Opened 2 years ago

Closed 2 years ago

#9778 closed defect (not a bug)

StarMap: Rosetta executables not found

Reported by: chimerax-bug-report@… Owned by: Wolfgang Lugmayr
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-13.5-arm64-arm-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> stmconfig

  
STARMAP_VERSION = 1.2.15  
ROSETTA_SCRIPTS_CMD = rosetta_scripts.static.macosclangrelease  
ROSETTA_SCRIPTS_MPI_CMD = rosetta_scripts.static.macosclangrelease  
ROSETTA_DENSITY_CMD = density_tools.static.macosclangrelease  
ROSETTA_SYMMDEF_CMD =
${ROSETTA3}/source/src/apps/public/symmetry/make_symmdef_file.pl  
MEDIC_SCRIPT_TEMPLATE = /Users/emullapudi/Library/Application
Support/ChimeraX/1.6/site-
packages/chimerax/starmap/templates/starmap_medic.tmpl.sh  
STARMAP_ROSETTA_SCRIPT = /Users/emullapudi/Library/Application
Support/ChimeraX/1.6/site-
packages/chimerax/starmap/templates/rosetta_tmpl_1.2.xml  
STARMAP_ROSETTA_APIX_SCRIPT = /Users/emullapudi/Library/Application
Support/ChimeraX/1.6/site-packages/chimerax/starmap/templates/rosetta_apix.xml  
STARMAP_SYMMETRY_CMD = /Users/emullapudi/Library/Application
Support/ChimeraX/1.6/site-packages/chimerax/starmap/contrib/check_symmetry.sh  
STARMAP_HELP = file:///Users/emullapudi/Library/Application
Support/ChimeraX/1.6/site-packages/chimerax/starmap/docs/starmap.html  
STARMAP_TEMPLATES_DIR = /Users/emullapudi/Library/Application
Support/ChimeraX/1.6/site-packages/chimerax/starmap/templates/  
STARMAP_USER1 = extra_res_cen  
STARMAP_USER2 = extra_res_fa  
STARMAP_USER3 =  
STARMAP_USER4 =  
STARMAP_USER5 =  
STARMAP_USER6 =  
STARMAP_USER7 =  
STARMAP_USER8 =  
PYTHON_SITE_PACKAGE = /Users/emullapudi/Library/Application
Support/ChimeraX/1.6/site-packages/chimerax/starmap  
LOCAL_CORES = 12  
FIX_FONT_SIZE = /Users/emullapudi/Library/Application
Support/ChimeraX/1.6/site-packages/chimerax/starmap/qtstarmapwidget.py  
  

> ui tool show StarMap

> starting StarMap 1.2.15  
> use command <stmhelp show> for the StarMap manual  

Populating font family aliases took 143 ms. Replace uses of missing font
family "Sans Serif" with one that exists to avoid this cost.  

> stmset usrlbl1=extra_res_cen

> stmset usrlbl2=extra_res_fa

Rosetta executables not found!  
Scripts can only be generated with default Rosetta executable names. Executing
them directly from ChimeraX will therefore fail!  

Traceback (most recent call last):  
File "/Users/emullapudi/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/starmap/tool.py", line 622, in _save_bash_apix_script  
self._save_apix_rosetta_script(apixFile)  
File "/Users/emullapudi/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/starmap/tool.py", line 651, in _save_apix_rosetta_script  
with open(STARMAP_ROSETTA_APIX_SCRIPT, encoding='utf-8') as f:  
FileNotFoundError: [Errno 2] No such file or directory: 'rosetta_apix.xml'  
  
FileNotFoundError: [Errno 2] No such file or directory: 'rosetta_apix.xml'  
  
File "/Users/emullapudi/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/starmap/tool.py", line 651, in _save_apix_rosetta_script  
with open(STARMAP_ROSETTA_APIX_SCRIPT, encoding='utf-8') as f:  
  
See log for complete Python traceback.  
  

