The following bug report has been submitted:
Platform: macOS-14.3.1-arm64-arm-64bit
ChimeraX Version: 1.8.dev202403290055 (2024-03-29 00:55:10 UTC)
Description
Tried to open a structure and MTZ file from PDB-Redo.
Log:
UCSF ChimeraX version: 1.8.dev202403290055 (2024-03-29)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 8gam format mmcif fromDatabase pdb
8gam title:
Exploiting Activation and Inactivation Mechanisms in Type I-C CRISPR-Cas3 for
Genome Editing Applications [more info...]
Chain information for 8gam #1
---
Chain | Description | UniProt
A B C D E F M | Cas7 | A0A378VEU0_NEILA 2-283
G H | Phage associated protein | A0A378VF47_NEILA 1-582
I J | Cas11 | A0A378VF47_NEILA 2-125
K | crRNA (43-MER) |
L | Target strand DNA (25-MER) |
N | Cas5 | D0W8X4_NEILA 2-206
O | Non target strand DNA (5'-D(P*AP*TP*GP*AP*AP*CP*TP*TP*CP*AP*AP*AP*A)-3') |
> log metadata #1
Metadata for 8gam #1
---
Title | Exploiting Activation and Inactivation Mechanisms in Type I-C CRISPR-Cas3 for Genome Editing Applications
Citation | Hu, C., Myers, M.T., Zhou, X., Hou, Z., Lozen, M.L., Nam, K.H., Zhang, Y., Ke, A. (2024). Exploiting activation and inactivation mechanisms in type I-C CRISPR-Cas3 for genome-editing applications. Mol.Cell, 84, 463-475.e5. PMID: 38242128. DOI: 10.1016/j.molcel.2023.12.034
Gene source | Neisseria lactamica
CryoEM Map | EMDB 29900 — open map
Experimental method | Electron microscopy
Resolution | 3.46Å
> close
> open 6c08 format mmcif fromDatabase pdb
6c08 title:
Zebrafish SLC38A9 with arginine bound in the cytosol open state [more info...]
Chain information for 6c08 #1
---
Chain | Description | UniProt
A D | antibody Fab Heavy Chain |
B E | antibody Fab light chain |
C F | Sodium-coupled neutral amino acid transporter 9 | S38A9_DANRE 71-549
Non-standard residues in 6c08 #1
---
ARG — arginine
6c08 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> log metadata #1
Metadata for 6c08 #1
---
Title | Zebrafish SLC38A9 with arginine bound in the cytosol open state
Citation | Lei, H.T., Ma, J., Sanchez Martinez, S., Gonen, T. (2018). Crystal structure of arginine-bound lysosomal transporter SLC38A9 in the cytosol-open state. Nat. Struct. Mol. Biol., 25, 522-527. PMID: 29872228. DOI: 10.1038/s41594-018-0072-2
Non-standard residue | ARG — arginine
Source (natural) | Mus musculus (house mouse)
Gene source | Danio rerio (zebrafish)
Experimental method | X-ray diffraction
Resolution | 3.100Å
> open 6c08 fromDatabase redo format mmcif
Summary of feedback from opening 6c08 fetched from redo
---
note | Fetching mmCIF 6c08 from https://pdb-redo.eu/db/6c08/6c08_final.cif
6c08 title:
Zebrafish SLC38A9 with arginine bound In the cytosol open state [more info...]
Chain information for 6c08 #2
---
Chain | Description | UniProt
A D | ANTIBODY FAB HEAVY CHAIN |
B E | ANTIBODY FAB LIGHT CHAIN |
C F | SODIUM-COUPLED NEUTRAL AMINO ACID TRANSPORTER 9 | S38A9_DANRE 71-549
Non-standard residues in 6c08 #2
---
ARG — arginine
6c08 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> hide #!1 models
> hide #!2 models
> show #!2 models
> show #!1 models
> usage open
open names [format format] [fromDatabase fromDatabase] [name a text string]
[id id] [format/database-specific arguments]
— read and display data
names: file names to open; a name of 'browse' will bring up a file browser
format: one of allxyz, aln, amber, amira, apbs, bild, brix, ccd, ccp4,
cellpack, clustal, cmap, cmd, cod, collada, com, compiled python, coords,
corecif, cube, dat, dcd, defattr, delphi, dicom, dock, dsn6, dv, dynamo,
emanhdf, fasta, fchk, fsc, generic_particles, geomodel, gltf, gopenmol, gro,
hdf, hssp, html, ihm, images, imagic, imod, imodmap, ims, iupac, log,
macmolplt, markers, mmcif, mmtf, model2point, mol2, mole, motivelist, motl,
mrc, msf, mtz, nbo31, nbo47, netcdfmap, nifti, nmrstar, nrrd, obj, out, pcod,
pdb, pdbqt, peet, pfam, photo, pif, pir, positions, priism, profec,
pseudobonds, psf, python, qout, relion, rmf, rsf, schrodinger maestro, sdf,
segger, session, sff, situs, smallcif, smiles, spider, sqmout, star, stl,
stockholm, storm, swc, swissdock, tbl, tom_em, trr, uhbd, uniprot, viperdb,
vtk, web fetch, xplor, xtc, xyz, or zdock
fromDatabase: one of alphafold, ccd, cellpack, cod, eds, edsdiff, emdb,
emdb_china, emdb_europe, emdb_fits, emdb_japan, emdb_us, esmfold, ftp, help,
http, https, iupac, pcod, pdb, pdb_nmr, pdbdev, pdbe, pdbe_bio, pdbj, pubchem,
rcsb_bio, redo, smiles, tcia, or uniprot
id: a model id
format/database-specific arguments: format- or database-specific arguments; to
see their syntax use 'usage open format format' or 'usage open database
database' commands respectively, where format and database are as per the
above
> usage open database pdbredo
Missing or invalid "database" argument: Should be one of 'alphafold', 'ccd',
'cellpack', 'cod', 'eds', 'edsdiff', 'emdb', 'emdb_china', 'emdb_europe',
'emdb_fits', 'emdb_japan', 'emdb_us', 'esmfold', 'ftp', 'help', 'http',
'https', 'iupac', 'pcod', 'pdb', 'pdb_nmr', 'pdbdev', 'pdbe', 'pdbe_bio',
'pdbj', 'pubchem', 'rcsb_bio', 'redo', 'smiles', 'tcia', or 'uniprot'
> usage open database redo
open names [ignoreCache true or false] [atomic true or false] [autoStyle true
or false] [combineSymAtoms true or false] [coordsets true or false] [logInfo
true or false] [maxModels an integer] [slider true or false] [overSampling a
number] [structureFactors true or false]
— read and display data
names: file names to open; a name of 'browse' will bring up a file browser
> close #2
> open 6c08 fromDatabase redo structureFactors true
Traceback (most recent call last):
File "/Users/goddard/Desktop/ChimeraX Apr 1
2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File "/Users/goddard/Desktop/ChimeraX Apr 1
2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2904, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/goddard/Desktop/ChimeraX Apr 1
