Showing DiffFit tool: OSError: [Errno 28] No space left on device

[houj2024@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  

> ui tool show "Model Panel"

UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> D:\\\project\\\Druantia\\\Constructing_atomic_models\\\3DVA\\\last_model\\\J322\\\J322_real_space_refined_004.cif

Summary of feedback from opening
D:\\\project\\\Druantia\\\Constructing_atomic_models\\\3DVA\\\last_model\\\J322\\\J322_real_space_refined_004.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' on line 1056  
Missing entity information. Treating each chain as a separate entity.  
Bad residue range for struct_conf "65" on line 195  
Invalid sheet range for struct_sheet_range "51 1" on line 998  
Invalid sheet range for struct_sheet_range "105 1" on line 1052  
Invalid sheet range for struct_sheet_range "106 1" on line 1054  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for J322_real_space_refined_004.cif #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> D:/project/Druantia/Constructing_atomic_models/3DVA/last_model/J399/J399_007_emready2.mrc

Opened J399_007_emready2.mrc as #2, grid size 735,735,735, pixel 0.5, shown at
step 1, values float32  

> volume #2 region 0,0,0,734,734,734 step 4

[Repeated 1 time(s)]

> volume #2 change image level -0.05455,0 level 5.529,0.8 level 14.07,1

> volume #2 level 2.546

> volume #2 step 1

> ui tool show DiffFit

loading settings...  
Traceback (most recent call last):  
File "C:\Users\22346\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\difffit\tool.py", line 816, in <lambda>  
button.clicked.connect(lambda: self.dependency_install_button_clicked())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\22346\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\difffit\tool.py", line 1798, in
dependency_install_button_clicked  
run_logged_pip(cmd_list, self.session.logger)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\python_utils.py", line 143, in run_logged_pip  
raise RuntimeError(s)  
RuntimeError: ERROR: Exception:  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 438, in _error_catcher  
yield  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 561, in read  
data = self._fp_read(amt) if not fp_closed else b""  
^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 527, in _fp_read  
return self._fp.read(amt) if amt is not None else self._fp.read()  
^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_vendor\cachecontrol\filewrapper.py", line 102, in read  
self.__buf.write(data)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\tempfile.py", line 483, in
func_wrapper  
return func(*args, **kwargs)  
^^^^^^^^^^^^^^^^^^^^^  
OSError: [Errno 28] No space left on device  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_internal\cli\base_command.py", line 105, in _run_wrapper  
status = _inner_run()  
^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_internal\cli\base_command.py", line 96, in _inner_run  
return self.run(options, args)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_internal\cli\req_command.py", line 67, in wrapper  
return func(self, options, args)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_internal\commands\install.py", line 379, in run  
requirement_set = resolver.resolve(  
^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_internal\resolution\resolvelib\resolver.py", line 95, in
resolve  
result = self._result = resolver.resolve(  
^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_vendor\resolvelib\resolvers.py", line 546, in resolve  
state = resolution.resolve(requirements, max_rounds=max_rounds)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_vendor\resolvelib\resolvers.py", line 397, in resolve  
self._add_to_criteria(self.state.criteria, r, parent=None)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_vendor\resolvelib\resolvers.py", line 173, in _add_to_criteria  
if not criterion.candidates:  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_vendor\resolvelib\structs.py", line 156, in __bool__  
return bool(self._sequence)  
^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_internal\resolution\resolvelib\found_candidates.py", line 174,
in __bool__  
return any(self)  
^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_internal\resolution\resolvelib\found_candidates.py", line 162,
in <genexpr>  
return (c for c in iterator if id(c) not in self._incompatible_ids)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_internal\resolution\resolvelib\found_candidates.py", line 53,
in _iter_built  
candidate = func()  
^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_internal\resolution\resolvelib\factory.py", line 186, in
_make_candidate_from_link  
base: Optional[BaseCandidate] = self._make_base_candidate_from_link(  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_internal\resolution\resolvelib\factory.py", line 232, in
_make_base_candidate_from_link  
self._link_candidate_cache[link] = LinkCandidate(  
^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_internal\resolution\resolvelib\candidates.py", line 303, in
__init__  
super().__init__(  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_internal\resolution\resolvelib\candidates.py", line 158, in
__init__  
self.dist = self._prepare()  
^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_internal\resolution\resolvelib\candidates.py", line 235, in
_prepare  
dist = self._prepare_distribution()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_internal\resolution\resolvelib\candidates.py", line 314, in
_prepare_distribution  
return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_internal\operations\prepare.py", line 527, in
prepare_linked_requirement  
return self._prepare_linked_requirement(req, parallel_builds)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_internal\operations\prepare.py", line 598, in
_prepare_linked_requirement  
local_file = unpack_url(  
^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_internal\operations\prepare.py", line 170, in unpack_url  
file = get_http_url(  
^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_internal\operations\prepare.py", line 111, in get_http_url  
from_path, content_type = download(link, temp_dir.path)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_internal\network\download.py", line 148, in __call__  
for chunk in chunks:  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_internal\network\utils.py", line 65, in response_chunks  
for chunk in response.raw.stream(  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 622, in stream  
data = self.read(amt=amt, decode_content=decode_content)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 560, in read  
with self._error_catcher():  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\contextlib.py", line 155, in
__exit__  
self.gen.throw(typ, value, traceback)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 455, in _error_catcher  
raise ProtocolError("Connection broken: %r" % e, e)  
pip._vendor.urllib3.exceptions.ProtocolError: ("Connection broken: OSError(28,
'No space left on device')", OSError(28, 'No space left on device'))  
  
