Opened 11 months ago

Closed 11 months ago

#16298 closed defect (nonchimerax)

Segger: realpath(): Operation not permitted

Reported by: Irene.Kiburu@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-14.2.1-arm64-arm-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
Trying to save a segmented region as .mrc

Get error
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/posixpath.py", line 380, in abspath
cwd = os.getcwd()

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Volumes/ikiburu-1/Documents/KRAS_degrader/Cryo-
> EM_Ternary_complex/GS-1630796/11062024/Maps/cryosparc_J610_map_sharp.mrc

Opened cryosparc_J610_map_sharp.mrc as #1, grid size 480,480,480, pixel 0.729,
shown at level 0.0494, step 2, values float32  

> volume #1 step 1

> volume #1 level 0.1512

> volume #1 level 0.1726

> volume gaussian #1 sDev 3.1

Opened cryosparc_J610_map_sharp.mrc gaussian as #2, grid size 480,480,480,
pixel 0.729, shown at step 1, values float32  

> ui tool show "Segment Map"

Segmenting cryosparc_J610_map_sharp.mrc gaussian, density threshold 0.005105  
Showing 41 region surfaces  
100 watershed regions, grouped to 41 regions  
Showing cryosparc_J610_map_sharp gaussian.seg - 41 regions, 41 surfaces  

> select add #3.1

1 model selected  

> select add #3.2

2 models selected  

> select add #3.16

3 models selected  

> select add #3.5

4 models selected  

> select add #3.4

5 models selected  

> select add #3.14

6 models selected  

> select add #3.20

7 models selected  

> select subtract #3.20

6 models selected  

> select subtract #3.14

5 models selected  

> select add #3.3

6 models selected  

> hide #!2 models

> select #3.20

1 model selected  

> hide #!3 models

> show #!3 models

> select add #3

42 models selected  

> select subtract #3

Nothing selected  

> select add #3

42 models selected  

> select subtract #3

Nothing selected  

> select add #3

42 models selected  

> select subtract #3

Nothing selected  

> hide #!3 models

> show #!3 models

> select #3.20

1 model selected  

> hide #!3 models

> show #!3 models

> select subtract #2

1 model selected  

> select add #2

3 models selected  

> select subtract #2

1 model selected  

> select add #3

42 models selected  

> select subtract #3

Nothing selected  

> hide #!3 models

> show #!3 models

> show #!2 models

> hide #!2 models

> select add #3

42 models selected  

> select subtract #3

Nothing selected  

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

Deleted 41 regions  
Select one or more regions to delete  
[Repeated 1 time(s)]

> hide #3 target m

> show #3 models

> select add #3

1 model selected  
Select one or more regions to delete  

> show #!2 models

> volume gaussian #1 sDev 3.1

Opened cryosparc_J610_map_sharp.mrc gaussian as #4, grid size 480,480,480,
pixel 0.729, shown at step 1, values float32  

> hide #3 models

> select subtract #3

Nothing selected  

> hide #!2 models

> select add #4

2 models selected  

> select subtract #4

Nothing selected  
Segmenting cryosparc_J610_map_sharp.mrc gaussian, density threshold 0.005105  
Showing 41 region surfaces  
100 watershed regions, grouped to 41 regions  
Showing cryosparc_J610_map_sharp gaussian.seg - 41 regions, 41 surfaces  

> select add #3.3

1 model selected  

> select add #3.5

2 models selected  

> select add #3.1

3 models selected  

> select add #3.4

4 models selected  

> select add #3.16

5 models selected  

> select add #3.2

6 models selected  

> select add #3.14

7 models selected  

> select subtract #3.16

6 models selected  

> hide #!4 models

> select add #3.20

7 models selected  

> select add #3.16

8 models selected  

> show #!4 models

> hide #!4 models

Drag select of 142, 144, 135, 140, 150, 133, 148, 141, 115, 113, 126, 143,
151, 42, 146, 134, 149, 117, 139, 1, 74, 125, 5, 14, 35, 11, 119, 118, 29, 62,
33, 24, 75  
Grouped 33 regions  

