Problem reading ORCA output file

[matthew.graneri@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
Tried to open ORCA output file but it didn't work. I tried the same thing with the ARM build of ChimeraX a few moments ago (submitted another bug report) and the same thing happened. I'll attach the output file itself this time.

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/matthewgraneri/Documents/Homework/PhD/calculations/p2/monomers/c3po/casscf/frequency/c3po-
> opt-freq-casscf-tz.out

Traceback (most recent call last):  
File
"/Applications/Chimera/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/Applications/Chimera/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/Chimera/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/Chimera/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/Applications/Chimera/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/Chimera/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/Applications/Chimera/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 457, in collated_open  
return remember_data_format()  
File
"/Applications/Chimera/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "/Users/matthewgraneri/Library/Application Support/ChimeraX/1.4/site-
packages/SEQCROW/__init__.py", line 429, in open  
return open_aarontools(  
File "/Users/matthewgraneri/Library/Application Support/ChimeraX/1.4/site-
packages/SEQCROW/io.py", line 27, in open_aarontools  
fr = FileReader(  
File "/Users/matthewgraneri/Library/Application Support/ChimeraX/1.4/site-
packages/AaronTools/fileIO.py", line 1006, in __init__  
self.read_orca_out(f, get_all, just_geom)  
File "/Users/matthewgraneri/Library/Application Support/ChimeraX/1.4/site-
packages/AaronTools/fileIO.py", line 1632, in read_orca_out  
self.atoms, n = get_atoms(f, n)  
File "/Users/matthewgraneri/Library/Application Support/ChimeraX/1.4/site-
packages/AaronTools/fileIO.py", line 1587, in get_atoms  
rv += [Atom(element=element, coords=coords, name=str(i))]  
File "/Users/matthewgraneri/Library/Application Support/ChimeraX/1.4/site-
packages/AaronTools/atoms.py", line 117, in __init__  
raise ValueError("Unknown element detected: %s" % element)  
ValueError: Unknown element detected: -  
  

Populating font family aliases took 288 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.  

ValueError: Unknown element detected: -  
  
File "/Users/matthewgraneri/Library/Application Support/ChimeraX/1.4/site-
packages/AaronTools/atoms.py", line 117, in __init__  
raise ValueError("Unknown element detected: %s" % element)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,2
      Processor Name: Unknown
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 10
      L2 Cache: 20 MB
      Memory: 64 GB

Software:

    System Software Overview:

      System Version: macOS 12.5 (21G72)
      Kernel Version: Darwin 21.6.0
      Time since boot: 58 minutes

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      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


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    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: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    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: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
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    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
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    Send2Trash: 1.8.0
    SEQCROW: 1.5
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
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    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0
File attachment: c3po-opt-freq-casscf-tz.out

c3po-opt-freq-casscf-tz.out​

[matthew.graneri@…]

Added by email2trac

[Tony Schaefer]

Matthew,

It looks like our file parser doesn't know how to handle the dummy atom in the ORCA output. I'll try to fix that soon

Tony
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Monday, August 15, 2022 12:08 PM
Cc: matthew.graneri@research.uwa.edu.au <matthew.graneri@research.uwa.edu.au>; Anthony James Schaefer <tony.schaefer@uga.edu>
Subject: Re: [ChimeraX] #7452: Problem reading ORCA output file (was: ChimeraX bug report submission)

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]


#7452: Problem reading ORCA output file
----------------------------------------+---------------------------
          Reporter:  matthew.graneri@…  |      Owner:  Tony Schaefer
              Type:  defect             |     Status:  assigned
          Priority:  normal             |  Milestone:
         Component:  Third Party        |    Version:
        Resolution:                     |   Keywords:
        Blocked By:                     |   Blocking:
Notify when closed:                     |   Platform:  all
           Project:  ChimeraX           |
----------------------------------------+---------------------------
Changes (by pett):

 * status:  new => assigned
 * component:  Unassigned => Third Party
 * project:   => ChimeraX
 * platform:   => all
 * owner:  (none) => Tony Schaefer


--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7452#comment:1>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[Tony Schaefer]

This should be fixed in the new version of SEQCROW (1.5.1). I'm able to open the file, view normal modes, and make a new input file using this structure. The dummy atom will be present in ORCA, Psi4, and Gaussian input files that are made through the QM Input Builder tool, but note that our input file builder doesn't handle dummy atoms for Q-Chem.

If you don't want to see the dummy atom, you can hide it by running the command "hide @@element==LP"​ or selecting it and running "hide sel"​. Replacing "hide"​ with "delete​" should work just as well if you want to get rid of the dummy for good.

Let me know if you notice more issues with dummy atoms or anything else

Best,

Tony
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Monday, August 15, 2022 2:20 PM
To: matthew.graneri@research.uwa.edu.au <matthew.graneri@research.uwa.edu.au>; Anthony James Schaefer <tony.schaefer@uga.edu>
Subject: Re: [ChimeraX] #7452: Problem reading ORCA output file

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]


#7452: Problem reading ORCA output file
----------------------------------------+---------------------------
          Reporter:  matthew.graneri@…  |      Owner:  Tony Schaefer
              Type:  defect             |     Status:  assigned
          Priority:  normal             |  Milestone:
         Component:  Third Party        |    Version:
        Resolution:                     |   Keywords:
        Blocked By:                     |   Blocking:
Notify when closed:                     |   Platform:  all
           Project:  ChimeraX           |
----------------------------------------+---------------------------

Comment (by Tony Schaefer):

 {{{
 Matthew,

 It looks like our file parser doesn't know how to handle the dummy atom in
 the ORCA output. I'll try to fix that soon

 Tony
 ________________________________
 From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
 Sent: Monday, August 15, 2022 12:08 PM
 Cc: matthew.graneri@research.uwa.edu.au
 <matthew.graneri@research.uwa.edu.au>; Anthony James Schaefer
 <tony.schaefer@uga.edu>
 Subject: Re: [ChimeraX] #7452: Problem reading ORCA output file (was:
 ChimeraX bug report submission)

 [EXTERNAL SENDER - PROCEED CAUTIOUSLY]


 #7452: Problem reading ORCA output file
 ----------------------------------------+---------------------------
           Reporter:  matthew.graneri@…  |      Owner:  Tony Schaefer
               Type:  defect             |     Status:  assigned
           Priority:  normal             |  Milestone:
          Component:  Third Party        |    Version:
         Resolution:                     |   Keywords:
         Blocked By:                     |   Blocking:
 Notify when closed:                     |   Platform:  all
            Project:  ChimeraX           |
 ----------------------------------------+---------------------------
 Changes (by pett):

  * status:  new => assigned
  * component:  Unassigned => Third Party
  * project:   => ChimeraX
  * platform:   => all
  * owner:  (none) => Tony Schaefer


 --
 Ticket URL:
 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7452#comment:1>
 ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
 ChimeraX Issue Tracker
 }}}

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7452#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker