Opened 4 years ago

Last modified 4 years ago

#5531 assigned defect

Problems connecting with Visual Studio Code

Reported by: Tristan Croll Owned by: Greg Couch
Priority: normal Milestone:
Component: Build System Version:
Keywords: Cc: chimera-programmers
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-3.10.0-1160.25.1.el7.x86_64-x86_64-with-glibc2.17
ChimeraX Version: 1.3rc202110301701 (2021-10-30 17:01:03 UTC)
Description
Trying to connect Visual Studio Code to ChimeraX's Python environment to make life a little easier. In Windows, giving it the ChimeraX executable works fine, with the minor side effect of launching a ChimeraX GUI window on first load. In Linux, I get this error message (I'm attaching the file it's actually trying to run). If I give it ChimeraX's Python executable, it connects without error but the user bundle directories aren't on the PYTHONPATH so I can't import ISOLDE (used, amongst other things, for live previewing of RestructuredText). Is there a way to make this work? Would wrapping the executable in a shell script that just extends the PYTHONPATH cause problems?

Log:
> alias preview_toolshed toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu; toolshed reload available

> alias production_toolshed toolshed url https://cxtoolshed.rbvi.ucsf.edu;
> toolshed reload available

> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  
UCSF ChimeraX version: 1.3rc202110301701 (2021-10-30)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/tic20/.vscode/extensions/ms-
> python.python-2021.5.926500501/pythonFiles/pyvsc-run-isolated.py

Traceback (most recent call last):  
File "/home/tic20/.vscode/extensions/ms-
python.python-2021.5.926500501/pythonFiles/pyvsc-run-isolated.py", line 5, in
<module>  
raise Exception("{} cannot be imported".format(__name__))  
Exception: ChimeraX_sandbox_1 cannot be imported  
  
Error opening python file /home/tic20/.vscode/extensions/ms-
python.python-2021.5.926500501/pythonFiles/pyvsc-run-isolated.py  

> open -c

'-c' has no suffix  

> open "import sys;print(sys.executable)"

Unrecognized file suffix '.executable)'  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/bug_reporter/bug_reporter_gui.py", line 190, in <lambda>  
sb.clicked.connect(lambda e: self.submit())  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/bug_reporter/bug_reporter_gui.py", line 237, in submit  
fields.extend(file_list)  
TypeError: 'NoneType' object is not iterable  
  
TypeError: 'NoneType' object is not iterable  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/bug_reporter/bug_reporter_gui.py", line 237, in submit  
fields.extend(file_list)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/bug_reporter/bug_reporter_gui.py", line 190, in <lambda>  
sb.clicked.connect(lambda e: self.submit())  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/bug_reporter/bug_reporter_gui.py", line 237, in submit  
fields.extend(file_list)  
TypeError: 'NoneType' object is not iterable  
  
TypeError: 'NoneType' object is not iterable  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/bug_reporter/bug_reporter_gui.py", line 237, in submit  
fields.extend(file_list)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 465.19.01
OpenGL renderer: NVIDIA TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            62G         11G        8.7G        426M         42G         50G
	Swap:          4.9G        3.8M        4.9G

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:11df]	
	Kernel driver in use: nvidia
Locale: ('en_GB', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.7
    ChimeraX-AddCharge: 1.1.5
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.30.2
    ChimeraX-AtomicLibrary: 4.1.5
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3rc202110301701
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    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: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.3.dev33
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.2
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.5
    ChimeraX-ModelPanel: 1.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-Phenix: 0.3
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-Sample: 0.1
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.5
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-Voyager: 0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.5.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jsonpickle: 2.0.0
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.2
    numexpr: 2.7.3
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.2
    ParmEd: 3.2.0
    parso: 0.8.2
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.21
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    python-igraph: 0.9.6
    pytz: 2021.3
    pyvis: 0.1.9
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.2
    RandomWords: 0.3.0
    rdkit-pypi: 2021.3.5.1
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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
    suds-jurko: 0.6
    tables: 3.6.1
    texttable: 1.6.4
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
File attachment: pyvsc-run-isolated.py

pyvsc-run-isolated.py​

Attachments (1)

pyvsc-run-isolated.py​ (900 bytes ) - added by Tristan Croll 4 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (5)

by Tristan Croll, 4 years ago

Attachment: pyvsc-run-isolated.py​ added

Added by email2trac

in reply to:  2 comment:1 by Tristan Croll, 4 years ago 

Also, when I run the ChimeraX python3.9 executable $home/.local/lib/python3.9/site-packages is on the PYTHONPATH, which is a recipe for interesting conflicts.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 03 November 2021 09:18
To: Tristan Croll <tic20@cam.ac.uk>
Subject: [ChimeraX] #5531: ChimeraX bug report submission