> show #!4 models

> hide #!4 models

Saving 1 regions to mrc file...  
Opened DDB1_J610_mask.mrc as #5, grid size 131,142,112, pixel 0.729, shown at
step 1, values float32  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/segment_dialog.py", line 1423, in
WriteSelRegionsMRCFile  
self.SaveRegsToMRC ( regs, dmap )  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/segment_dialog.py", line 1400, in SaveRegsToMRC  
nv.write_file ( path, "mrc" )  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1757, in write_file  
format = save_grid_data(d, path, self.session, format, options)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/fileformats.py", line 297, in save_grid_data  
if matching_grid_path(glist, path):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/fileformats.py", line 339, in matching_grid_path  
if _realpath(gp) == rp:  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/fileformats.py", line 348, in _realpath  
return realpath(path)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/posixpath.py",
line 393, in realpath  
return abspath(path)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/posixpath.py",
line 380, in abspath  
cwd = os.getcwd()  
PermissionError: [Errno 1] Operation not permitted  
  
PermissionError: [Errno 1] Operation not permitted  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/posixpath.py",
line 380, in abspath  
cwd = os.getcwd()  
  
See log for complete Python traceback.  
  
Saving 1 regions to mrc file...  
Opened cryosparc_J610_map_sharp_region_152.mrc as #6, grid size 131,142,112,
pixel 0.729, shown at step 1, values float32  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/segment_dialog.py", line 1423, in
WriteSelRegionsMRCFile  
self.SaveRegsToMRC ( regs, dmap )  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/segment_dialog.py", line 1400, in SaveRegsToMRC  
nv.write_file ( path, "mrc" )  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1757, in write_file  
format = save_grid_data(d, path, self.session, format, options)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/fileformats.py", line 297, in save_grid_data  
if matching_grid_path(glist, path):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/fileformats.py", line 339, in matching_grid_path  
if _realpath(gp) == rp:  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/fileformats.py", line 348, in _realpath  
return realpath(path)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/posixpath.py",
line 393, in realpath  
return abspath(path)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/posixpath.py",
line 380, in abspath  
cwd = os.getcwd()  
PermissionError: [Errno 1] Operation not permitted  
  
PermissionError: [Errno 1] Operation not permitted  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/posixpath.py",
line 380, in abspath  
cwd = os.getcwd()  
  
See log for complete Python traceback.  
  

> hide #!5 models

> hide #!3 models

> select add #3

10 models selected  

> select subtract #3

Nothing selected  

> select add #6

2 models selected  

> volume #6 level 0.0347

> show #!5 models

> select add #5

4 models selected  

> hide #!6 models

> select subtract #6

2 models selected  

> select add #6

4 models selected  

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!5 models

> select subtract #5

2 models selected  
Please select one ore more regions to save to .mrc file  




OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,1
      Model Number: MK193LL/A
      Chip: Apple M1 Pro
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 10151.61.4
      OS Loader Version: 10151.61.4

Software:

    System Software Overview:

      System Version: macOS 14.2.1 (23C71)
      Kernel Version: Darwin 23.2.0
      Time since boot: 20 minutes, 59 seconds

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL U4021QW:
          Resolution: 5120 x 2160 (Ultra-wide 5K)
          UI Looks like: 2560 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    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: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 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-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    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-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    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: 2.7.2
    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
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.6
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    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
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0

Change History (2)

comment:1 by Eric Pettersen, 11 months ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Segger: realpath(): Operation not permitted

comment:2 by Tom Goddard, 11 months ago

Resolution: → nonchimerax
Status: assigned → closed

This error means ChimeraX has been started in a directory that you don't have permission to read, or started in a directory that has been deleted. This causes an error whenever the code tries to determine the current directory.

When you start ChimeraX by clicking on the application icon it starts in your Desktop directory, so I would expect you have permission to read that directory and it exists. But since you are at a company I have no idea how your computer security is set up which causes ChimeraX to start in a directory where you do not have read permission.

You could try typing the ChimeraX command "cd ~/Desktop" to change the current directory to the desktop and that may fix your problem for this ChimeraX session. But to fix it for future uses of ChimeraX you may need to ask your IT department to figure out how the application is starting in a directory where you don't have read permission, and to fix that so it starts in a directory where you do have read permission.

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