Permission denied saving .cmap file

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:\Users\bradr\Downloads\cryosparc_P63_J21_040_volume_map_sharp.mrc
> format mrc

Opened cryosparc_P63_J21_040_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.29, shown at level 0.203, step 1, values float32  

> volume #1 level 0.335

> ui mousemode right "map eraser"

> volume erase #1 center 171.56,207.21,159.28 radius 50.322 outside true

Opened cryosparc_P63_J21_040_volume_map_sharp.mrc copy as #3, grid size
256,256,256, pixel 1.29, shown at step 1, values float32  

> volume erase #3 center 224.61,151.46,149.8 radius 50.217

> volume erase #3 center 109.85,165.2,178.28 radius 50.217

> volume erase #3 center 153.33,121.69,179.76 radius 50.217

> volume erase #3 center 160.72,120.47,165.01 radius 50.217

No map chosen to save  

> select #3

2 models selected  
No map chosen to save  

> hide #2 models

> save "C:/Program Files/ChimeraX 1.2.5/lib/SEN dimer.cmap" models #3

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 87, in provider_save  
provider_info.bundle_info.run_provider(session, provider_info.format_name,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\map\\__init__.py", line 164, in save  
save_map(session, path, _name, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\map\volume.py", line 3974, in save_map  
save_grid_data(grids, path, session, format_name, options)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\map_data\fileformats.py", line 314, in save_grid_data  
ff.save_func(garg, tpath, options = options, progress = p)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\map_data\cmap\write_cmap.py", line 81, in
write_grid_as_chimera_map  
h5file = tables.open_file(path, mode = mode)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\tables\file.py",
line 315, in open_file  
return File(filename, mode, title, root_uep, filters, **kwargs)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\tables\file.py",
line 778, in __init__  
self._g_new(filename, mode, **params)  
File "tables\hdf5extension.pyx", line 492, in tables.hdf5extension.File._g_new  
tables.exceptions.HDF5ExtError: HDF5 error back trace  
  
File "D:\pytables_hdf5\CMake-hdf5-1.10.5\hdf5-1.10.5\src\H5F.c", line 444, in
H5Fcreate  
unable to create file  
File "D:\pytables_hdf5\CMake-hdf5-1.10.5\hdf5-1.10.5\src\H5Fint.c", line 1509,
in H5F_open  
unable to open file: time = Tue Jul 20 11:18:03 2021  
, name = 'C:/Program Files/ChimeraX 1.2.5/lib/SEN dimer.cmap', tent_flags = 13  
File "D:\pytables_hdf5\CMake-hdf5-1.10.5\hdf5-1.10.5\src\H5FD.c", line 734, in
H5FD_open  
open failed  
File "D:\pytables_hdf5\CMake-hdf5-1.10.5\hdf5-1.10.5\src\H5FDsec2.c", line
346, in H5FD_sec2_open  
unable to open file: name = 'C:/Program Files/ChimeraX 1.2.5/lib/SEN
dimer.cmap', errno = 13, error message = 'Permission denied', flags = 13,
o_flags = 302  
  
End of HDF5 error back trace  
  
Unable to open/create file 'C:/Program Files/ChimeraX 1.2.5/lib/SEN
dimer.cmap'  
  
tables.exceptions.HDF5ExtError: HDF5 error back trace  
  
File "D:\pytables_hdf5\CMake-hdf5-1.10.5\hdf5-1.10.5\src\H5F.c", line 444, in
H5Fcreate  
unable to create file  
File "D:\pytables_hdf5\CMake-hdf5-1.10.5\hdf5-1.10.5\src\H5Fint.c", line 1509,
in H5F_open  
unable to open file: time = Tue Jul 20 11:18:03 2021  
, name = 'C:/Program Files/ChimeraX 1.2.5/lib/SEN dimer.cmap', tent_flags = 13  
File "D:\pytables_hdf5\CMake-hdf5-1.10.5\hdf5-1.10.5\src\H5FD.c", line 734, in
H5FD_open  
open failed  
File "D:\pytables_hdf5\CMake-hdf5-1.10.5\hdf5-1.10.5\src\H5FDsec2.c", line
346, in H5FD_sec2_open  
unable to open file: name = 'C:/Program Files/ChimeraX 1.2.5/lib/SEN
dimer.cmap', errno = 13, error message = 'Permission denied', flags = 13,
o_flags = 302  
  
End of HDF5 error back trace  
  
Unable to open/create file 'C:/Program Files/ChimeraX 1.2.5/lib/SEN
dimer.cmap'  
  
File "tables\hdf5extension.pyx", line 492, in tables.hdf5extension.File._g_new  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 457.71
OpenGL renderer: GeForce GTX 1050 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Inspiron 15 7000 Gaming
OS: Microsoft Windows 10 Home (Build 18363)
Memory: 17,039,704,064
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-7300HQ CPU @ 2.50GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
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: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    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: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    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: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    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: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    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: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    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: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    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: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pywin32: 228
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    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: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

[Tom Goddard]

User tried to save a file to a directory where they did not have permission.
Normally this would give a simple error message and no traceback. Unfortunately PyTables does not give an IOError in this situation so the simple permission denied error message is not given.
I never saw this reported before, don't think it is worth trying to inspect the HDF exception and convert it to IOError unless this is reported again.