phenix connect command traceback when wrong Phenix directory given

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
Used phenix connect command.  File browser appeared and I chose /Applications/phenix-1.19.2-4158 and pressed Open and got this error.  Maybe it wants some subdirectory specified.  I'll try that.

Would be good to log a message saying what Phenix directory must be specified.

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show

Downloading bundle ChimeraX_Phenix-0.3-py3-none-any.whl  
Successfully installed ChimeraX-Phenix-0.3  
Installed ChimeraX-Phenix (0.3)  

> open 7cki structureFactors true

Summary of feedback from opening 7cki fetched from pdb  
---  
errors | Unknown invert atom type: N3 for atom 9E0 /A:401 N01  
Unknown invert atom type: N3 for atom 9E0 /A:401 N01  
Unknown invert atom type: N3 for atom 9E0 /A:401 N01  
notes | Fetching compressed mmCIF 7cki from
http://files.rcsb.org/download/7cki.cif  
Fetching CCD 9E0 from http://ligand-expo.rcsb.org/reports/9/9E0/9E0.cif  
Fetching compressed 7cki structure factors from
http://files.rcsb.org/download/7cki-sf.cif  
Resolution: 2.159386109870212  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 40,38,36, pixel
0.646,0.646,0.681, shown at level 0.581, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 40,38,36, pixel
0.646,0.646,0.681, shown at level -0.161,0.161, step 1, values float32  
Opened (LIVE) 2mFo-DFc_smooth_12 as #1.1.1.4, grid size 40,38,36, pixel
0.646,0.646,0.681, shown at level 0.486, step 1, values float32  
Opened (STATIC) pdbx_DELFWT, pdbx_DELPHWT as #1.1.1.5, grid size 40,38,36,
pixel 0.646,0.646,0.681, shown at level -0.319,0.319, step 1, values float32  
Opened (STATIC) pdbx_FWT, pdbx_PHWT as #1.1.1.6, grid size 40,38,36, pixel
0.646,0.646,0.681, shown at level -0.976,0.976, step 1, values float32  
7cki title:  
Crystal structure of Tryptophanyl-tRNA synthetase from Bacillus
stearothermophilus in complex with chuangxinmycin and ATP [more info...]  
  
Chain information for 7cki  
---  
Chain | Description  
1.2/A | Tryptophan--tRNA ligase  
  
Non-standard residues in 7cki #1.2  
---  
9E0 —
(5~{S},6~{R})-5-methyl-7-thia-2-azatricyclo[6.3.1.0^{4,12}]dodeca-1(12),3,8,10-tetraene-6-carboxylic
acid  
ATP — adenosine-5'-triphosphate  
K — potassium ion  
MG — magnesium ion  
  
7cki mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> select :ATP

31 atoms, 33 bonds, 1 residue, 1 model selected  

> view sel

> delete sel

> phenix connect

Traceback (most recent call last):  
File "/Users/goddard/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/phenix/__init__.py", line 25, in _choose_phenix_directory  
subprocess.call([os.path.join(result,'phenix.version')])  
File
"/Users/goddard/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/subprocess.py",
line 340, in call  
with Popen(*popenargs, **kwargs) as p:  
File
"/Users/goddard/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/subprocess.py",
line 858, in __init__  
self._execute_child(args, executable, preexec_fn, close_fds,  
File
"/Users/goddard/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/subprocess.py",
line 1706, in _execute_child  
raise child_exception_type(errno_num, err_msg, err_filename)  
FileNotFoundError: [Errno 2] No such file or directory:
'/Applications/phenix-1.19.2-4158/phenix.version'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Users/goddard/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 280, in execute  
cmd.run(cmd_text)  
File
"/Users/goddard/Desktop/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "/Users/goddard/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/phenix/cmd.py", line 45, in phenix_connect  
sufficient, version = check_for_phenix(session)  
File "/Users/goddard/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/phenix/__init__.py", line 77, in check_for_phenix  
version = check_for_phenix_version(session)  
File "/Users/goddard/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/phenix/__init__.py", line 50, in check_for_phenix_version  
phenix_path = _choose_phenix_directory(session)  
File "/Users/goddard/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/phenix/__init__.py", line 28, in _choose_phenix_directory  
choice = QMessageBox.warning(parent, 'This directory does not appear to
contain Phenix executables. Would you like to try again?',  
TypeError: warning(QWidget, str, str, buttons:
Union[QMessageBox.StandardButtons, QMessageBox.StandardButton] =
QMessageBox.Ok, defaultButton: QMessageBox.StandardButton =
QMessageBox.NoButton): argument 3 has unexpected type 'StandardButtons'  
  
TypeError: warning(QWidget, str, str, buttons:
Union[QMessageBox.StandardButtons, QMessageBox.StandardButton] =
QMessageBox.Ok, defaultButton: QMessageBox.StandardButton =
QMessageBox.NoButton): argument 3 has unexpected type 'StandardButtons'  
  
File "/Users/goddard/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/phenix/__init__.py", line 28, in _choose_phenix_directory  
choice = QMessageBox.warning(parent, 'This directory does not appear to
contain Phenix executables. Would you like to try again?',  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.10.19
OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,3
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.4 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: 1554.100.64.0.0 (iBridge: 18.16.14556.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H1030)
      Kernel Version: Darwin 19.6.0
      Time since boot: 62 days 21:43

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1

    Radeon Pro Vega 20:

      Chipset Model: Radeon Pro Vega 20
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x69af
      Revision ID: 0x00c0
      ROM Revision: 113-D2060I-087
      VBIOS Version: 113-D20601MA0T-016
      Option ROM Version: 113-D20601MA0T-016
      EFI Driver Version: 01.01.087
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
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    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    biopython: 1.78
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-Clipper: 0.16.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    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: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
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    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.2.2
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
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    ChimeraX-Map: 1.0.2
    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: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
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    ChimeraX-ModelSeries: 1.0
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    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
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    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
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    ChimeraX-PDBBio: 1.0
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    ChimeraX-PDBMatrices: 1.0
    ChimeraX-Phenix: 0.3
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    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
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    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
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    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    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
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    comtypes: 1.1.7
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    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0

[goddard@…]

By trial and error found it wanted /Applications/phinx-1.19.2-4156/build/bin

[Tom Goddard]

The QMessageBox did not appear, I guess due to the error.

[Tristan Croll]

Obsolete now, due to the R24 ChimeraX-Phenix interface.