemode right "crop volume"
> volume #1 region 0,0,0,1646,1505,465
> volume #1 region 0,0,0,1646,1505,1349
[Repeated 1 time(s)]
> view name p2
> view orient
> view name p1
> view list
Named views: p1, p2
> save
> Y:/Edoardo/ChimeraX_processing/F107A_binaries_bin2/F107_A1_bin1_session.cxs
——— End of log from Mon Jun 27 13:14:10 2022 ———
opened ChimeraX session
> view list
Named views: p1, p2
> vieww p2
Unknown command: vieww p2
> view p2
> open
> Y:/Edoardo/ChimeraX_processing/F107A_binaries_bin2/data/nuclei_f107a_flipz.mrc
Opened nuclei_f107a_flipz.mrc as #2, grid size 1647,1506,1350, pixel 300,
shown at step 1, values int8
> volume #1 region 0,0,0,1646,1505,1349
> volume #2 region 0,0,0,1646,1505,1349 step 8
> volume #2 region 0,0,0,1646,1505,1349 step 1 colorMode opaque8
> showOutlineBox true imageMode "box faces"
> volume #2 style surface level 0.8 color #5555ff step 2 level 100
> ~ribbon disp#1
> cartoon hide disp#1
Expected an atoms specifier or a keyword
> ~display #1
> lighting soft
> display #1
> volume #2 region 0,0,0,1646,1505,1350
> ui mousemode right "crop volume"
C:\Users\imprima\ChimeraX 1.4\bin\lib\site-
packages\chimerax\map\volume_viewer.py:2749: RuntimeWarning: invalid value
encountered in log
h.show_data(log(counts + 1))
> volume #1 region 0,0,0,1646,1505,1188
> volume #1 region 0,0,0,1646,1505,918
> volume all region 0,0,0,1646,1505,1349
> volume all region 0,0,0,1646,1505,1300
> volume all region 0,0,0,1646,1505,1310
> lighting gentle
> volume all region 0,0,0,1646,1505,1320
> volume all region 0,0,0,1646,1505,1330
> volume all region 0,0,0,1646,1505,1340
> volume all region 0,0,0,1646,1505,1345
> volume all region 0,0,0,1646,1505,1344
> save C:/Users/imprima/Desktop/F107A_binaries_bin2/F107_A1_bin1_session.cxs
> open
> Y:/Edoardo/ChimeraX_processing/F107A_binaries_bin2/data/mitos_f107a_flipz.mrc
Opened mitos_f107a_flipz.mrc as #3, grid size 1647,1506,1350, pixel 300, shown
at step 1, values int8
> ~display #1
> volume all region 0,0,0,1646,1505,1344
> volume #3 style surface level 0.8 color #aa557f step 2 level 100
> lighting soft
> open
> Y:/Edoardo/ChimeraX_processing/F107A_binaries_bin2/data/actin_f107a_flipz.mrc
Opened actin_f107a_flipz.mrc as #4, grid size 1647,1506,1350, pixel 300, shown
at step 1, values int8
> volume all region 0,0,0,1646,1505,1344
> volume #4 style surface level 0.8 color #f514fd step 2 level 100
> open
> Y:/Edoardo/ChimeraX_processing/F107A_binaries_bin2/data/junctions_f107a_flipz.mrc
Opened junctions_f107a_flipz.mrc as #5, grid size 1647,1506,1350, pixel 300,
shown at step 1, values int8
> volume all region 0,0,0,1646,1505,1344
> volume #5 style surface level 0.8 color #11ffcc step 2 level 100
> save C:/Users/imprima/Desktop/F107A_binaries_bin2/F107_A1_bin1_session.cxs
> open
> Y:/Edoardo/ChimeraX_processing/F107A_binaries_bin2/data/phantom_f107a_flipz.mrc
Opened phantom_f107a_flipz.mrc as #6, grid size 1647,1506,1350, pixel 300,
shown at step 1, values int8
> volume all region 0,0,0,1646,1505,1344
> volume #6 style surface level 0.8 color #ff9429 step 2 level 100
> save C:/Users/imprima/Desktop/F107A_binaries_bin2/F107_A1_bin1_session.cxs
> volume all region 0,0,0,1646,1505,120
> volume all region 0,0,0,1646,1505,60
> volume all region 0,0,0,1646,1505,1344
> save C:/Users/imprima/Desktop/F107A_binaries_bin2/F107_A1_bin1_session.cxs
——— End of log from Mon Jun 27 14:15:40 2022 ———
opened ChimeraX session
> fly p2 p1 100
> wait
> display #1
> volume #2-6 transparency 0.8
> 2dlabels text Nuclei color #5555ff size 18 xpos .03 ypos .92 bold true
> bgColor black margin 5
> 2dlabels text Mitochondria color #aa557f size 18 xpos .03 ypos .87 bold true
> bgColor black margin 5
> 2dlabels text "Actin bundles" color #f514fd size 18 xpos .03 ypos .82 bold
> true bgColor black margin 5
> 2dlabels text "Cell junctions" color #11ffcc size 18 xpos .03 ypos .77 bold
> true bgColor black margin 5
> 2dlabels text "Entotic cell" color #ff9429 size 18 xpos .03 ypos .72 bold
> true bgColor black margin 5
> volume all planes z,1344,60
> wait 1284
> ~display #1
OSError: [Errno 28] No space left on device
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Users\imprima\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "C:\Users\imprima\ChimeraX 1.4\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 350, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "C:\Users\imprima\ChimeraX 1.4\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add
self._history.enqueue((item, typed))
File "C:\Users\imprima\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue
self.save()
File "C:\Users\imprima\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save
self._history.save(self._queue)
File "C:\Users\imprima\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "C:\Users\imprima\ChimeraX 1.4\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 "C:\Users\imprima\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\safesave.py", line 85, in __exit__
self._f.close()
See log for complete Python traceback.
> display #1
OSError: [Errno 28] No space left on device
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Users\imprima\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "C:\Users\imprima\ChimeraX 1.4\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 350, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "C:\Users\imprima\ChimeraX 1.4\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add
self._history.enqueue((item, typed))
File "C:\Users\imprima\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue
self.save()
File "C:\Users\imprima\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save
self._history.save(self._queue)
File "C:\Users\imprima\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "C:\Users\imprima\ChimeraX 1.4\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 "C:\Users\imprima\ChimeraX 1.4\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 452.77
OpenGL renderer: GRID V100S-8Q/PCI/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: windows
Manufacturer: VMware, Inc.
Model: VMware Virtual Platform
OS: Microsoft Windows 10 Education (Build 17763)
Memory: 137,438,347,264
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Xeon(R) Gold 6226R CPU @ 2.90GHz
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2022.5.18.1
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
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: 2.2.4
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4
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: 1.1
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
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: 1.1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
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: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
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: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
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: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.6
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: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.3
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
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: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
comtypes: 1.1.10
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pywin32: 303
pyzmq: 23.1.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
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-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
WMI: 1.5.1
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Hi Edoardo,
--Eric