#5531: ChimeraX bug report submission
---------------------------+-----------------------------
 Reporter:  Tristan Croll  |                Type:  defect
   Status:  new            |            Priority:  normal
Component:  Unassigned     |          Blocked By:
 Blocking:                 |  Notify when closed:
---------------------------+-----------------------------
 {{{
 The following bug report has been submitted:
 Platform:        Linux-3.10.0-1160.25.1.el7.x86_64-x86_64-with-glibc2.17
 ChimeraX Version: 1.3rc202110301701 (2021-10-30 17:01:03 UTC)
 Description
 Trying to connect Visual Studio Code to ChimeraX's Python environment to
 make life a little easier. In Windows, giving it the ChimeraX executable
 works fine, with the minor side effect of launching a ChimeraX GUI window
 on first load. In Linux, I get this error message (I'm attaching the file
 it's actually trying to run). If I give it ChimeraX's Python executable,
 it connects without error but the user bundle directories aren't on the
 PYTHONPATH so I can't import ISOLDE (used, amongst other things, for live
 previewing of RestructuredText). Is there a way to make this work? Would
 wrapping the executable in a shell script that just extends the PYTHONPATH
 cause problems?

 Log:
 > alias preview_toolshed toolshed url https://cxtoolshed-
 > preview.rbvi.ucsf.edu; toolshed reload available

 > alias production_toolshed toolshed url https://cxtoolshed.rbvi.ucsf.edu;
 > toolshed reload available

 > isolde shorthand


     Initialising ISOLDE-specific command aliases:
     Alias       Equivalent full command
     -------------------------------------------------
     st  isolde step {arguments}
     aw  isolde add water {arguments}
     awsf        isolde add water {arguments} sim false
     al  isolde add ligand {arguments}
     aa  isolde add aa $1 sel {arguments}
     ht  isolde mod his sel {arguments}
     so  setattr sel atoms occupancy {arguments}
     ab  isolde adjust bfactors {arguments}
     ss  isolde sim start sel
     rt  isolde release torsions sel {arguments}
     rd  isolde release distances sel {arguments}
     ra  rd; rt
     pf  isolde pepflip sel
     cf  isolde cisflip sel
     cbb color bfactor {arguments}
     cbo color byattr occupancy {arguments}
     cbc color {arguments} bychain; color {arguments} byhet
     cs  clipper set contourSensitivity {arguments}



 UCSF ChimeraX version: 1.3rc202110301701 (2021-10-30)
 © 2016-2021 Regents of the University of California. All rights reserved.
 How to cite UCSF ChimeraX

 > open /home/tic20/.vscode/extensions/ms-
 > python.python-2021.5.926500501/pythonFiles/pyvsc-run-isolated.py

 Traceback (most recent call last):
 File "/home/tic20/.vscode/extensions/ms-
 python.python-2021.5.926500501/pythonFiles/pyvsc-run-isolated.py", line 5,
 in
 <module>
 raise Exception("{} cannot be imported".format(__name__))
 Exception: ChimeraX_sandbox_1 cannot be imported

 Error opening python file /home/tic20/.vscode/extensions/ms-
 python.python-2021.5.926500501/pythonFiles/pyvsc-run-isolated.py

 > open -c

 '-c' has no suffix

 > open "import sys;print(sys.executable)"

 Unrecognized file suffix '.executable)'
 Traceback (most recent call last):
 File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
 packages/chimerax/bug_reporter/bug_reporter_gui.py", line 190, in <lambda>
 sb.clicked.connect(lambda e: self.submit())
 File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
 packages/chimerax/bug_reporter/bug_reporter_gui.py", line 237, in submit
 fields.extend(file_list)
 TypeError: 'NoneType' object is not iterable

 TypeError: 'NoneType' object is not iterable

 File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
 packages/chimerax/bug_reporter/bug_reporter_gui.py", line 237, in submit
 fields.extend(file_list)

 See log for complete Python traceback.

 Traceback (most recent call last):
 File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
 packages/chimerax/bug_reporter/bug_reporter_gui.py", line 190, in <lambda>
 sb.clicked.connect(lambda e: self.submit())
 File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
 packages/chimerax/bug_reporter/bug_reporter_gui.py", line 237, in submit
 fields.extend(file_list)
 TypeError: 'NoneType' object is not iterable

 TypeError: 'NoneType' object is not iterable

 File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
 packages/chimerax/bug_reporter/bug_reporter_gui.py", line 237, in submit
 fields.extend(file_list)

 See log for complete Python traceback.





