Opened 3 years ago

Closed 3 years ago

#8056 closed defect (fixed)

Problem opening Gaussian output: Unknown element detected: Variables

Reported by: matthew.graneri@… Owned by: Tony Schaefer
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-13.0.1-arm64-arm-64bit
ChimeraX Version: 1.5rc202211171732 (2022-11-17 17:32:15 UTC)
Description
Tried to upload Gaussian output file, and error comes up.

Log:
UCSF ChimeraX version: 1.5rc202211171732 (2022-11-17)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/matthewgraneri/Documents/Homework/PhD/calculations/p2/complexes/ma.h2s/c1/b3lyp-d3/coulomb/gau_ma.h2s-opt-
> freq-b3lyp-d3-qzvppd.log

Summary of feedback from opening
/Users/matthewgraneri/Documents/Homework/PhD/calculations/p2/complexes/ma.h2s/c1/b3lyp-d3/coulomb/gau_ma.h2s-opt-
freq-b3lyp-d3-qzvppd.log  
---  
error | unable to open gau_ma.h2s-opt-freq-b3lyp-d3-qzvppd.log  
  
Traceback (most recent call last):  
File
"/Applications/Chimera/ChimeraX-1.5-rc2022.11.17.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-1.5-rc2022.11.17.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-1.5-rc2022.11.17.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-1.5-rc2022.11.17.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-1.5-rc2022.11.17.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-1.5-rc2022.11.17.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-1.5-rc2022.11.17.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-1.5-rc2022.11.17.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/1.5/site-
packages/SEQCROW/__init__.py", line 414, in open  
return open_aarontools(  
File "/Users/matthewgraneri/Library/Application Support/ChimeraX/1.5/site-
packages/SEQCROW/io.py", line 40, in open_aarontools  
raise e  
File "/Users/matthewgraneri/Library/Application Support/ChimeraX/1.5/site-
packages/SEQCROW/io.py", line 32, in open_aarontools  
fr = FileReader(  
File "/Users/matthewgraneri/Library/Application Support/ChimeraX/1.5/site-
packages/AaronTools/fileIO.py", line 1002, in __init__  
self.read_log(f, get_all, just_geom, scan_read_all)  
File "/Users/matthewgraneri/Library/Application Support/ChimeraX/1.5/site-
packages/AaronTools/fileIO.py", line 2605, in read_log  
self.atoms, n = get_input(f, n)  
File "/Users/matthewgraneri/Library/Application Support/ChimeraX/1.5/site-
packages/AaronTools/fileIO.py", line 2459, in get_input  
rv += [Atom(element=line[0], name=str(a), coords=np.zeros(3))]  
File "/Users/matthewgraneri/Library/Application Support/ChimeraX/1.5/site-
packages/AaronTools/atoms.py", line 117, in __init__  
raise ValueError("Unknown element detected: %s" % element)  
ValueError: Unknown element detected: Variables:  
  
ValueError: Unknown element detected: Variables:  
  
File "/Users/matthewgraneri/Library/Application Support/ChimeraX/1.5/site-
packages/AaronTools/atoms.py", line 117, in __init__  
raise ValueError("Unknown element detected: %s" % element)  
  
See log for complete Python traceback.  
  

> open
> /Users/matthewgraneri/Documents/Homework/PhD/calculations/p2/complexes/ma.h2s/c1/b3lyp-d3/coulomb/gau_ma.h2s-opt-
> freq-b3lyp-d3-qzvppd.log

Summary of feedback from opening
/Users/matthewgraneri/Documents/Homework/PhD/calculations/p2/complexes/ma.h2s/c1/b3lyp-d3/coulomb/gau_ma.h2s-opt-
freq-b3lyp-d3-qzvppd.log  
---  
error | unable to open gau_ma.h2s-opt-freq-b3lyp-d3-qzvppd.log  
  
Traceback (most recent call last):  
File
"/Applications/Chimera/ChimeraX-1.5-rc2022.11.17.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-1.5-rc2022.11.17.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-1.5-rc2022.11.17.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-1.5-rc2022.11.17.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-1.5-rc2022.11.17.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-1.5-rc2022.11.17.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-1.5-rc2022.11.17.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-1.5-rc2022.11.17.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/1.5/site-
packages/SEQCROW/__init__.py", line 414, in open  
return open_aarontools(  
File "/Users/matthewgraneri/Library/Application Support/ChimeraX/1.5/site-
packages/SEQCROW/io.py", line 40, in open_aarontools  
raise e  
File "/Users/matthewgraneri/Library/Application Support/ChimeraX/1.5/site-
packages/SEQCROW/io.py", line 32, in open_aarontools  
fr = FileReader(  
File "/Users/matthewgraneri/Library/Application Support/ChimeraX/1.5/site-
packages/AaronTools/fileIO.py", line 1002, in __init__  
self.read_log(f, get_all, just_geom, scan_read_all)  
File "/Users/matthewgraneri/Library/Application Support/ChimeraX/1.5/site-
packages/AaronTools/fileIO.py", line 2605, in read_log  
self.atoms, n = get_input(f, n)  
File "/Users/matthewgraneri/Library/Application Support/ChimeraX/1.5/site-
packages/AaronTools/fileIO.py", line 2459, in get_input  
rv += [Atom(element=line[0], name=str(a), coords=np.zeros(3))]  
File "/Users/matthewgraneri/Library/Application Support/ChimeraX/1.5/site-
packages/AaronTools/atoms.py", line 117, in __init__  
raise ValueError("Unknown element detected: %s" % element)  
ValueError: Unknown element detected: Variables:  
  
