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Opened 5 months ago
Closed 5 months ago
#17817 closed defect (fixed)
Mutation Scores: NotImplementedError: cannot remove artist
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Analysis | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.3-arm64-arm-64bit
ChimeraX Version: 1.9rc202412100036 (2024-12-10 00:36:39 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
UCSF ChimeraX version: 1.9rc202412100036 (2024-12-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 7pqg
7pqg title:
Structure of thermostabilised human NTCP in complex with nanobody 87 [more
info...]
Chain information for 7pqg #1
---
Chain | Description | UniProt
A | Sodium/bile acid cotransporter | NTCP_HUMAN 3-328
B | Nanobody 87 |
> select /B
955 atoms, 979 bonds, 124 residues, 1 model selected
> hide sel cartoons
> set bgColor white
> lighting soft
> graphics silhouettes true
> ui tool show "Color Actions"
> color sel slate gray
> select /a
2296 atoms, 2346 bonds, 299 residues, 1 model selected
> ui tool show "Color Actions"
> color sel slate gray
> select clear
> open /Users/everodonnell/Documents/ntcp/ntcp_merged_scofes_.csv chain /A
No such file/path: /Users/everodonnell/Documents/ntcp/ntcp_merged_scofes_.csv
> open /Users/everodonnell/Documents/ntcp/ntcp_merged_scores_.csv chain /A
Summary of feedback from opening
/Users/everodonnell/Documents/ntcp/ntcp_merged_scores_.csv
---
warning | Did not associate chain /A because sequence does not match mutation set ntcp_merged_scores_ at 7 positions, first mistmatch is VAL 33
note | Plotted 6471 mutations with effect_se_hbv_125 on x-axis and effect_se_hbv_187 on y-axis
Opened deep mutational scan data for 6718 mutations of 341 residues with score
names effect_se_hbv_125, effect_se_hbv_187, effect_se_hbv_250,
effect_se_hbv_62, effect_se_nb79_125, effect_se_nb79_187, effect_se_nb79_250,
effect_se_nb79_62, effect_se_nb79_93, effect_se_nb87_125, effect_se_nb87_187,
effect_se_nb87_250, effect_se_nb87_62, effect_se_nb87_93, lfsr_abundance,
lfsr_hbv_125, lfsr_hbv_187, lfsr_hbv_250, lfsr_hbv_62, lfsr_nb79_125,
lfsr_nb79_187, lfsr_nb79_250, lfsr_nb79_62, lfsr_nb79_93, lfsr_nb87_125,
lfsr_nb87_187, lfsr_nb87_250, lfsr_nb87_62, lfsr_nb87_93,
pos_effect_abundance, pos_effect_hbv_125, pos_effect_hbv_187,
pos_effect_hbv_250, pos_effect_hbv_62, pos_effect_nb79_125,
pos_effect_nb79_187, pos_effect_nb79_250, pos_effect_nb79_62,
pos_effect_nb79_93, pos_effect_nb87_125, pos_effect_nb87_187,
pos_effect_nb87_250, pos_effect_nb87_62, pos_effect_nb87_93,
pos_effect_se_abundance, pos_effect_se_hbv_125, pos_effect_se_hbv_187,
pos_effect_se_hbv_250, pos_effect_se_hbv_62, pos_effect_se_nb79_125,
pos_effect_se_nb79_187, pos_effect_se_nb79_250, pos_effect_se_nb79_62,
pos_effect_se_nb79_93, pos_effect_se_nb87_125, pos_effect_se_nb87_187,
pos_effect_se_nb87_250, pos_effect_se_nb87_62, pos_effect_se_nb87_93,
pos_sd_abundance, pos_sd_hbv_125, pos_sd_hbv_187, pos_sd_hbv_250,
pos_sd_hbv_62, pos_sd_nb79_125, pos_sd_nb79_187, pos_sd_nb79_250,
pos_sd_nb79_62, pos_sd_nb79_93, pos_sd_nb87_125, pos_sd_nb87_187,
pos_sd_nb87_250, pos_sd_nb87_62, pos_sd_nb87_93, pos_sd_se_abundance,
pos_sd_se_hbv_125, pos_sd_se_hbv_187, pos_sd_se_hbv_250, pos_sd_se_hbv_62,
pos_sd_se_nb79_125, pos_sd_se_nb79_187, pos_sd_se_nb79_250, pos_sd_se_nb79_62,
pos_sd_se_nb79_93, pos_sd_se_nb87_125, pos_sd_se_nb87_187, pos_sd_se_nb87_250,
pos_sd_se_nb87_62, pos_sd_se_nb87_93, position, score_abundance,
score_hbv_125, score_hbv_187, score_hbv_250, score_hbv_62, score_nb79_125,
score_nb79_187, score_nb79_250, score_nb79_62, score_nb79_93, score_nb87_125,
score_nb87_187, score_nb87_250, score_nb87_62, score_nb87_93, score_tca_100,
se_abundance. Assigned scores to 292 of 299 residues of chain /A. Found scores
for 49 residues not present in atomic model.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9-rc2024.12.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_scatter_plot.py", line 119, in
_menu_selection_changed
self.set_plot_data(x_score_name, y_score_name, mutation_set_name,
File
"/Applications/ChimeraX-1.9-rc2024.12.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_scatter_plot.py", line 183, in
set_plot_data
self._set_nodes(xy, point_names=point_names, colors=colors,
stack_order=stack_order,
File
"/Applications/ChimeraX-1.9-rc2024.12.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_scatter_plot.py", line 202, in _set_nodes
self.draw_graph()
File
"/Applications/ChimeraX-1.9-rc2024.12.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/interfaces/graph.py", line 237, in draw_graph
node_pos = self._draw_nodes()
^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9-rc2024.12.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/interfaces/graph.py", line 264, in _draw_nodes
self._node_artist.remove()
File "/Users/everodonnell/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/matplotlib/artist.py", line 256,
in remove
raise NotImplementedError('cannot remove artist')
NotImplementedError: cannot remove artist
NotImplementedError: cannot remove artist
File "/Users/everodonnell/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/matplotlib/artist.py", line 256,
in remove
raise NotImplementedError('cannot remove artist')
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9-rc2024.12.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_scatter_plot.py", line 119, in
_menu_selection_changed
self.set_plot_data(x_score_name, y_score_name, mutation_set_name,
File
"/Applications/ChimeraX-1.9-rc2024.12.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_scatter_plot.py", line 183, in
set_plot_data
self._set_nodes(xy, point_names=point_names, colors=colors,
stack_order=stack_order,
File
"/Applications/ChimeraX-1.9-rc2024.12.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_scatter_plot.py", line 202, in _set_nodes
self.draw_graph()
File