 OpenGL version: 3.3.0 NVIDIA 465.19.01
 OpenGL renderer: NVIDIA TITAN Xp/PCIe/SSE2
 OpenGL vendor: NVIDIA Corporation
 Manufacturer: Dell Inc.
 Model: Precision T5600
 OS: CentOS Linux 7 Core
 Architecture: 64bit ELF
 Virutal Machine: none
 CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
 Cache Size: 20480 KB
 Memory:
                       total        used        free      shared
 buff/cache   available
         Mem:            62G         11G        8.7G        426M
 42G         50G
         Swap:          4.9G        3.8M        4.9G

 Graphics:
         03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102
 [TITAN Xp] [10de:1b02] (rev a1)
         Subsystem: NVIDIA Corporation Device [10de:11df]
         Kernel driver in use: nvidia
 Locale: ('en_GB', 'UTF-8')
 PyQt5 5.15.2, Qt 5.15.2
 Installed Packages:
     alabaster: 0.7.12
     appdirs: 1.4.4
     Babel: 2.9.1
     backcall: 0.2.0
     blockdiag: 2.0.1
     certifi: 2021.10.8
     cftime: 1.5.1.1
     charset-normalizer: 2.0.7
     ChimeraX-AddCharge: 1.1.5
     ChimeraX-AddH: 2.1.10
     ChimeraX-AlignmentAlgorithms: 2.0
     ChimeraX-AlignmentHdrs: 3.2
     ChimeraX-AlignmentMatrices: 2.0
     ChimeraX-Alignments: 2.2.3
     ChimeraX-AlphaFold: 1.0
     ChimeraX-AltlocExplorer: 1.0.1
     ChimeraX-AmberInfo: 1.0
     ChimeraX-Arrays: 1.0
     ChimeraX-Atomic: 1.30.2
     ChimeraX-AtomicLibrary: 4.1.5
     ChimeraX-AtomSearch: 2.0
     ChimeraX-AtomSearchLibrary: 1.0
     ChimeraX-AxesPlanes: 2.0
     ChimeraX-BasicActions: 1.1
     ChimeraX-BILD: 1.0
     ChimeraX-BlastProtein: 2.0
     ChimeraX-BondRot: 2.0
     ChimeraX-BugReporter: 1.0
     ChimeraX-BuildStructure: 2.6
     ChimeraX-Bumps: 1.0
     ChimeraX-BundleBuilder: 1.1
     ChimeraX-ButtonPanel: 1.0
     ChimeraX-CageBuilder: 1.0
     ChimeraX-CellPack: 1.0
     ChimeraX-Centroids: 1.2
     ChimeraX-ChemGroup: 2.0
     ChimeraX-Clashes: 2.2.2
     ChimeraX-Clipper: 0.17.0
     ChimeraX-ColorActions: 1.0
     ChimeraX-ColorGlobe: 1.0
     ChimeraX-ColorKey: 1.5
     ChimeraX-CommandLine: 1.1.5
     ChimeraX-ConnectStructure: 2.0
     ChimeraX-Contacts: 1.0
     ChimeraX-Core: 1.3rc202110301701
     ChimeraX-CoreFormats: 1.1
     ChimeraX-coulombic: 1.3.1
     ChimeraX-Crosslinks: 1.0
     ChimeraX-Crystal: 1.0
     ChimeraX-CrystalContacts: 1.0
     ChimeraX-DataFormats: 1.2.2
     ChimeraX-Dicom: 1.0
     ChimeraX-DistMonitor: 1.1.5
     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: 1.1
     ChimeraX-Hbonds: 2.1.2
     ChimeraX-Help: 1.2
     ChimeraX-HKCage: 1.3
     ChimeraX-IHM: 1.1
     ChimeraX-ImageFormats: 1.2
     ChimeraX-IMOD: 1.0
     ChimeraX-IO: 1.0.1
     ChimeraX-ISOLDE: 1.3.dev33
     ChimeraX-ItemsInspection: 1.0
     ChimeraX-Label: 1.1
     ChimeraX-LinuxSupport: 1.0
     ChimeraX-ListInfo: 1.1.1
     ChimeraX-Log: 1.1.4
     ChimeraX-LookingGlass: 1.1
     ChimeraX-Maestro: 1.8.1
     ChimeraX-Map: 1.1
     ChimeraX-MapData: 2.0
     ChimeraX-MapEraser: 1.0
     ChimeraX-MapFilter: 2.0
     ChimeraX-MapFit: 2.0
     ChimeraX-MapSeries: 2.1
     ChimeraX-Markers: 1.0
     ChimeraX-Mask: 1.0
     ChimeraX-MatchMaker: 2.0.2
     ChimeraX-MDcrds: 2.6
     ChimeraX-MedicalToolbar: 1.0.1
     ChimeraX-Meeting: 1.0
     ChimeraX-MLP: 1.1
     ChimeraX-mmCIF: 2.4
     ChimeraX-MMTF: 2.1
     ChimeraX-Modeller: 1.2.5
     ChimeraX-ModelPanel: 1.2
     ChimeraX-ModelSeries: 1.0
     ChimeraX-Mol2: 2.0
     ChimeraX-Morph: 1.0
     ChimeraX-MouseModes: 1.1
     ChimeraX-Movie: 1.0
     ChimeraX-Neuron: 1.0
     ChimeraX-Nucleotides: 2.0.2
     ChimeraX-OpenCommand: 1.7
     ChimeraX-PDB: 2.6.5
     ChimeraX-PDBBio: 1.0
     ChimeraX-PDBLibrary: 1.0.2
     ChimeraX-PDBMatrices: 1.0
     ChimeraX-Phenix: 0.3