> stmconfig

  
STARMAP_VERSION = 1.2.15  
ROSETTA_SCRIPTS_CMD = rosetta_scripts.static.macosclangrelease  
ROSETTA_SCRIPTS_MPI_CMD = rosetta_scripts.static.macosclangrelease  
ROSETTA_DENSITY_CMD = density_tools.static.macosclangrelease  
ROSETTA_SYMMDEF_CMD =
${ROSETTA3}/source/src/apps/public/symmetry/make_symmdef_file.pl  
MEDIC_SCRIPT_TEMPLATE = /Users/emullapudi/Library/Application
Support/ChimeraX/1.6/site-
packages/chimerax/starmap/templates/starmap_medic.tmpl.sh  
STARMAP_ROSETTA_SCRIPT = /Users/emullapudi/Library/Application
Support/ChimeraX/1.6/site-
packages/chimerax/starmap/templates/rosetta_tmpl_1.2.xml  
STARMAP_ROSETTA_APIX_SCRIPT = /Users/emullapudi/Library/Application
Support/ChimeraX/1.6/site-packages/chimerax/starmap/templates/rosetta_apix.xml  
STARMAP_SYMMETRY_CMD = /Users/emullapudi/Library/Application
Support/ChimeraX/1.6/site-packages/chimerax/starmap/contrib/check_symmetry.sh  
STARMAP_HELP = file:///Users/emullapudi/Library/Application
Support/ChimeraX/1.6/site-packages/chimerax/starmap/docs/starmap.html  
STARMAP_TEMPLATES_DIR = /Users/emullapudi/Library/Application
Support/ChimeraX/1.6/site-packages/chimerax/starmap/templates/  
STARMAP_USER1 = extra_res_cen  
STARMAP_USER2 = extra_res_fa  
STARMAP_USER3 =  
STARMAP_USER4 =  
STARMAP_USER5 =  
STARMAP_USER6 =  
STARMAP_USER7 =  
STARMAP_USER8 =  
PYTHON_SITE_PACKAGE = /Users/emullapudi/Library/Application
Support/ChimeraX/1.6/site-packages/chimerax/starmap  
LOCAL_CORES = 12  
FIX_FONT_SIZE = /Users/emullapudi/Library/Application
Support/ChimeraX/1.6/site-packages/chimerax/starmap/qtstarmapwidget.py  
  
Traceback (most recent call last):  
File "/Users/emullapudi/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/starmap/tool.py", line 622, in _save_bash_apix_script  
self._save_apix_rosetta_script(apixFile)  
File "/Users/emullapudi/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/starmap/tool.py", line 651, in _save_apix_rosetta_script  
with open(STARMAP_ROSETTA_APIX_SCRIPT, encoding='utf-8') as f:  
FileNotFoundError: [Errno 2] No such file or directory: 'rosetta_apix.xml'  
  
FileNotFoundError: [Errno 2] No such file or directory: 'rosetta_apix.xml'  
  
File "/Users/emullapudi/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/starmap/tool.py", line 651, in _save_apix_rosetta_script  
with open(STARMAP_ROSETTA_APIX_SCRIPT, encoding='utf-8') as f:  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,5
      Model Number: Z17J001F6D/A
      Chip: Apple M2 Max
      Total Number of Cores: 12 (8 performance and 4 efficiency)
      Memory: 64 GB
      System Firmware Version: 8422.141.2
      OS Loader Version: 8422.141.2

Software:

    System Software Overview:

      System Version: macOS 13.5 (22G74)
      Kernel Version: Darwin 22.6.0
      Time since boot: 3 days, 5 hours, 6 minutes

Graphics/Displays:

    Apple M2 Max:

      Chipset Model: Apple M2 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 30
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        DELL P2419H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
        DELL P2720D:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    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: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.21.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    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-ISOLDE: 1.6.0
    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: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NIHPresets: 1.1.12
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-OpenCommands: 1.1
    ChimeraX-PDB: 2.7.2
    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-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    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-StarMap: 1.2.15
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    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: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    pyqtgraph: 0.13.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    Send2Trash: 1.8.2
    SEQCROW: 1.7.3
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

Change History (2)

comment:1 by Eric Pettersen, 2 years ago

Component: Unassigned → Third Party
Owner: set to Wolfgang Lugmayr
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → StarMap: Rosetta executables not found

comment:2 by Wolfgang Lugmayr, 2 years ago

Resolution: → not a bug
Status: assigned → closed

This message is a warning that the external Rosetta software suite was not installed or the executables are not visible to ChimeraX/StarMap.

Due license and download size reasons the user must download Rosetta outside the ChimeraX toolshed.

A short guide on how to download, extract the binaries and add it to your environment is in the StarMap manual (type 'stmhelp show' in the ChimeraX commandline) in section "Troubleshooting and HOWTOs" -> "Rosetta HOWTO".

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