Opened 2 years ago
Closed 2 years ago
#9452 closed defect (fixed)
StarMap: Permission denied: 'run_starmap_medic.sh'
Reported by: | 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: Windows-10-10.0.19044 ChimeraX Version: 1.7.dev202307150241 (2023-07-15 02:41:29 UTC) Description it says "permission denied: run_starmap_medic.sh". Shoud I change the permissions of this file shomewhere? Log: UCSF ChimeraX version: 1.7.dev202307150241 (2023-07-15) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > ui tool show StarMap > starting StarMap 1.2.15 > use command <stmhelp show> for the StarMap manual starmap> checking WSL2 installation by calling: starmap> wsl.exe --status wsl> starmap> ERROR using the default Windows Subsystem for Linux (WSL2)!!! starmap> Is WSL properly installed? > 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! Exception in thread Thread-1 (_readerthread): Traceback (most recent call last): File "C:\Users\ChimeraX\bin\Lib\threading.py", line 1038, in _bootstrap_inner self.run() File "C:\Users\ChimeraX\bin\Lib\threading.py", line 975, in run self._target(*self._args, **self._kwargs) File "C:\Users\ChimeraX\bin\Lib\subprocess.py", line 1552, in _readerthread buffer.append(fh.read()) ^^^^^^^^^ UnicodeDecodeError: 'cp950' codec can't decode byte 0x98 in position 1: illegal multibyte sequence > stmconfig STARMAP_VERSION = 1.2.15 ROSETTA_SCRIPTS_CMD = rosetta_scripts.static.linuxgccrelease ROSETTA_SCRIPTS_MPI_CMD = rosetta_scripts.static.linuxgccrelease ROSETTA_DENSITY_CMD = density_tools.static.linuxgccrelease ROSETTA_SYMMDEF_CMD = make_symmdef_file.pl MEDIC_SCRIPT_TEMPLATE = C:/Users/User1/AppData/Local/UCSF/ChimeraX/1.7/site- packages/chimerax/starmap/templates/starmap_medic.tmpl.sh STARMAP_ROSETTA_SCRIPT = C:/Users/User1/AppData/Local/UCSF/ChimeraX/1.7/site- packages/chimerax/starmap/templates/rosetta_tmpl_1.2.xml STARMAP_ROSETTA_APIX_SCRIPT = C:/Users/User1/AppData/Local/UCSF/ChimeraX/1.7/site- packages/chimerax/starmap/templates/rosetta_apix.xml STARMAP_SYMMETRY_CMD = C:/Users/User1/AppData/Local/UCSF/ChimeraX/1.7/site- packages/chimerax/starmap/contrib/check_symmetry.sh STARMAP_HELP = file:///C:/Users/User1/AppData/Local/UCSF/ChimeraX/1.7/site- packages/chimerax/starmap/docs/starmap.html STARMAP_TEMPLATES_DIR = C:/Users/User1/AppData/Local/UCSF/ChimeraX/1.7/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 = WSL = C:/Windows/system32/wsl.exe TEMP = C:/Users/User1/AppData/Local/Temp/ PYTHON_SITE_PACKAGE = C:/Users/User1/AppData/Local/UCSF/ChimeraX/1.7/site- packages/chimerax/starmap LOCAL_CORES = 16 FIX_FONT_SIZE = C:/Users/User1/AppData/Local/UCSF/ChimeraX/1.7/site- packages/chimerax/starmap/qtstarmapwidget.py Traceback (most recent call last): File "C:\Users\User1\AppData\Local\UCSF\ChimeraX\1.7\site- packages\chimerax\starmap\tool.py", line 601, in _save_bash_medic_script target = open(self.stmBashMedicFile, 'w', newline='\n') ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ PermissionError: [Errno 13] Permission denied: 'run_starmap_medic.sh' PermissionError: [Errno 13] Permission denied: 'run_starmap_medic.sh' File "C:\Users\User1\AppData\Local\UCSF\ChimeraX\1.7\site- packages\chimerax\starmap\tool.py", line 601, in _save_bash_medic_script target = open(self.stmBashMedicFile, 'w', newline='\n') ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. Traceback (most recent call last): File "C:\Users\User1\AppData\Local\UCSF\ChimeraX\1.7\site- packages\chimerax\starmap\tool.py", line 601, in _save_bash_medic_script target = open(self.stmBashMedicFile, 'w', newline='\n') ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ PermissionError: [Errno 13] Permission denied: 'run_starmap_medic.sh' PermissionError: [Errno 13] Permission denied: 'run_starmap_medic.sh' File "C:\Users\User1\AppData\Local\UCSF\ChimeraX\1.7\site- packages\chimerax\starmap\tool.py", line 601, in _save_bash_medic_script target = open(self.stmBashMedicFile, 'w', newline='\n') ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 456.71 OpenGL renderer: GeForce GT 730/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.2 Locale: zh_TW.cp950 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: windows Manufacturer: Dell Inc. Model: OptiPlex 7090 OS: Microsoft Windows 10 專業版 (Build 19044) Memory: 16,887,386,112 MaxProcessMemory: 137,438,953,344 CPU: 16 11th Gen Intel(R) Core(TM) i7-11700 @ 2.50GHz OSLanguage: zh-TW Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2023.5.7 cftime: 1.6.2 charset-normalizer: 3.2.0 ChimeraX-AddCharge: 1.5.11 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.46 ChimeraX-AtomicLibrary: 10.0.8 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: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.4 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-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: 1.7.dev202307150241 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: 1.1.2 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-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.2 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: 2.1 ChimeraX-MCopy: 1.0 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: 1.4 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: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.2 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0.1 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: 1.2 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: 2.9 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: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StarMap: 1.2.15 ChimeraX-StdCommands: 1.12.1 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: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.30.2 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2.2 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 comtypes: 1.1.14 contourpy: 1.1.0 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: 4.41.0 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.9.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2023.3.16 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.7 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.3.1 jupyterlab-widgets: 3.0.8 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 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: 23.1 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.8.1 prompt-toolkit: 3.0.39 psutil: 5.9.4 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.6 PyOpenGL-accelerate: 3.1.6 pyparsing: 3.1.0 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 pywin32: 305 pyzmq: 25.1.0 qtconsole: 5.4.3 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 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: 3.8.0 tcia-utils: 1.5.1 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.2 traitlets: 5.9.0 typing-extensions: 4.7.1 tzdata: 2023.3 urllib3: 2.0.3 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.8 WMI: 1.5.1
Change History (4)
comment:1 by , 2 years ago
Component: | Unassigned → Third Party |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → StarMap: Permission denied: 'run_starmap_medic.sh' |
comment:2 by , 2 years ago
Dear Lou, it seems you try to save the script to a working folder which your login user is not allowed to access. In the StarMap workflow it is assumed you create a working folder on Windows e.g. C:\Users\username\MyProject Then copy the MRC and PDB file into this working folder. In ChimeraX then go to "File -> Set Working Folder ..." and choose this folder. Open StarMap and go to 'Analysis -> Input' and choose the MRC and PDB and set the map resolution. Now switch to 'MEDIC -> Save/Run' and press the Save button again and the 'Execute' button should be enabled. The execution will fail because you need a Linux distribution to execute the script. From your log: starmap> checking WSL2 installation by calling: starmap> wsl.exe --status wsl> starmap> ERROR using the default Windows Subsystem for Linux (WSL2)!!! starmap> Is WSL properly installed? Please download/install a Ubuntu from the Microsoft Store. Once you have installed Ubuntu open a Windows Powershell and type: wsl.exe /usr/bin/bash You should get a different command prompt. StarMap then will call later something like: wsl.exe /usr/bin/bash C:/Users/username/MyProject/run_starmap_medic.sh and this will do the MEDIC run inside the WSL2 and the commandline script execution messages will be