Opened 2 years ago

Closed 2 years ago

#9461 closed defect (limitation)

Session save: DLL load failed while importing _serialize

Reported by: 383365989@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Sessions Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "J:/TB/pAGO/Cryo-EM Structure/monomer with
> NT/monomer_dna_rna_P30_J641-coot-0.pdb"

Chain information for monomer_dna_rna_P30_J641-coot-0.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  

> set bgColor white

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> select /A:313

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select /A:309-313

37 atoms, 37 bonds, 5 residues, 1 model selected  

> select /A:271

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:1-271

1890 atoms, 1941 bonds, 1 pseudobond, 229 residues, 2 models selected  

> color (#!1 & sel) hot pink

> select /A:272

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select /A:272-507

1881 atoms, 1926 bonds, 236 residues, 1 model selected  

> color sel magenta

> ui tool show "Show Sequence Viewer"

> sequence chain /B

Alignment identifier is 1/B  

> select /B:163-164

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select /B:1-164

1340 atoms, 1368 bonds, 164 residues, 1 model selected  

> color sel cornflower blue

> select /B:183-184

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select /B:165-184

174 atoms, 180 bonds, 20 residues, 1 model selected  

> color sel dark gray

> select /B:242-243

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select /B:185-242

516 atoms, 534 bonds, 58 residues, 1 model selected  

> color sel cyan

> select /B:243

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /B:243-409

1397 atoms, 1427 bonds, 167 residues, 1 model selected  

> select /B:415-416

18 atoms, 18 bonds, 2 residues, 1 model selected  

> select /B:241-415

1460 atoms, 1492 bonds, 175 residues, 1 model selected  

> color sel dark gray

> select /B:417

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /B:417-449

256 atoms, 256 bonds, 33 residues, 1 model selected  

> select /B:450

10 atoms, 9 bonds, 1 residue, 1 model selected  

> select /B:415-450

284 atoms, 285 bonds, 36 residues, 1 model selected  

> color sel blue

> select /C

480 atoms, 535 bonds, 24 residues, 1 model selected  

> color sel yellow

> select /D

454 atoms, 508 bonds, 21 residues, 1 model selected  

> color sel lime

> open "J:/TB/pAGO/Cryo-EM Structure/monomer with
> NT/cryosparc_P30_J641_002_volume_map.mrc"

Opened cryosparc_P30_J641_002_volume_map.mrc as #2, grid size 230,230,230,
pixel 1.04, shown at level 0.0255, step 1, values float32  

> ui tool show "Color Zone"

> color zone #2 near #1 distance 6.24

> set bgColor white

> lighting soft

> volume #2 level 0.1148

> hide #!1 models

> volume #2 level 0.0983

> volume #2 level 0.1216

> save C:/Users/GXP/Desktop/compar/first.cxs includeMaps true

Traceback (most recent call last):  
File "D:\program files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\program files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 597, in save  
from . import serialize  
File "D:\program files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\serialize.py", line 41, in <module>  
from . import _serialize  
ImportError: DLL load failed while importing _serialize: 拒绝访问。  
  
ImportError: DLL load failed while importing _serialize: 拒绝访问。  
  
File "D:\program files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\serialize.py", line 41, in  
from . import _serialize  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\program files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "D:\program files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "D:\program files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "D:\program files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\program files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\program files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "D:\program files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\program files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "D:\program files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "D:\program files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\program files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 597, in save  
from . import serialize  
File "D:\program files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\serialize.py", line 41, in <module>  
from . import _serialize  
ImportError: DLL load failed while importing _serialize: 拒绝访问。  
  
ImportError: DLL load failed while importing _serialize: 拒绝访问。  
  
File "D:\program files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\serialize.py", line 41, in  
from . import _serialize  
  
See log for complete Python traceback.  
  

> save C:/Users/GXP/Desktop/compar/fisr.cxs

Traceback (most recent call last):  
File "D:\program files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\program files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 597, in save  
from . import serialize  
File "D:\program files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\serialize.py", line 41, in <module>  
from . import _serialize  
ImportError: DLL load failed while importing _serialize: 拒绝访问。  
  
ImportError: DLL load failed while importing _serialize: 拒绝访问。  
  
File "D:\program files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\serialize.py", line 41, in  
from . import _serialize  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\program files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "D:\program files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "D:\program files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "D:\program files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\program files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\program files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "D:\program files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\program files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "D:\program files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "D:\program files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\program files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 597, in save  
from . import serialize  
File "D:\program files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\serialize.py", line 41, in <module>  
from . import _serialize  
ImportError: DLL load failed while importing _serialize: 拒绝访问。  
  
ImportError: DLL load failed while importing _serialize: 拒绝访问。  
  
File "D:\program files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\serialize.py", line 41, in  
from . import _serialize  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 474.14
OpenGL renderer: NVIDIA GeForce GT 730/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: zh_CN.cp936
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: windows

Manufacturer: Dell Inc.
Model: Inspiron 3910
OS: Microsoft Windows 11 家庭中文版 (Build 22621)
Memory: 16,924,782,592
MaxProcessMemory: 137,438,953,344
CPU: 20 12th Gen Intel(R) Core(TM) i7-12700F
OSLanguage: zh-CN

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2022.5.18.1
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    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: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    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-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    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: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    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: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    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: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pywin32: 303
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    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-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (2)

comment:1 by pett, 2 years ago

Component: Unassigned → Sessions
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Session save: DLL load failed while importing _serialize

comment:2 by Greg Couch, 2 years ago

Resolution: → limitation
Status: assigned → closed

It looks like your ChimeraX installation got corrupted some how. Using Google translate, " 拒绝访问" means "access denied". Which means that the file permissions for the "C:\Program Files\ChimeraX 1.4\bin\Lib\site-packages\chimerax\core\_serialize.cp39-win_amd64.pyd" file are incorrect. I recommend removing your existing version of ChimeraX and upgrading to ChimeraX 1.6.

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