Opened 2 years ago

Closed 2 years ago

#9452 closed defect (fixed)

StarMap: Permission denied: 'run_starmap_medic.sh'

Reported by: scluo@… 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 pett, 2 years ago

Component: UnassignedThird Party
Owner: set to Wolfgang Lugmayr
Platform: all
Project: ChimeraX
Status: newassigned
Summary: ChimeraX bug report submissionStarMap: Permission denied: 'run_starmap_medic.sh'

Reported by Shih-Chi Luo

comment:2 by wolfgang.lugmayr@…, 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 wolfgang.lugmayr@…, 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
 }}}

comment:4 by pett, 2 years ago

Resolution: fixed
Status: assignedclosed

Fixed in starmap 1.2.17

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