Save spin movie to desktop: Operation not permitted

[jithesh.kottur@…]

The following bug report has been submitted:
Platform:        Darwin-19.3.0-x86_64-i386-64bit
ChimeraX Version: 1.1.dev202007230715 (2020-07-23 07:15:08 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.1.dev202007230715 (2020-07-23)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 3w7f format mmcif fromDatabase pdb

3w7f title:  
Crystal structure of the C(30) carotenoid dehydrosqualene synthase from
staphylococcus aureus complexed with farnesyl thiopyrophosphate [more info...]  
  
Chain information for 3w7f #1  
---  
Chain | Description  
A B | Dehydrosqualene synthase  
  
Non-standard residues in 3w7f #1  
---  
FPS — S-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienyl] trihydrogen
thiodiphosphate (farnesyl thiopyrophosphate)  
MG — magnesium ion  
  
3w7f mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> delete /B

> show ligand

> view ligand

> label ligand

> select :Tyr248

Nothing selected  

> select :248

12 atoms, 12 bonds, 1 model selected  

> view /248

Failed command: view /248  
No objects specified.  

> view :248

> toolshed show Rotamers

Failed command: toolshed show Rotamers  
Cannot find bundle 'Rotamers' in Toolshed  

> mlp

Map values for surface "3w7f_A SES surface": minimum -26.45, mean -3.954,
maximum 24.82  

> lighting full

> lighting full

> lighting soft

> lighting soft

> lighting simple

> set bgColor white

> set bgColor white

> lighting full

> mlp

Map values for surface "3w7f_A SES surface": minimum -26.45, mean -3.954,
maximum 24.82  

> surface ligand @<6.3 visiblePatvhes 1

Failed command: surface ligand @<6.3 visiblePatvhes 1  
Expected a keyword  

> surface ligand @<6.3 visiblePatches 1

> hide ribbons

> hide protein

> preset sticks

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> set bgColor black

> style ligand shpere

Failed command: style ligand shpere  
Expected a keyword  

> style ligand sphere

Changed 48 atom styles  

> color byattribute bfactor

2617 atoms, 463 residues, 1 surfaces, atom bfactor range 18.3 to 95.2  

> color byattribute bfactor palette rainbow range 25, 75

2617 atoms, 463 residues, 1 surfaces, atom bfactor range 18.3 to 95.2  

> open 2zco

Summary of feedback from opening 2zco fetched from pdb  
---  
note | Fetching compressed mmCIF 2zco from
http://files.rcsb.org/download/2zco.cif  
  
2zco title:  
Crystal structure of the C(30) carotenoid dehydrosqualene synthase from
Staphylococcus aureus [more info...]  
  
Chain information for 2zco #2  
---  
Chain | Description  
A | Dehydrosqualene synthase  
  

> preset original

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> mmaker #2 to #1 showAlignment true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 3w7f, chain A (#1) with 2zco, chain A (#2), sequence alignment
score = 1499.3  
Alignment identifier is 1  
RMSD between 277 pruned atom pairs is 0.608 angstroms; (across all 284 pairs:
0.886)  
  

> select ~sel

961 atoms, 160 bonds, 18 pseudobonds, 6 models selected  

> display sel & protein

> select clear

> morph #1,2 wrap true frames 60

Associated Morph - 3w7f chain A to 2zco, chain A with 0 mismatches  
Computed 121 frame morph #3  

> coordset #3 1,121

> movie record

> movie encode /Users/jitheshkottur/Desktop/movie.mp4 framerate 25.0

Movie saved to /Users/jitheshkottur/Desktop/movie.mp4  
  

> show #3:lys

> hide #3:lys

> show #!1 models

> hide #1 surfaces, ribbons, atoms

> show #1:fps,mg

> delete /#1

Failed command: delete /#1  
Missing or invalid "atoms" argument: invalid atoms specifier  

> delete #1

> delete #2

> delete #3

> open 2bbv

Summary of feedback from opening 2bbv fetched from pdb  
---  
notes | Fetching compressed mmCIF 2bbv from
http://files.rcsb.org/download/2bbv.cif  
Fetching CCD CA from http://ligand-expo.rcsb.org/reports/C/CA/CA.cif  
  
2bbv title:  
The refined three-dimensional structure of an insect virus At 2.8 angstroms
resolution [more info...]  
  
Chain information for 2bbv #1  
---  
Chain | Description  
A B C | protein (black beetle virus capsid protein)  
D E F | protein (black beetle virus capsid protein)  
N | RNA (5'-R(*up*CP*up*up*ap*up*ap*up*CP*U)-3')  
  
Non-standard residues in 2bbv #1  
---  
CA — calcium ion  
  
2bbv mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
6| crystal asymmetric unit, crystal frame  
  

> style /b stick

Changed 2382 atom styles  

> hide cartoons

> hide /c

> ribbon /c

> select /A:157@CB

1 atom, 1 model selected  
Drag select of 39 atoms  
Drag select of 8 atoms  
Drag select of 282 atoms, 4 residues, 7 bonds  

> select up

262 atoms, 213 bonds, 1 model selected  

> select up

459 atoms, 440 bonds, 1 model selected  

> select up

1422 atoms, 1440 bonds, 1 model selected  

> select down

459 atoms, 440 bonds, 1 model selected  

> surface #1

> select clear

> style solvent sphere

Changed 208 atom styles  

> style ~solvent stick

Changed 7609 atom styles  

> ~style

Failed command: ~style  
Unknown command: ~style  

> sym#1

Failed command: sym#1  
Unknown command: sym#1  

> sym #1

2bbv mmCIF Assemblies  
---  
1| complete icosahedral assembly| 60 copies of chains A-F,N  
2| icosahedral asymmetric unit| 1 copy of chains A-F,N  
3| icosahedral pentamer| 5 copies of chains A-F,N  
4| icosahedral 23 hexamer| 6 copies of chains A-F,N  
5| icosahedral asymmetric unit, std point frame| 1 copy of chains A-F,N  
6| crystal asymmetric unit, crystal frame| 5 copies of chains A-F,N  
  

> sym #1 assembly 3 newModel false

> view

> set bgColor white

> set silhouettes true

> save~/Desktop/2bbv.png

Failed command: save~/Desktop/2bbv.png  
Unknown command: save~/Desktop/2bbv.png  

> save /Users/jitheshkottur/Desktop/2bbv.png

Traceback (most recent call last):  
File
"/private/var/folders/t1/fm6zcq7d6vb_vktd7fm9ngsc0000gn/T/AppTranslocation/427A67FE-287A-48B1-BBB9-CE656815DAE1/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/tool.py", line 162, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/private/var/folders/t1/fm6zcq7d6vb_vktd7fm9ngsc0000gn/T/AppTranslocation/427A67FE-287A-48B1-BBB9-CE656815DAE1/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 363, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/private/var/folders/t1/fm6zcq7d6vb_vktd7fm9ngsc0000gn/T/AppTranslocation/427A67FE-287A-48B1-BBB9-CE656815DAE1/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1607, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File
"/private/var/folders/t1/fm6zcq7d6vb_vktd7fm9ngsc0000gn/T/AppTranslocation/427A67FE-287A-48B1-BBB9-CE656815DAE1/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/shortcuts/__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File
"/private/var/folders/t1/fm6zcq7d6vb_vktd7fm9ngsc0000gn/T/AppTranslocation/427A67FE-287A-48B1-BBB9-CE656815DAE1/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 1212, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File
"/private/var/folders/t1/fm6zcq7d6vb_vktd7fm9ngsc0000gn/T/AppTranslocation/427A67FE-287A-48B1-BBB9-CE656815DAE1/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 375, in try_shortcut  
self.run_shortcut(keys)  
File
"/private/var/folders/t1/fm6zcq7d6vb_vktd7fm9ngsc0000gn/T/AppTranslocation/427A67FE-287A-48B1-BBB9-CE656815DAE1/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 393, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File
"/private/var/folders/t1/fm6zcq7d6vb_vktd7fm9ngsc0000gn/T/AppTranslocation/427A67FE-287A-48B1-BBB9-CE656815DAE1/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 312, in run  
f(s)  
File
"/private/var/folders/t1/fm6zcq7d6vb_vktd7fm9ngsc0000gn/T/AppTranslocation/427A67FE-287A-48B1-BBB9-CE656815DAE1/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 1144, in save_spin_movie  
% unused_file_name(directory, basename, suffix))  
File
"/private/var/folders/t1/fm6zcq7d6vb_vktd7fm9ngsc0000gn/T/AppTranslocation/427A67FE-287A-48B1-BBB9-CE656815DAE1/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 1158, in unused_file_name  
files = listdir(dir)  
PermissionError: [Errno 1] Operation not permitted:
'/Users/jitheshkottur/Desktop'  
  
PermissionError: [Errno 1] Operation not permitted:
'/Users/jitheshkottur/Desktop'  
  
File
"/private/var/folders/t1/fm6zcq7d6vb_vktd7fm9ngsc0000gn/T/AppTranslocation/427A67FE-287A-48B1-BBB9-CE656815DAE1/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 1158, in unused_file_name  
files = listdir(dir)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.5.5
OpenGL renderer: AMD Radeon Pro 580X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac19,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 3.6 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      Boot ROM Version: 1037.80.34.0.0
      SMC Version (system): 2.46f13

Software:

    System Software Overview:

      System Version: macOS 10.15.3 (19D76)
      Kernel Version: Darwin 19.3.0
      Time since boot: 5:48

Graphics/Displays:

    Radeon Pro 580X:

      Chipset Model: Radeon Pro 580X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c0
      ROM Revision: 113-D0008A-042
      VBIOS Version: 113-D0008A1X-009
      EFI Driver Version: 01.B1.042
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: 5120 x 2880 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        iMac:
          Display Type: LCD
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: DisplayPort

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
    appnope: 0.1.0
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.0
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 1.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.5.1
    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: 1.1.2
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1.dev202007230715
    ChimeraX-CoreFormats: 1.0
    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: 1.0
    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-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    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: 1.2.1
    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: 1.0.3
    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-Tug: 1.0
    ChimeraX-UI: 1.2.2
    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: 0.3.0
    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: 0.16
    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
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.1.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.5
    psutil: 5.7.0
    ptyprocess: 0.6.0
    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
    pyzmq: 19.0.1
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 47.3.0
    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: 4.3.3
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

[Tom Goddard]

Appears you denied permission for ChimeraX to access your Desktop so it gives an error trying to save a spin movie to the desktop. You'd have to give it permssion, macOS system preferences Security & Privacy / Files and Folders / UCSF ChimeraX / Desktop Folder.

I've made this error give a simpler message saying Desktop permission was denied.