Opened 5 years ago

Closed 5 years ago

#4431 closed enhancement (fixed)

More user-friendly session error handling

Reported by: mmaldo@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Sessions Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC)
Description
Hi,
I'm not sure if this is a bug, but it keeps suggesting I report it. 
Does it have to do with the view matrix command? My labmates are able to use it. We wrote a simple script to open files, align them, take pictures and save the session. We get the view matrix parameters by positioning the models by hand, then writing "view matrix" and then copy/pasting those values in the script so we have them for next time.

Thank you,
Maria

Log:
UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/mmaldo/Desktop/test.cxs

Failed opening file /Users/mmaldo/Desktop/test.cxs:  
could not find MARK  

> open /Users/mmaldo/Desktop/test.cxs

Traceback (most recent call last):  
File
"/opt/sbgrid/i386-mac/chimerax/1.1.1/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/open_command/dialog.py", line 150, in _qt_safe  
if data_format is None else " format " +
StringArg.unparse(data_format.nicknames[0])))  
File
"/opt/sbgrid/i386-mac/chimerax/1.1.1/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/opt/sbgrid/i386-mac/chimerax/1.1.1/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/opt/sbgrid/i386-mac/chimerax/1.1.1/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 100, in cmd_open  
return Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/opt/sbgrid/i386-mac/chimerax/1.1.1/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/opt/sbgrid/i386-mac/chimerax/1.1.1/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 154, in provider_open  
name or model_name_from_path(fi.file_name)), provider_kw)  
File
"/opt/sbgrid/i386-mac/chimerax/1.1.1/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 390, in collated_open  
return func(*func_args, **func_kw)  
File
"/opt/sbgrid/i386-mac/chimerax/1.1.1/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 26, in open  
return cxs_open(session, data, **kw)  
File
"/opt/sbgrid/i386-mac/chimerax/1.1.1/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 925, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File
"/opt/sbgrid/i386-mac/chimerax/1.1.1/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 608, in restore  
version = serialize.pickle_deserialize(stream)  
File
"/opt/sbgrid/i386-mac/chimerax/1.1.1/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/serialize.py", line 57, in pickle_deserialize  
return unpickler.load()  
_pickle.UnpicklingError: could not find MARK  
  
_pickle.UnpicklingError: could not find MARK  
  
File
"/opt/sbgrid/i386-mac/chimerax/1.1.1/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/serialize.py", line 57, in pickle_deserialize  
return unpickler.load()  
  
See log for complete Python traceback.  
  

> open /Users/mmaldo/Downloads/Chimera_test_Matrix.cxc

> open
> /Users/apadavan/Desktop/Tetrahymena_Model_Building/Refinement/Refinement_MA/Refinement_MA_210317/pdb_extract_20864.cif

No such file/path:
/Users/apadavan/Desktop/Tetrahymena_Model_Building/Refinement/Refinement_MA/Refinement_MA_210317/pdb_extract_20864.cif  




OpenGL version: 4.1 NVIDIA-12.0.24 355.11.10.50.10.103
OpenGL renderer: NVIDIA GeForce GT 750M OpenGL Engine
OpenGL vendor: NVIDIA CorporationHardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac14,3
      Processor Name: Intel Core i7
      Processor Speed: 3.1 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 430.0.0.0.0
      SMC Version (system): 2.17f7

Software:

    System Software Overview:

      System Version: macOS 10.14.6 (18G8022)
      Kernel Version: Darwin 18.7.0
      Time since boot: 1:08

Graphics/Displays:

    NVIDIA GeForce GT 750M:

      Chipset Model: NVIDIA GeForce GT 750M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 1 GB
      Vendor: NVIDIA (0x10de)
      Device ID: 0x0fe9
      Revision ID: 0x00a2
      ROM Revision: 3762
      Metal: Supported, feature set macOS GPUFamily1 v4
      Displays:
        iMac:
          Display Type: LCD
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: DisplayPort
        HP VH240a:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60 Hz
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Display Serial Number: 6CM0210YQB  
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No

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: 2.1.3
    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-Clipper: 0.15.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1.1
    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-ISOLDE: 1.1.0
    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
    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: 0.7.1
    pexpect: 4.8.0
    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
    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: 19.0.2
    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
File attachment: test.cxs

test.cxs​

Attachments (1)

test.cxs​ (430 bytes ) - added by mmaldo@… 5 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (4)

by mmaldo@…, 5 years ago

Attachment: test.cxs​ added

Added by email2trac

in reply to:  2 comment:1 by mmaldo@…, 5 years ago 

I'm so sorry, I think the error was due to me using .cxs rather than .cxc. Sorry about that.

Best wishes,
Maria 

On 3/29/21, 5:10 PM, "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:

    #4431: ChimeraX bug report submission
    ------------------------+-----------------------------
     Reporter:  mmaldo@…    |                Type:  defect
       Status:  new         |            Priority:  normal
    Component:  Unassigned  |          Blocked By:
     Blocking:              |  Notify when closed:
    ------------------------+-----------------------------
     {{{
     The following bug report has been submitted:
     Platform:        Darwin-18.7.0-x86_64-i386-64bit
     ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC)
     Description
     Hi,
     I'm not sure if this is a bug, but it keeps suggesting I report it.
     Does it have to do with the view matrix command? My labmates are able to
     use it. We wrote a simple script to open files, align them, take pictures
     and save the session. We get the view matrix parameters by positioning the
     models by hand, then writing "view matrix" and then copy/pasting those
     values in the script so we have them for next time.

     Thank you,
     Maria

     Log:
     UCSF ChimeraX version: 1.1.1 (2020-10-07)
     © 2016-2020 Regents of the University of California. All rights reserved.
     How to cite UCSF ChimeraX

     > open /Users/mmaldo/Desktop/test.cxs

     Failed opening file /Users/mmaldo/Desktop/test.cxs:
     could not find MARK

     > open /Users/mmaldo/Desktop/test.cxs

     Traceback (most recent call last):
     File
     "/opt/sbgrid/i386-mac/chimerax/1.1.1/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
     packages/chimerax/open_command/dialog.py", line 150, in _qt_safe
     if data_format is None else " format " +
     StringArg.unparse(data_format.nicknames[0])))
     File
     "/opt/sbgrid/i386-mac/chimerax/1.1.1/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
     packages/chimerax/core/commands/run.py", line 31, in run
     results = command.run(text, log=log)
     File
     "/opt/sbgrid/i386-mac/chimerax/1.1.1/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
     packages/chimerax/core/commands/cli.py", line 2805, in run
     result = ci.function(session, **kw_args)
     File
     "/opt/sbgrid/i386-mac/chimerax/1.1.1/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
     packages/chimerax/open_command/cmd.py", line 100, in cmd_open
     return Command(session, registry=registry).run(provider_cmd_text, log=log)
     File
     "/opt/sbgrid/i386-mac/chimerax/1.1.1/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
     packages/chimerax/core/commands/cli.py", line 2805, in run
     result = ci.function(session, **kw_args)
     File
     "/opt/sbgrid/i386-mac/chimerax/1.1.1/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
     packages/chimerax/open_command/cmd.py", line 154, in provider_open
     name or model_name_from_path(fi.file_name)), provider_kw)
     File
     "/opt/sbgrid/i386-mac/chimerax/1.1.1/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
     packages/chimerax/open_command/cmd.py", line 390, in collated_open
     return func(*func_args, **func_kw)
     File
     "/opt/sbgrid/i386-mac/chimerax/1.1.1/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
     packages/chimerax/core_formats/__init__.py", line 26, in open
     return cxs_open(session, data, **kw)
     File
     "/opt/sbgrid/i386-mac/chimerax/1.1.1/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
     packages/chimerax/core/session.py", line 925, in open
     session.restore(stream, path=path, resize_window=resize_window)
     File
     "/opt/sbgrid/i386-mac/chimerax/1.1.1/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
     packages/chimerax/core/session.py", line 608, in restore
     version = serialize.pickle_deserialize(stream)
     File
     "/opt/sbgrid/i386-mac/chimerax/1.1.1/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
     packages/chimerax/core/serialize.py", line 57, in pickle_deserialize
     return unpickler.load()
     _pickle.UnpicklingError: could not find MARK

     _pickle.UnpicklingError: could not find MARK

     File
     "/opt/sbgrid/i386-mac/chimerax/1.1.1/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
     packages/chimerax/core/serialize.py", line 57, in pickle_deserialize
     return unpickler.load()

     See log for complete Python traceback.