     ChimeraX-PickBlobs: 1.0
     ChimeraX-Positions: 1.0
     ChimeraX-PresetMgr: 1.0.1
     ChimeraX-PubChem: 2.1
     ChimeraX-ReadPbonds: 1.0
     ChimeraX-Registration: 1.1
     ChimeraX-RemoteControl: 1.0
     ChimeraX-ResidueFit: 1.0
     ChimeraX-RestServer: 1.1
     ChimeraX-RNALayout: 1.0
     ChimeraX-RotamerLibMgr: 2.0
     ChimeraX-RotamerLibsDunbrack: 2.0
     ChimeraX-RotamerLibsDynameomics: 2.0
     ChimeraX-RotamerLibsRichardson: 2.0
     ChimeraX-Sample: 0.1
     ChimeraX-SaveCommand: 1.5
     ChimeraX-SchemeMgr: 1.0
     ChimeraX-SDF: 2.0
     ChimeraX-Segger: 1.0
     ChimeraX-Segment: 1.0
     ChimeraX-SelInspector: 1.0
     ChimeraX-SeqView: 2.4.5
     ChimeraX-Shape: 1.0.1
     ChimeraX-Shell: 1.0
     ChimeraX-Shortcuts: 1.1
     ChimeraX-ShowAttr: 1.0
     ChimeraX-ShowSequences: 1.0
     ChimeraX-SideView: 1.0
     ChimeraX-Smiles: 2.1
     ChimeraX-SmoothLines: 1.0
     ChimeraX-SpaceNavigator: 1.0
     ChimeraX-StdCommands: 1.6
     ChimeraX-STL: 1.0
     ChimeraX-Storm: 1.0
     ChimeraX-Struts: 1.0
     ChimeraX-Surface: 1.0
     ChimeraX-SwapAA: 2.0
     ChimeraX-SwapRes: 2.1
     ChimeraX-TapeMeasure: 1.0
     ChimeraX-Test: 1.0
     ChimeraX-Toolbar: 1.1
     ChimeraX-ToolshedUtils: 1.2
     ChimeraX-Tug: 1.0
     ChimeraX-UI: 1.13.7
     ChimeraX-uniprot: 2.2
     ChimeraX-UnitCell: 1.0
     ChimeraX-ViewDockX: 1.0.1
     ChimeraX-VIPERdb: 1.0
     ChimeraX-Vive: 1.1
     ChimeraX-VolumeMenu: 1.0
     ChimeraX-Voyager: 0.1
     ChimeraX-VTK: 1.0
     ChimeraX-WavefrontOBJ: 1.0
     ChimeraX-WebCam: 1.0
     ChimeraX-WebServices: 1.0
     ChimeraX-Zone: 1.0
     colorama: 0.4.4
     cxservices: 1.1
     cycler: 0.11.0
     Cython: 0.29.24
     decorator: 5.1.0
     distro: 1.6.0
     docutils: 0.17.1
     filelock: 3.0.12
     funcparserlib: 0.3.6
     grako: 3.16.5
     h5py: 3.5.0
     html2text: 2020.1.16
     idna: 3.3
     ihm: 0.21
     imagecodecs: 2021.4.28
     imagesize: 1.2.0
     ipykernel: 5.5.5
     ipython: 7.23.1
     ipython-genutils: 0.2.0
     jedi: 0.18.0
     Jinja2: 3.0.1
     jsonpickle: 2.0.0
     jupyter-client: 6.1.12
     jupyter-core: 4.9.1
     kiwisolver: 1.3.2
     line-profiler: 3.3.0
     lxml: 4.6.3
     lz4: 3.1.3
     MarkupSafe: 2.0.1
     matplotlib: 3.4.3
     matplotlib-inline: 0.1.3
     msgpack: 1.0.2
     netCDF4: 1.5.7
     networkx: 2.6.2
     numexpr: 2.7.3
     numpy: 1.21.2
     openvr: 1.16.801
     packaging: 21.2
     ParmEd: 3.2.0
     parso: 0.8.2
     pexpect: 4.8.0
     pickleshare: 0.7.5
     Pillow: 8.3.2
     pip: 21.2.4
     pkginfo: 1.7.1
     prompt-toolkit: 3.0.21
     psutil: 5.8.0
     ptyprocess: 0.7.0
     pycollada: 0.7.1
     pydicom: 2.1.2
     Pygments: 2.10.0
     PyOpenGL: 3.1.5
     PyOpenGL-accelerate: 3.1.5
     pyparsing: 2.4.7
     PyQt5-commercial: 5.15.2
     PyQt5-sip: 12.8.1
     PyQtWebEngine-commercial: 5.15.2
     python-dateutil: 2.8.2
     python-igraph: 0.9.6
     pytz: 2021.3
     pyvis: 0.1.9
     pyzmq: 22.3.0
     qtconsole: 5.1.1
     QtPy: 1.11.2
     RandomWords: 0.3.0
     rdkit-pypi: 2021.3.5.1
     requests: 2.26.0
     scipy: 1.7.1
     setuptools: 57.5.0
     sfftk-rw: 0.7.1
     six: 1.16.0
     snowballstemmer: 2.1.0
     sortedcontainers: 2.4.0
     Sphinx: 4.2.0
     sphinx-autodoc-typehints: 1.12.0
     sphinxcontrib-applehelp: 1.0.2
     sphinxcontrib-blockdiag: 2.0.0
     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
     suds-jurko: 0.6
     tables: 3.6.1
     texttable: 1.6.4
     tifffile: 2021.4.8
     tinyarray: 1.2.3
     tornado: 6.1
     traitlets: 5.1.1
     urllib3: 1.26.7
     wcwidth: 0.2.5
     webcolors: 1.11.1
     wheel: 0.37.0
     wheel-filename: 1.3.0
 File attachment: pyvsc-run-isolated.py

 }}}

 [attachment:"pyvsc-run-isolated.py"]

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5531>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

in reply to:  3 ; comment:2 by Tristan Croll, 4 years ago 

Answered my own question. If I add the ChimeraX user directory to PYTHONPATH and attempt to import ISOLDE, I get:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/tic20/.local/share/ChimeraX/1.3/site-packages/chimerax/isolde/__init__.py", line 28, in <module>
    initialize_openmm()
  File "/home/tic20/.local/share/ChimeraX/1.3/site-packages/chimerax/isolde/__init__.py", line 26, in initialize_openmm
    from chimerax import app_lib_dir
ImportError: cannot import name 'app_lib_dir' from 'chimerax' (unknown location)

... so clearly there's a bunch more internal organisation being done by the ChimeraX executable.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 03 November 2021 09:23
To: Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #5531: ChimeraX bug report submission

#5531: ChimeraX bug report submission
------------------------------------+--------------------
          Reporter:  Tristan Croll  |      Owner:  (none)
              Type:  defect         |     Status:  new
          Priority:  normal         |  Milestone:
         Component:  Unassigned     |    Version:
        Resolution:                 |   Keywords:
        Blocked By:                 |   Blocking:
Notify when closed:                 |
------------------------------------+--------------------

Comment (by Tristan Croll):

 {{{
 Also, when I run the ChimeraX python3.9 executable
 $home/.local/lib/python3.9/site-packages is on the PYTHONPATH, which is a
 recipe for interesting conflicts.
 ________________________________
 From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
 Sent: 03 November 2021 09:18
 To: Tristan Croll <tic20@cam.ac.uk>
 Subject: [ChimeraX] #5531: ChimeraX bug report submission

 #5531: ChimeraX bug report submission
 ---------------------------+-----------------------------
  Reporter:  Tristan Croll  |                Type:  defect
    Status:  new            |            Priority:  normal
 Component:  Unassigned     |          Blocked By:
  Blocking:                 |  Notify when closed:
 ---------------------------+-----------------------------
  {{{
  The following bug report has been submitted:
  Platform:        Linux-3.10.0-1160.25.1.el7.x86_64-x86_64-with-glibc2.17
  ChimeraX Version: 1.3rc202110301701 (2021-10-30 17:01:03 UTC)
  Description
  Trying to connect Visual Studio Code to ChimeraX's Python environment to
  make life a little easier. In Windows, giving it the ChimeraX executable
  works fine, with the minor side effect of launching a ChimeraX GUI window
  on first load. In Linux, I get this error message (I'm attaching the file
  it's actually trying to run). If I give it ChimeraX's Python executable,
  it connects without error but the user bundle directories aren't on the
  PYTHONPATH so I can't import ISOLDE (used, amongst other things, for live
  previewing of RestructuredText). Is there a way to make this work? Would
  wrapping the executable in a shell script that just extends the
 PYTHONPATH
  cause problems?

  Log:
  > alias preview_toolshed toolshed url https://cxtoolshed-
  > preview.rbvi.ucsf.edu; toolshed reload available

  > alias production_toolshed toolshed url
 https://cxtoolshed.rbvi.ucsf.edu;
  > toolshed reload available

  > isolde shorthand


      Initialising ISOLDE-specific command aliases:
      Alias       Equivalent full command
      -------------------------------------------------
      st  isolde step {arguments}
      aw  isolde add water {arguments}
      awsf        isolde add water {arguments} sim false
      al  isolde add ligand {arguments}
      aa  isolde add aa $1 sel {arguments}
      ht  isolde mod his sel {arguments}
      so  setattr sel atoms occupancy {arguments}
      ab  isolde adjust bfactors {arguments}
      ss  isolde sim start sel
      rt  isolde release torsions sel {arguments}
      rd  isolde release distances sel {arguments}
      ra  rd; rt
      pf  isolde pepflip sel
      cf  isolde cisflip sel
      cbb color bfactor {arguments}
      cbo color byattr occupancy {arguments}
      cbc color {arguments} bychain; color {arguments} byhet
      cs  clipper set contourSensitivity {arguments}