ValueError: Unknown element detected: Variables:  
  
File "/Users/matthewgraneri/Library/Application Support/ChimeraX/1.5/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 - 83
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,2
      Model Number: Z14X000EVX/A
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 64 GB
      System Firmware Version: 8419.41.10
      OS Loader Version: 8419.41.10

Software:

    System Software Overview:

      System Version: macOS 13.0.1 (22A400)
      Kernel Version: Darwin 22.1.0
      Time since boot: 1 hour, 37 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 Support: Metal 3
      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
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5rc202211171732
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    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: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.3
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.0.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.0.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.32
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.6
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    Send2Trash: 1.8.0
    SEQCROW: 1.5.8
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    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
    stack-data: 0.6.1
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.12
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.10.0
File attachment: gau_ma.h2s-opt-freq-b3lyp-d3-qzvppd.log

gau_ma.h2s-opt-freq-b3lyp-d3-qzvppd.log​

Attachments (1)

gau_ma.h2s-opt-freq-b3lyp-d3-qzvppd.log​ (1.9 MB ) - added by matthew.graneri@… 3 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (6)

by matthew.graneri@…, 3 years ago

Attachment: gau_ma.h2s-opt-freq-b3lyp-d3-qzvppd.log​ added

Added by email2trac

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Third Party
Owner: set to Tony Schaefer
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Problem opening Gaussian output: Unknown element detected: Variables

in reply to:  3 comment:2 by Tony Schaefer, 3 years ago 

Our Gaussian file parser doesn't handle z-matrices. I'll work on adding that.

As a temporary workaround, you can delete the "Variables" section that starts on line 123 of the output, and the file will open. The first coordinate set will have all the atoms at the origin, but the rest of the coordinate sets will be the standard/input orientation from the optimization.

Tony
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Monday, November 21, 2022 10:17 AM
Cc: matthew.graneri@research.uwa.edu.au <matthew.graneri@research.uwa.edu.au>; Anthony James Schaefer <tony.schaefer@uga.edu>
Subject: Re: [ChimeraX] #8056: Problem opening Gaussian output: Unknown element detected: Variables (was: ChimeraX bug report submission)

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]


#8056: Problem opening Gaussian output: Unknown element detected: Variables
----------------------------------------+---------------------------
          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/8056#comment:1>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

in reply to:  4 ; comment:3 by Tony Schaefer, 3 years ago 

Fixed in SEQCROW 1.5.9. You can update through the toolshed (Tools -> More Tools... on the ChimeraX menu).

best,

Tony
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Monday, November 21, 2022 10:57 AM
To: matthew.graneri@research.uwa.edu.au <matthew.graneri@research.uwa.edu.au>; Anthony James Schaefer <tony.schaefer@uga.edu>
Subject: Re: [ChimeraX] #8056: Problem opening Gaussian output: Unknown element detected: Variables

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]


#8056: Problem opening Gaussian output: Unknown element detected: Variables
----------------------------------------+---------------------------
          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):

 {{{
 Our Gaussian file parser doesn't handle z-matrices. I'll work on adding
 that.

 As a temporary workaround, you can delete the "Variables" section that
 starts on line 123 of the output, and the file will open. The first
 coordinate set will have all the atoms at the origin, but the rest of the
 coordinate sets will be the standard/input orientation from the
 optimization.

 Tony
 ________________________________
 From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
 Sent: Monday, November 21, 2022 10:17 AM
 Cc: matthew.graneri@research.uwa.edu.au
 <matthew.graneri@research.uwa.edu.au>; Anthony James Schaefer
 <tony.schaefer@uga.edu>
 Subject: Re: [ChimeraX] #8056: Problem opening Gaussian output: Unknown
 element detected: Variables (was: ChimeraX bug report submission)

 [EXTERNAL SENDER - PROCEED CAUTIOUSLY]


 #8056: Problem opening Gaussian output: Unknown element detected:
 Variables
 ----------------------------------------+---------------------------
           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/8056#comment:1>
 ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
 ChimeraX Issue Tracker
 }}}

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/8056#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

in reply to:  5 ; comment:4 by matthew.graneri@…, 3 years ago 

Hi Tony,

Thank you!

Regards

Matthew

comment:5 by Eric Pettersen, 3 years ago

Resolution: → fixed
Status: assigned → closed
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