Better write-permission error handling

[chimerax-bug-report@…]

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
(Describe the actions that caused this problem to occur here)

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\rosat\OneDrive\Documents\Universidad\Cuarto\Biología
> estructural computacional\Trabajo final\Estructuras\2qeh.pdb" format pdb

2qeh.pdb title:  
Crystal structure of anopheles gambiae D7R4-serotonin complex [more info...]  
  
Chain information for 2qeh.pdb #1  
---  
Chain | Description  
A | D7-related 4 protein  
  
Non-standard residues in 2qeh.pdb #1  
---  
SRO — serotonin (3-(2-aminoethyl)-1H-indol-5-ol)  
  

> Background Opaque

Unknown command: Background Opaque  

> set bgColor gray

> select :SRO

13 atoms, 14 bonds, 1 residue, 1 model selected  

> select /A:0-144

1193 atoms, 1219 bonds, 145 residues, 1 model selected  

> select :SRO

13 atoms, 14 bonds, 1 residue, 1 model selected  

> select :SRO

13 atoms, 14 bonds, 1 residue, 1 model selected  

> hide sel atoms

> hide sel atoms

> show sel atoms

> select /A:0-144

1193 atoms, 1219 bonds, 145 residues, 1 model selected  

> hide sel cartoons

> hide sel cartoons

> hide sel atoms

> save "C:/Users/rosat/OneDrive/Documents/Universidad/Cuarto/Biología
> estructural computacional/Trabajo final/Estructuras/serotonina.cxs"

> close session

> open "C:\Users\rosat\OneDrive\Documents\Universidad\Cuarto\Biología
> estructural computacional\Trabajo final\Estructuras\2qeh.pdb" format pdb

2qeh.pdb title:  
Crystal structure of anopheles gambiae D7R4-serotonin complex [more info...]  
  
Chain information for 2qeh.pdb #1  
---  
Chain | Description  
A | D7-related 4 protein  
  
Non-standard residues in 2qeh.pdb #1  
---  
SRO — serotonin (3-(2-aminoethyl)-1H-indol-5-ol)  
  

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select up

57 atoms, 57 bonds, 6 residues, 1 model selected  

> select up

1327 atoms, 1233 bonds, 267 residues, 1 model selected  

> select down

57 atoms, 57 bonds, 6 residues, 1 model selected  

> select down

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select down

2 atoms, 1 bond, 1 residue, 1 model selected  

> ui tool show Rotamers

> swapaa interactive sel GLN rotLib Dunbrack

/A TYR 24: phi 64.7, psi 20.7 trans  
Changed 648 bond radii  

> open "C:/Users/rosat/OneDrive/Documents/Universidad/Cuarto/Biología
> estructural computacional/Trabajo final/Estructuras/2qeh.pdb"

2qeh.pdb title:  
Crystal structure of anopheles gambiae D7R4-serotonin complex [more info...]  
  
Chain information for 2qeh.pdb #2  
---  
Chain | Description  
A | D7-related 4 protein  
  
Non-standard residues in 2qeh.pdb #2  
---  
SRO — serotonin (3-(2-aminoethyl)-1H-indol-5-ol)  
  

> close session

> open "C:/Users/rosat/OneDrive/Documents/Universidad/Cuarto/Biología
> estructural computacional/Trabajo final/Estructuras/2qeh.pdb"

2qeh.pdb title:  
Crystal structure of anopheles gambiae D7R4-serotonin complex [more info...]  
  
Chain information for 2qeh.pdb #1  
---  
Chain | Description  
A | D7-related 4 protein  
  
Non-standard residues in 2qeh.pdb #1  
---  
SRO — serotonin (3-(2-aminoethyl)-1H-indol-5-ol)  
  

> ui tool show "Show Sequence Viewer"

> hide #1 models

> show #1 models

> select #1

1327 atoms, 1233 bonds, 267 residues, 1 model selected  

> hide #1 models

> show #1 models

> ~select #1

Nothing selected  

> ui mousemode right select

Drag select of 5 atoms, 2 residues, 4 bonds  
Drag select of 1 atoms, 1 residues  

> select clear

Drag select of 5 atoms, 2 residues, 4 bonds  
Drag select of 3 atoms, 6 residues, 1 bonds  

> select /A:39

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:140

9 atoms, 8 bonds, 1 residue, 1 model selected  
Drag select of 22 atoms, 45 residues, 18 bonds  

> select /A:140

9 atoms, 8 bonds, 1 residue, 1 model selected  
Drag select of 17 atoms, 37 residues, 14 bonds  

> select clear

Drag select of 11 atoms, 3 residues, 10 bonds  

> select /A:35

10 atoms, 10 bonds, 1 residue, 1 model selected  
Drag select of 1 atoms, 1 bonds  

> select clear

Drag select of 7 atoms, 1 residues, 12 bonds  

> select clear

> select clear

Drag select of 6 atoms, 6 bonds  
Drag select of 1 atoms, 2 bonds  

> select clear

> select /A

1327 atoms, 1233 bonds, 267 residues, 1 model selected  

> select ligand

13 atoms, 14 bonds, 1 residue, 1 model selected  

> select ligand

13 atoms, 14 bonds, 1 residue, 1 model selected  

> save "C:/Users/rosat/OneDrive/Documents/Universidad/Cuarto/Biología
> estructural computacional/Trabajo final/Estructuras/serotonin pdb.pdb"
> selectedOnly true relModel #1

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 48, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\pdb\\__init__.py", line 71, in save  
pdb.save_pdb(session, path, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\pdb\pdb.py", line 119, in save_pdb  
(serial_numbering == "h36"), polymeric_res_names)  
OSError: Unable to open file
'C:/Users/rosat/OneDrive/Documents/Universidad/Cuarto/Biología estructural
computacional/Trabajo final/Estructuras/serotonin pdb.pdb' for writing  
  
OSError: Unable to open file
'C:/Users/rosat/OneDrive/Documents/Universidad/Cuarto/Biología estructural
computacional/Trabajo final/Estructuras/serotonin pdb.pdb' for writing  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\pdb\pdb.py", line 119, in save_pdb  
(serial_numbering == "h36"), polymeric_res_names)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.13474 Core Profile Forward-Compatible Context 22.19.163.1792
OpenGL renderer: AMD Radeon(TM) R5 Graphics
OpenGL vendor: ATI Technologies Inc.
Manufacturer: Acer
Model: Aspire A315-21
OS: Microsoft Windows 10 Home (Build 19041)
Memory: 12,303,327,232
MaxProcessMemory: 137,438,953,344
CPU: 2 AMD A9-9420 RADEON R5, 5 COMPUTE CORES 2C+3G   "
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

[Eric Pettersen]

Why do we get OSError instead of IOError when the C++ is setting PyExc_IOError? If we do manage to fix it to raise IOError, is it caught and converted to non-bug?