  UCSF ChimeraX version: 1.3rc202110301701 (2021-10-30)
  © 2016-2021 Regents of the University of California. All rights reserved.
  How to cite UCSF ChimeraX

  > open /home/tic20/.vscode/extensions/ms-
  > python.python-2021.5.926500501/pythonFiles/pyvsc-run-isolated.py

  Traceback (most recent call last):
  File "/home/tic20/.vscode/extensions/ms-
  python.python-2021.5.926500501/pythonFiles/pyvsc-run-isolated.py", line
 5,
  in
  <module>
  raise Exception("{} cannot be imported".format(__name__))
  Exception: ChimeraX_sandbox_1 cannot be imported

  Error opening python file /home/tic20/.vscode/extensions/ms-
  python.python-2021.5.926500501/pythonFiles/pyvsc-run-isolated.py

  > open -c

  '-c' has no suffix

  > open "import sys;print(sys.executable)"

  Unrecognized file suffix '.executable)'
  Traceback (most recent call last):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
  packages/chimerax/bug_reporter/bug_reporter_gui.py", line 190, in
 <lambda>
  sb.clicked.connect(lambda e: self.submit())
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
  packages/chimerax/bug_reporter/bug_reporter_gui.py", line 237, in submit
  fields.extend(file_list)
  TypeError: 'NoneType' object is not iterable

  TypeError: 'NoneType' object is not iterable

  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
  packages/chimerax/bug_reporter/bug_reporter_gui.py", line 237, in submit
  fields.extend(file_list)

  See log for complete Python traceback.

  Traceback (most recent call last):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
  packages/chimerax/bug_reporter/bug_reporter_gui.py", line 190, in
 <lambda>
  sb.clicked.connect(lambda e: self.submit())
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
  packages/chimerax/bug_reporter/bug_reporter_gui.py", line 237, in submit
  fields.extend(file_list)
  TypeError: 'NoneType' object is not iterable

  TypeError: 'NoneType' object is not iterable

  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
  packages/chimerax/bug_reporter/bug_reporter_gui.py", line 237, in submit
  fields.extend(file_list)

  See log for complete Python traceback.





  OpenGL version: 3.3.0 NVIDIA 465.19.01
  OpenGL renderer: NVIDIA TITAN Xp/PCIe/SSE2
  OpenGL vendor: NVIDIA Corporation
  Manufacturer: Dell Inc.
  Model: Precision T5600
  OS: CentOS Linux 7 Core
  Architecture: 64bit ELF
  Virutal Machine: none
  CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
  Cache Size: 20480 KB
  Memory:
                        total        used        free      shared
  buff/cache   available
          Mem:            62G         11G        8.7G        426M
  42G         50G
          Swap:          4.9G        3.8M        4.9G