displayed in the StarMap Log tab. Did setting the working folder in ChimeraX solve your problem? Cheers, Wolfgang ----- Original Message ----- From: "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu> To: "scluo" <scluo@gate.sinica.edu.tw>, "starmap" <starmap@marlovitslab.org> Sent: Tuesday, 25 July, 2023 18:13:42 Subject: Re: [ChimeraX] #9452: StarMap: Permission denied: 'run_starmap_medic.sh' (was: ChimeraX bug report submission) #9452: StarMap: Permission denied: 'run_starmap_medic.sh' ----------------------------------+------------------------------ Reporter: scluo@\u2026 | Owner: Wolfgang Lugmayr 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): * component: Unassigned => Third Party * owner: (none) => Wolfgang Lugmayr * platform: => all * project: => ChimeraX * status: new => assigned * summary: ChimeraX bug report submission => StarMap: Permission denied: 'run_starmap_medic.sh' Comment: Reported by Shih-Chi Luo
comment:3 by , 2 years ago
Added a popup warning window with the name of the directory where StarMap could not write. This happens only if ChimeraX is started from the main Windows menu. When its started by a desktop/quicklaunch icon, the default data location is the users desktop and there its writeable. Fixed on github in v1.2.17, I will wait for more MEDIC issues until I release a new toolshed version. Cheers, Wolfgang ----- Original Message ----- From: "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu> To: "scluo" <scluo@gate.sinica.edu.tw>, "starmap" <starmap@marlovitslab.org> Sent: Wednesday, 26 July, 2023 11:19:32 Subject: Re: [ChimeraX] #9452: StarMap: Permission denied: 'run_starmap_medic.sh' #9452: StarMap: Permission denied: 'run_starmap_medic.sh' ----------------------------------+------------------------------ Reporter: scluo@\u2026 | Owner: Wolfgang Lugmayr 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 wolfgang.lugmayr@\u2026): {{{ Dear Lou, it seems you try to save the script to a working folder which your login user is not allowed to access. In the StarMap workflow it is assumed you create a working folder on Windows e.g. C:\Users\username\MyProject Then copy the MRC and PDB file into this working folder. In ChimeraX then go to "File -> Set Working Folder ..." and choose this folder. Open StarMap and go to 'Analysis -> Input' and choose the MRC and PDB and set the map resolution. Now switch to 'MEDIC -> Save/Run' and press the Save button again and the 'Execute' button should be enabled. The execution will fail because you need a Linux distribution to execute the script. From your log: starmap> checking WSL2 installation by calling: starmap> wsl.exe --status wsl> starmap> ERROR using the default Windows Subsystem for Linux (WSL2)!!! starmap> Is WSL properly installed? Please download/install a Ubuntu from the Microsoft Store. Once you have installed Ubuntu open a Windows Powershell and type: wsl.exe /usr/bin/bash You should get a different command prompt. StarMap then will call later something like: wsl.exe /usr/bin/bash C:/Users/username/MyProject/run_starmap_medic.sh and this will do the MEDIC run inside the WSL2 and the commandline script execution messages will be displayed in the StarMap Log tab. Did setting the working folder in ChimeraX solve your problem? Cheers, Wolfgang ----- Original Message ----- From: "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu> To: "scluo" <scluo@gate.sinica.edu.tw>, "starmap" <starmap@marlovitslab.org> Sent: Tuesday, 25 July, 2023 18:13:42 Subject: Re: [ChimeraX] #9452: StarMap: Permission denied: 'run_starmap_medic.sh' (was: ChimeraX bug report submission) #9452: StarMap: Permission denied: 'run_starmap_medic.sh' ----------------------------------+------------------------------ Reporter: scluo@\u2026 | Owner: Wolfgang Lugmayr 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): * component: Unassigned => Third Party * owner: (none) => Wolfgang Lugmayr * platform: => all * project: => ChimeraX * status: new => assigned * summary: ChimeraX bug report submission => StarMap: Permission denied: 'run_starmap_medic.sh' Comment: Reported by Shih-Chi Luo }}}
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Reported by Shih-Chi Luo