  
RuntimeError: ERROR: Exception:  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 438, in _error_catcher  
yield  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 561, in read  
data = self._fp_read(amt) if not fp_closed else b""  
^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 527, in _fp_read  
return self._fp.read(amt) if amt is not None else self._fp.read()  
^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_vendor\cachecontrol\filewrapper.py", line 102, in read  
self.__buf.write(data)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\tempfile.py", line 483, in
func_wrapper  
return func(*args, **kwargs)  
^^^^^^^^^^^^^^^^^^^^^  
OSError: [Errno 28] No space left on device  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_internal\cli\base_command.py", line 105, in _run_wrapper  
status = _inner_run()  
^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_internal\cli\base_command.py", line 96, in _inner_run  
return self.run(options, args)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_internal\cli\req_command.py", line 67, in wrapper  
return func(self, options, args)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_internal\commands\install.py", line 379, in run  
requirement_set = resolver.resolve(  
^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_internal\resolution\resolvelib\resolver.py", line 95, in
resolve  
result = self._result = resolver.resolve(  
^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_vendor\resolvelib\resolvers.py", line 546, in resolve  
state = resolution.resolve(requirements, max_rounds=max_rounds)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_vendor\resolvelib\resolvers.py", line 397, in resolve  
self._add_to_criteria(self.state.criteria, r, parent=None)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_vendor\resolvelib\resolvers.py", line 173, in _add_to_criteria  
if not criterion.candidates:  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_vendor\resolvelib\structs.py", line 156, in __bool__  
return bool(self._sequence)  
^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_internal\resolution\resolvelib\found_candidates.py", line 174,
in __bool__  
return any(self)  
^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_internal\resolution\resolvelib\found_candidates.py", line 162,
in  
return (c for c in iterator if id(c) not in self._incompatible_ids)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_internal\resolution\resolvelib\found_candidates.py", line 53,
in _iter_built  
candidate = func()  
^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_internal\resolution\resolvelib\factory.py", line 186, in
_make_candidate_from_link  
base: Optional[BaseCandidate] = self._make_base_candidate_from_link(  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_internal\resolution\resolvelib\factory.py", line 232, in
_make_base_candidate_from_link  
self._link_candidate_cache[link] = LinkCandidate(  
^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_internal\resolution\resolvelib\candidates.py", line 303, in
__init__  
super().__init__(  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_internal\resolution\resolvelib\candidates.py", line 158, in
__init__  
self.dist = self._prepare()  
^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_internal\resolution\resolvelib\candidates.py", line 235, in
_prepare  
dist = self._prepare_distribution()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_internal\resolution\resolvelib\candidates.py", line 314, in
_prepare_distribution  
return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_internal\operations\prepare.py", line 527, in
prepare_linked_requirement  
return self._prepare_linked_requirement(req, parallel_builds)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_internal\operations\prepare.py", line 598, in
_prepare_linked_requirement  
local_file = unpack_url(  
^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_internal\operations\prepare.py", line 170, in unpack_url  
file = get_http_url(  
^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_internal\operations\prepare.py", line 111, in get_http_url  
from_path, content_type = download(link, temp_dir.path)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_internal\network\download.py", line 148, in __call__  
for chunk in chunks:  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_internal\network\utils.py", line 65, in response_chunks  
for chunk in response.raw.stream(  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 622, in stream  
data = self.read(amt=amt, decode_content=decode_content)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 560, in read  
with self._error_catcher():  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\contextlib.py", line 155, in
__exit__  
self.gen.throw(typ, value, traceback)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 455, in _error_catcher  
raise ProtocolError("Connection broken: %r" % e, e)  
pip._vendor.urllib3.exceptions.ProtocolError: ("Connection broken: OSError(28,
'No space left on device')", OSError(28, 'No space left on device'))  
  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\python_utils.py", line 143, in run_logged_pip  
raise RuntimeError(s)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 566.14
OpenGL renderer: NVIDIA GeForce RTX 4060 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: zh_CN.cp936
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: XIAOMI
Model: Redmi G Pro 2024
OS: Microsoft Windows 11 家庭中文版 (Build 26100)
Memory: 16,944,259,072
MaxProcessMemory: 137,438,953,344
CPU: 24 Intel(R) Core(TM) i7-14650HX
OSLanguage: zh-CN

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    autocommand: 2.2.2
    babel: 2.16.0
    backports.tarfile: 1.2.0
    beautifulsoup4: 4.12.3
    biopython: 1.83
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2024.8.30
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-Clipper: 0.24.0
    ChimeraX-clix: 0.2.1
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    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: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ISOLDE: 1.9
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-QScore: 1.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.5
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    DiffFit: 0.7.0
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    fsspec: 2025.7.0
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    importlib_metadata: 8.0.0
    importlib_resources: 6.4.0
    inflect: 7.3.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jaraco.context: 5.3.0
    jaraco.functools: 4.0.1
    jaraco.text: 3.12.1
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    MolecularDynamicsViewer: 1.6
    more-itertools: 10.3.0
    mpmath: 1.3.0
    mrcfile: 1.5.0
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    ordered-set: 4.1.0
    packaging: 23.2
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    platformdirs: 4.2.2
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pywin32: 306
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    sympy: 1.14.0
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tomli: 2.0.1
    torch: 2.2.1
    tornado: 6.4.2
    traitlets: 5.14.3
    typeguard: 4.3.0
    typing_extensions: 4.12.2
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    WMI: 1.5.1
    zipp: 3.19.2

[Tom Goddard]

The error message when you tried to use DiffFit "No space left on device" means you have no disk space. DiffFit was trying to install some Python package but you ran out of disk space.