  Graphics:
          03:00.0 VGA compatible controller [0300]: NVIDIA Corporation
 GP102
  [TITAN Xp] [10de:1b02] (rev a1)
          Subsystem: NVIDIA Corporation Device [10de:11df]
          Kernel driver in use: nvidia
  Locale: ('en_GB', 'UTF-8')
  PyQt5 5.15.2, Qt 5.15.2
  Installed Packages:
      alabaster: 0.7.12
      appdirs: 1.4.4
      Babel: 2.9.1
      backcall: 0.2.0
      blockdiag: 2.0.1
      certifi: 2021.10.8
      cftime: 1.5.1.1
      charset-normalizer: 2.0.7
      ChimeraX-AddCharge: 1.1.5
      ChimeraX-AddH: 2.1.10
      ChimeraX-AlignmentAlgorithms: 2.0
      ChimeraX-AlignmentHdrs: 3.2
      ChimeraX-AlignmentMatrices: 2.0
      ChimeraX-Alignments: 2.2.3
      ChimeraX-AlphaFold: 1.0
      ChimeraX-AltlocExplorer: 1.0.1
      ChimeraX-AmberInfo: 1.0
      ChimeraX-Arrays: 1.0
      ChimeraX-Atomic: 1.30.2
      ChimeraX-AtomicLibrary: 4.1.5
      ChimeraX-AtomSearch: 2.0
      ChimeraX-AtomSearchLibrary: 1.0
      ChimeraX-AxesPlanes: 2.0
      ChimeraX-BasicActions: 1.1
      ChimeraX-BILD: 1.0
      ChimeraX-BlastProtein: 2.0
      ChimeraX-BondRot: 2.0
      ChimeraX-BugReporter: 1.0
      ChimeraX-BuildStructure: 2.6
      ChimeraX-Bumps: 1.0
      ChimeraX-BundleBuilder: 1.1
      ChimeraX-ButtonPanel: 1.0
      ChimeraX-CageBuilder: 1.0
      ChimeraX-CellPack: 1.0
      ChimeraX-Centroids: 1.2
      ChimeraX-ChemGroup: 2.0
      ChimeraX-Clashes: 2.2.2
      ChimeraX-Clipper: 0.17.0
      ChimeraX-ColorActions: 1.0
      ChimeraX-ColorGlobe: 1.0
      ChimeraX-ColorKey: 1.5
      ChimeraX-CommandLine: 1.1.5
      ChimeraX-ConnectStructure: 2.0
      ChimeraX-Contacts: 1.0
      ChimeraX-Core: 1.3rc202110301701
      ChimeraX-CoreFormats: 1.1
      ChimeraX-coulombic: 1.3.1
      ChimeraX-Crosslinks: 1.0
      ChimeraX-Crystal: 1.0
      ChimeraX-CrystalContacts: 1.0
      ChimeraX-DataFormats: 1.2.2
      ChimeraX-Dicom: 1.0
      ChimeraX-DistMonitor: 1.1.5
      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: 1.1
      ChimeraX-Hbonds: 2.1.2
      ChimeraX-Help: 1.2
      ChimeraX-HKCage: 1.3
      ChimeraX-IHM: 1.1
      ChimeraX-ImageFormats: 1.2
      ChimeraX-IMOD: 1.0
      ChimeraX-IO: 1.0.1
      ChimeraX-ISOLDE: 1.3.dev33
      ChimeraX-ItemsInspection: 1.0
      ChimeraX-Label: 1.1
      ChimeraX-LinuxSupport: 1.0
      ChimeraX-ListInfo: 1.1.1
      ChimeraX-Log: 1.1.4
      ChimeraX-LookingGlass: 1.1
      ChimeraX-Maestro: 1.8.1
      ChimeraX-Map: 1.1
      ChimeraX-MapData: 2.0
      ChimeraX-MapEraser: 1.0
      ChimeraX-MapFilter: 2.0
      ChimeraX-MapFit: 2.0
      ChimeraX-MapSeries: 2.1
      ChimeraX-Markers: 1.0
      ChimeraX-Mask: 1.0
      ChimeraX-MatchMaker: 2.0.2
      ChimeraX-MDcrds: 2.6
      ChimeraX-MedicalToolbar: 1.0.1
      ChimeraX-Meeting: 1.0
      ChimeraX-MLP: 1.1
      ChimeraX-mmCIF: 2.4
      ChimeraX-MMTF: 2.1
      ChimeraX-Modeller: 1.2.5
      ChimeraX-ModelPanel: 1.2
      ChimeraX-ModelSeries: 1.0
      ChimeraX-Mol2: 2.0
      ChimeraX-Morph: 1.0
      ChimeraX-MouseModes: 1.1
      ChimeraX-Movie: 1.0
      ChimeraX-Neuron: 1.0
      ChimeraX-Nucleotides: 2.0.2
      ChimeraX-OpenCommand: 1.7
      ChimeraX-PDB: 2.6.5
      ChimeraX-PDBBio: 1.0
      ChimeraX-PDBLibrary: 1.0.2
      ChimeraX-PDBMatrices: 1.0
      ChimeraX-Phenix: 0.3
      ChimeraX-PickBlobs: 1.0
      ChimeraX-Positions: 1.0
      ChimeraX-PresetMgr: 1.0.1
      ChimeraX-PubChem: 2.1
      ChimeraX-ReadPbonds: 1.0
      ChimeraX-Registration: 1.1
      ChimeraX-RemoteControl: 1.0
      ChimeraX-ResidueFit: 1.0
      ChimeraX-RestServer: 1.1
      ChimeraX-RNALayout: 1.0
      ChimeraX-RotamerLibMgr: 2.0
      ChimeraX-RotamerLibsDunbrack: 2.0
      ChimeraX-RotamerLibsDynameomics: 2.0
      ChimeraX-RotamerLibsRichardson: 2.0
      ChimeraX-Sample: 0.1
      ChimeraX-SaveCommand: 1.5
      ChimeraX-SchemeMgr: 1.0
      ChimeraX-SDF: 2.0
      ChimeraX-Segger: 1.0
      ChimeraX-Segment: 1.0
      ChimeraX-SelInspector: 1.0
      ChimeraX-SeqView: 2.4.5
      ChimeraX-Shape: 1.0.1
      ChimeraX-Shell: 1.0
      ChimeraX-Shortcuts: 1.1
      ChimeraX-ShowAttr: 1.0
      ChimeraX-ShowSequences: 1.0
      ChimeraX-SideView: 1.0
      ChimeraX-Smiles: 2.1
      ChimeraX-SmoothLines: 1.0
      ChimeraX-SpaceNavigator: 1.0
      ChimeraX-StdCommands: 1.6
      ChimeraX-STL: 1.0
      ChimeraX-Storm: 1.0
      ChimeraX-Struts: 1.0
      ChimeraX-Surface: 1.0
      ChimeraX-SwapAA: 2.0
      ChimeraX-SwapRes: 2.1
      ChimeraX-TapeMeasure: 1.0
      ChimeraX-Test: 1.0
      ChimeraX-Toolbar: 1.1
      ChimeraX-ToolshedUtils: 1.2
      ChimeraX-Tug: 1.0
      ChimeraX-UI: 1.13.7
      ChimeraX-uniprot: 2.2
      ChimeraX-UnitCell: 1.0
      ChimeraX-ViewDockX: 1.0.1
      ChimeraX-VIPERdb: 1.0
      ChimeraX-Vive: 1.1
      ChimeraX-VolumeMenu: 1.0
      ChimeraX-Voyager: 0.1
      ChimeraX-VTK: 1.0
      ChimeraX-WavefrontOBJ: 1.0
      ChimeraX-WebCam: 1.0
      ChimeraX-WebServices: 1.0
      ChimeraX-Zone: 1.0
      colorama: 0.4.4
      cxservices: 1.1
      cycler: 0.11.0
      Cython: 0.29.24
      decorator: 5.1.0
      distro: 1.6.0
      docutils: 0.17.1
      filelock: 3.0.12
      funcparserlib: 0.3.6
      grako: 3.16.5
      h5py: 3.5.0
      html2text: 2020.1.16
      idna: 3.3
      ihm: 0.21
      imagecodecs: 2021.4.28
      imagesize: 1.2.0
      ipykernel: 5.5.5
      ipython: 7.23.1
      ipython-genutils: 0.2.0
      jedi: 0.18.0
      Jinja2: 3.0.1
      jsonpickle: 2.0.0
      jupyter-client: 6.1.12
      jupyter-core: 4.9.1
      kiwisolver: 1.3.2
      line-profiler: 3.3.0
      lxml: 4.6.3
      lz4: 3.1.3
      MarkupSafe: 2.0.1
      matplotlib: 3.4.3
      matplotlib-inline: 0.1.3
      msgpack: 1.0.2
      netCDF4: 1.5.7
      networkx: 2.6.2
      numexpr: 2.7.3
      numpy: 1.21.2
      openvr: 1.16.801
      packaging: 21.2
      ParmEd: 3.2.0
      parso: 0.8.2
      pexpect: 4.8.0
      pickleshare: 0.7.5
      Pillow: 8.3.2
      pip: 21.2.4
      pkginfo: 1.7.1
      prompt-toolkit: 3.0.21
      psutil: 5.8.0
      ptyprocess: 0.7.0
      pycollada: 0.7.1
      pydicom: 2.1.2
      Pygments: 2.10.0
      PyOpenGL: 3.1.5
      PyOpenGL-accelerate: 3.1.5
      pyparsing: 2.4.7
      PyQt5-commercial: 5.15.2
      PyQt5-sip: 12.8.1
      PyQtWebEngine-commercial: 5.15.2
      python-dateutil: 2.8.2
      python-igraph: 0.9.6
      pytz: 2021.3
      pyvis: 0.1.9
      pyzmq: 22.3.0
      qtconsole: 5.1.1
      QtPy: 1.11.2
      RandomWords: 0.3.0
      rdkit-pypi: 2021.3.5.1
      requests: 2.26.0
      scipy: 1.7.1
      setuptools: 57.5.0
      sfftk-rw: 0.7.1
      six: 1.16.0
      snowballstemmer: 2.1.0
      sortedcontainers: 2.4.0
      Sphinx: 4.2.0
      sphinx-autodoc-typehints: 1.12.0
      sphinxcontrib-applehelp: 1.0.2
      sphinxcontrib-blockdiag: 2.0.0
      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
      suds-jurko: 0.6
      tables: 3.6.1
      texttable: 1.6.4
      tifffile: 2021.4.8
      tinyarray: 1.2.3
      tornado: 6.1
      traitlets: 5.1.1
      urllib3: 1.26.7
      wcwidth: 0.2.5
      webcolors: 1.11.1
      wheel: 0.37.0
      wheel-filename: 1.3.0
  File attachment: pyvsc-run-isolated.py

  }}}

  [attachment:"pyvsc-run-isolated.py"]

 --
 Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5531>
 ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
 ChimeraX Issue Tracker
 }}}

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5531#comment:1>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:3 by Eric Pettersen, 4 years ago

Cc: chimera-programmers added
Component: Unassigned → Build System
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Problems connecting with Visual Studio Code

comment:4 by Tom Goddard, 4 years ago

ISOLDE tries to initialize OpenMM when it is imported. And that uses chimerax.app_lib_dir which is an attribute that the ChimeraX application initializes at startup. So just starting Python won't have done that initialization. We plan to make a PyPi ChimeraX module as part of our CZI grant and will need to solve this problem where various modules are broken unless some initialization is done first. In general the modules should not be relying on some global initialization, especially this should not be needed just to import the Python code. I would suggest that ISOLDE should not be calling initialize_openmm() in its init.py. These kinds of side effects from importing a module lead to difficult problems to debug because you never know how early ISOLDE is going to be imported, so it fails to control the order in which routines get called. Instead the routines that actually need openmm to be initialized should be doing the initialization, so initialization only happens when the code that needs it gets used, not on import.

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