Opened 7 days ago
Last modified 7 days ago
#20597 assigned defect
Opening mutation score .csv file does to show the scores in the order used in the file
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Analysis | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-26.5.2-arm64-arm-64bit
ChimeraX Version: 1.13.dev202607062341 (2026-07-06 23:41:36 UTC)
Description
Opening mutation scores .csv file does not list the scores in the order they appear in the header line of the .csv file.
Log:
UCSF ChimeraX version: 1.13.dev202607062341 (2026-07-06)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/goddard/Downloads/urn_mavedb_00001222-b-2_scores.csv format ms
Summary of feedback from opening
/Users/goddard/Downloads/urn_mavedb_00001222-b-2_scores.csv
---
note | Ignored 121 variants: 121 stop codons p.Ser1Ter, p.Pro3Ter, p.Ser4Ter ...
Opened deep mutational scan data for 2150 mutations of 286 residues with score
names control_score, score, control_rep1_score, var, control_rep3_score,
control_rep4_score, control_rep2_score, control_std, rep1_score, std,
control_var, rep4_score, rep3_score, rep2_score.
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M2 Ultra
OpenGL vendor: Apple
Python: 3.11.15
Locale: en_US.UTF-8
Qt version: PySide6 6.11.1, Qt 6.11.1
Qt runtime version: 6.11.1
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac Studio
Model Identifier: Mac14,14
Model Number: Z1800003VLL/A
Chip: Apple M2 Ultra
Total Number of Cores: 24 (16 Performance and 8 Efficiency)
Memory: 64 GB
System Firmware Version: 18000.121.3
OS Loader Version: 18000.121.3
Software:
System Software Overview:
System Version: macOS 26.5.2 (25F84)
Kernel Version: Darwin 25.5.0
Time since boot: 8 days, 22 hours, 59 minutes
Graphics/Displays:
Apple M2 Ultra:
Chipset Model: Apple M2 Ultra
Type: GPU
Bus: Built-In
Total Number of Cores: 60
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
PHL 278B1:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
accessible-pygments: 0.0.5
aiohappyeyeballs: 2.7.1
aiohttp: 3.13.4
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.14.1
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 26.1.0
babel: 2.18.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 4.7.0
build: 1.5.0
certifi: 2026.6.17
cftime: 1.6.5
charset-normalizer: 3.4.8
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.3.1
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.2
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.2.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.70
ChimeraX-AtomicLibrary: 14.4.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4.1
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.4
ChimeraX-Cluster: 1.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.1
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.13.dev202607062341
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.6
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DAQplugin: 1.0.0
ChimeraX-DataFormats: 1.2.4
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.2.2
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.4
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.8.4
ChimeraX-Label: 1.5
ChimeraX-LightingGUI: 1.0
ChimeraX-ListInfo: 1.3.1
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.3
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-MatchAlign: 1.2.1
ChimeraX-MatchMaker: 2.4.1
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.2.0
ChimeraX-MDcrds: 2.19.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.4.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.17
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.24
ChimeraX-ModelPanel: 1.6.1
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: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.16.2
ChimeraX-OpenFold: 1.0
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.13
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.10.2
ChimeraX-ProNA3D: 0.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.8.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.12
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.19.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
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-SNFG: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.20
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: 2.5.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.4
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.53
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.6.4
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: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.4.2
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.15.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.2.4
debugpy: 1.8.21
decorator: 5.3.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
flatbuffers: 25.12.19
fonttools: 4.63.0
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.16.0
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.18
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 2.0.0
iniconfig: 2.3.0
ipykernel: 7.3.0
ipython: 9.14.1
ipython_pygments_lexers: 1.1.1
jedi: 0.20.0
Jinja2: 3.1.6
joblib: 1.5.3
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.9.1
jupyter_core: 5.9.1
kiwisolver: 1.5.0
line_profiler: 5.0.0
llvmlite: 0.47.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
markdown-it-py: 4.2.0
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.2
mcp: 1.18.0
mdurl: 0.1.2
mlx: 0.31.2
mlx-metal: 0.31.2
mrcfile: 1.5.4
msgpack: 1.1.1
multidict: 6.7.1
narwhals: 2.23.0
ndindex: 1.10.1
nest-asyncio2: 1.7.2
netCDF4: 1.7.4
networkx: 3.3
numba: 0.65.1
numexpr: 2.14.1
numpy: 2.4.6
onnxruntime: 1.26.0
OpenMM: 8.4.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.7
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 26.1.2
pkginfo: 1.12.1.2
platformdirs: 4.10.0
plotly: 6.8.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.5.2
protobuf: 7.34.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.13.4
pydantic-settings: 2.14.2
pydantic_core: 2.46.4
pydata-sphinx-theme: 0.19.0
Pygments: 2.18.0
pyKVFinder: 0.9.3
pynmrstar: 3.5.1
pynndescent: 0.6.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PySide6: 6.11.1
PySide6_Addons: 6.11.1
PySide6_Essentials: 6.11.1
pytest: 9.1.1
pytest-cov: 7.1.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.2
python-multipart: 0.0.32
pyzmq: 27.1.0
qtconsole: 5.7.2
QtPy: 2.4.3
qtshim: 1.2.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
rich: 15.0.0
roman-numerals: 4.1.0
rpds-py: 2026.6.3
scikit-learn: 1.9.0
scipy: 1.17.1
setuptools: 82.0.1
sfftk-rw: 0.8.1
shiboken6: 6.11.1
six: 1.17.0
snowballstemmer: 3.1.1
sortedcontainers: 2.4.0
soupsieve: 2.8.4
Sphinx: 9.0.4
sphinx-autodoc-typehints: 3.6.1
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
sse-starlette: 3.4.5
stack-data: 0.6.3
starlette: 1.3.1
superqt: 0.7.6
tables: 3.11.1
threadpoolctl: 3.6.0
tifffile: 2025.3.13
tinyarray: 1.2.5
tomlkit: 0.15.0
tornado: 6.5.7
tqdm: 4.68.3
traitlets: 5.15.1
typing-inspection: 0.4.2
typing_extensions: 4.16.0
umap-learn: 0.5.12
urllib3: 2.7.0
uvicorn: 0.50.2
wcwidth: 0.8.2
webcolors: 24.11.1
wheel: 0.47.0
wheel-filename: 1.4.2
yarl: 1.24.2
Change History (2)
comment:1 by , 7 days ago
| Component: | Unassigned → Structure Analysis |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Opening mutation score .csv file does to show the scores in the order used in the file |
comment:2 by , 7 days ago
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The score names are put in alphabetical order. Some code that was not checked in from my development build made them appear in random order (an option to include computed names was added and it used set() which disordered the names).
I'm not sure if the score names should use alphabetical order or the order listed in the .csv file header. It may be alphabetical is better.