2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 131, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/goddard/Desktop/ChimeraX Apr 1
2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2904, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/goddard/Desktop/ChimeraX Apr 1
2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 166, in provider_open
models, status = collated_open(session, database_name, ident,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/goddard/Desktop/ChimeraX Apr 1
2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 513, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File "/Users/goddard/Desktop/ChimeraX Apr 1
2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 484, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/goddard/Desktop/ChimeraX Apr 1
2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mmcif/__init__.py", line 109, in fetch
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "src/mmcif.pyx", line 519, in chimerax.mmcif.mmcif.fetch_pdb_redo
File "/Users/goddard/Desktop/ChimeraX Apr 1
2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/manager.py", line 217, in open_data
return provider_open(self.session, [path], _return_status=True,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/goddard/Desktop/ChimeraX Apr 1
2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 213, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/goddard/Desktop/ChimeraX Apr 1
2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 514, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File "/Users/goddard/Desktop/ChimeraX Apr 1
2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 484, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/goddard/Desktop/ChimeraX Apr 1
2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mmcif/__init__.py", line 54, in open
return mmcif.open_mmcif(session, data, file_name, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "src/mmcif.pyx", line 90, in chimerax.mmcif.mmcif.open_mmcif
TypeError: open_mmcif() got an unexpected keyword argument 'structure_factors'
TypeError: open_mmcif() got an unexpected keyword argument 'structure_factors'
File "src/mmcif.pyx", line 90, in chimerax.mmcif.mmcif.open_mmcif
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,2
Model Number: MK1H3LL/A
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 GB
System Firmware Version: 10151.81.1
OS Loader Version: 10151.81.1
Software:
System Software Overview:
System Version: macOS 14.3.1 (23D60)
Kernel Version: Darwin 23.3.0
Time since boot: 36 days, 6 hours, 6 minutes
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 32
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
alphashape: 1.3.1
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.14.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.1.1
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.16
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.3
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.5
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.56
ChimeraX-AtomicLibrary: 14.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
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: 2.12.1
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: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8.dev202403290055
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4.2
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.9
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.15
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-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.3
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
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: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2
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-TetraScapeCommand: 0.1
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: 1.37.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
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: 1.1.3
ChimeraX-Zone: 1.0.1
click: 8.1.7
click-log: 0.4.0
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.9
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.1
fonttools: 4.50.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.10.0
html2text: 2024.2.26
idna: 3.6
ihm: 0.43
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.2
jedi: 0.19.1
Jinja2: 3.1.3
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.10
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.1.0
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.3
matplotlib-inline: 0.1.6
msgpack: 1.0.8
ndindex: 1.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.2.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.9.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.3
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.2.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.0
prompt-toolkit: 3.0.43
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.3.0
pygments: 2.17.2
pynmrstar: 3.3.2
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3302
pyparsing: 3.1.2
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.2
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.2
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 25.1.2
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
Rtree: 1.1.0
scipy: 1.12.0
setuptools: 69.2.0
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
shapely: 2.0.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.0
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.1
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.1
trimesh: 4.0.8
typing-extensions: 4.10.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.10
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Usage no longer reports overSampling or structureFactors as legal keywords for 'redo'