     > open /Users/mmaldo/Downloads/Chimera_test_Matrix.cxc

     > open
     >
     /Users/apadavan/Desktop/Tetrahymena_Model_Building/Refinement/Refinement_MA/Refinement_MA_210317/pdb_extract_20864.cif

     No such file/path:
     /Users/apadavan/Desktop/Tetrahymena_Model_Building/Refinement/Refinement_MA/Refinement_MA_210317/pdb_extract_20864.cif




     OpenGL version: 4.1 NVIDIA-12.0.24 355.11.10.50.10.103
     OpenGL renderer: NVIDIA GeForce GT 750M OpenGL Engine
     OpenGL vendor: NVIDIA CorporationHardware:

         Hardware Overview:

           Model Name: iMac
           Model Identifier: iMac14,3
           Processor Name: Intel Core i7
           Processor Speed: 3.1 GHz
           Number of Processors: 1
           Total Number of Cores: 4
           L2 Cache (per Core): 256 KB
           L3 Cache: 8 MB
           Hyper-Threading Technology: Enabled
           Memory: 16 GB
           Boot ROM Version: 430.0.0.0.0
           SMC Version (system): 2.17f7

     Software:

         System Software Overview:

           System Version: macOS 10.14.6 (18G8022)
           Kernel Version: Darwin 18.7.0
           Time since boot: 1:08

     Graphics/Displays:

         NVIDIA GeForce GT 750M:

           Chipset Model: NVIDIA GeForce GT 750M
           Type: GPU
           Bus: PCIe
           PCIe Lane Width: x16
           VRAM (Total): 1 GB
           Vendor: NVIDIA (0x10de)
           Device ID: 0x0fe9
           Revision ID: 0x00a2
           ROM Revision: 3762
           Metal: Supported, feature set macOS GPUFamily1 v4
           Displays:
             iMac:
               Display Type: LCD
               Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
               UI Looks like: 1920 x 1080
               Framebuffer Depth: 24-Bit Color (ARGB8888)
               Main Display: Yes
               Mirror: Off
               Online: Yes
               Rotation: Supported
               Automatically Adjust Brightness: No
               Connection Type: DisplayPort
             HP VH240a:
               Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
               UI Looks like: 1920 x 1080 @ 60 Hz
               Framebuffer Depth: 24-Bit Color (ARGB8888)
               Display Serial Number: 6CM0210YQB
               Mirror: Off
               Online: Yes
               Rotation: Supported
               Automatically Adjust Brightness: No

     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: 2.1.3
         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-Clipper: 0.15.0
         ChimeraX-ColorActions: 1.0
         ChimeraX-ColorGlobe: 1.0
         ChimeraX-CommandLine: 1.1.3
         ChimeraX-ConnectStructure: 2.0
         ChimeraX-Contacts: 1.0
         ChimeraX-Core: 1.1.1
         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-ISOLDE: 1.1.0
         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
         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: 0.7.1
         pexpect: 4.8.0
         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
         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: 19.0.2
         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
     File attachment: test.cxs

     }}}

     [attachment:"test.cxs"]

    --
    Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4431>
    ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
    ChimeraX Issue Tracker

comment:2 by Eric Pettersen, 5 years ago

Component: Unassigned → Sessions
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → More user-friendly session error handling
Type: defect → enhancement

It would be nice if ChimeraX could detect that a file is simply not a session file at all and report that.

comment:3 by Greg Couch, 5 years ago

Resolution: → fixed
Status: assigned → closed

The bug is probably that the session file was written using the ChimeraX daily build. Unfortunately, this can only be fixed by upgrading your version of ChimeraX. Starting with ChimeraX 1.2, if this situation happens, an error message is generated rather than a Python traceback.

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