"/Applications/ChimeraX-1.9-rc2024.12.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/interfaces/graph.py", line 237, in draw_graph
node_pos = self._draw_nodes()
^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9-rc2024.12.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/interfaces/graph.py", line 264, in _draw_nodes
self._node_artist.remove()
File "/Users/everodonnell/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/matplotlib/artist.py", line 256,
in remove
raise NotImplementedError('cannot remove artist')
NotImplementedError: cannot remove artist
NotImplementedError: cannot remove artist
File "/Users/everodonnell/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/matplotlib/artist.py", line 256,
in remove
raise NotImplementedError('cannot remove artist')
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,7
Model Number: MNEH3LL/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 10151.101.3
OS Loader Version: 10151.81.1
Software:
System Software Overview:
System Version: macOS 14.3 (23D56)
Kernel Version: Darwin 23.3.0
Time since boot: 1 day, 13 hours, 18 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.7.1
build: 1.2.1
certifi: 2023.11.17
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-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: 1.9rc202412100036
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-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-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
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.2
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h5py: 3.12.1
html2text: 2024.2.26
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
joblib: 1.4.2
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
llvmlite: 0.44.0
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.10.3
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
narwhals: 1.41.0
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numba: 0.61.0
numexpr: 2.10.2
numpy: 2.2.6
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
plotly: 6.0.1
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pyKVFinder: 0.8.0
pynmrstar: 3.3.4
pynndescent: 0.5.13
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
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scikit-learn: 1.6.1
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
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
tables: 3.10.1
tcia_utils: 1.5.1
threadpoolctl: 3.6.0
tifffile: 2024.7.24
tinyarray: 1.2.4
tomlkit: 0.13.2
tornado: 6.4.2
tqdm: 4.67.1
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
umap-learn: 0.5.7
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Attachments (1)
Change History (8)
comment:1 by , 5 months ago
| Component: | Unassigned → Structure Analysis |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Mutation Scores: NotImplementedError: cannot remove artist |
comment:2 by , 5 months ago
| Cc: | added |
|---|---|
| Reporter: | changed from to |
comment:3 by , 5 months ago
Hey Tom,
Thanks for the quick reply! I got the same error with the most recent daily build, i downloaded it this morning.
Best,
Ever
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Tuesday, May 27, 2025 3:19 PM
To: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; O'Donnell, Ever <Ever.ODonnell@ucsf.edu>
Cc: PETTERSEN, ERIC <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #17817: Mutation Scores: NotImplementedError: cannot remove artist
!-------------------------------------------------------------------|
This Message Is From an External Sender
This message came from outside your organization.
|-------------------------------------------------------------------!
#17817: Mutation Scores: NotImplementedError: cannot remove artist
-----------------------------------------+-------------------------
Reporter: Ever.ODonnell@… | Owner: Tom Goddard
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Structure Analysis | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
-----------------------------------------+-------------------------
Changes (by Tom Goddard):
* cc: pett (added)
* reporter: chimerax-bug-report@… => Ever.ODonnell@…
Comment:
Hi Ever,
I'm puzzled by this error when you changed the scatter plot axes after
open /Users/everodonnell/Documents/ntcp/ntcp_merged_scores_.csv chain
/A
The error comes from matplotlib, the plotting package that is trying to
draw the scatter plot. Could you try this with the ChimeraX 1.10 release
candidate?
One theory I have is that it is caused by ChimeraX having two different
versions of matplotlib installed (3.9.2 and 3.10.3). I think the newer
one of those matplotlib versions (3.10.3) got installed by some other
ChimeraX tool from the Toolshed while 3.9.2 was what ChimeraX had built
in.
Tom
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/17817#comment:2 >
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/ >
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=?utf-8?B?U2NyZWVuc2hvdCAyMDI1LTA1LTI3IGF0IDMuMzguMDHigK9QTS5wbmc=?=
by , 5 months ago
| Attachment: | =?utf-8?B?U2NyZWVuc2hvdCAyMDI1LTA1LTI3IGF0IDMuMzguMDHigK9QTS5wbmc=?= added |
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Added by email2trac
comment:4 by , 5 months ago
Ok, I see I get that error too. I must have changed some code a month ago that broke this. I'll investigate and fix hopefully today.
comment:5 by , 5 months ago
I raised the Matplotlib prereq to 3.10 so that MD plotting could access an API (MouseEvent.button) only available starting with that version.
comment:6 by , 5 months ago
Tests show the error happens in matplotlib 3.10 from an April 23, 2025 ChimeraX daily build but does not happen with matplotlib 3.9 from a February 23, 2025 ChimeraX. Replacing matplotlib 3.10 with 3.9 in the current ChimeraX daily build fixes the problem. So this bug is caused by matplotlib 3.10. Will need to investigate possible fixes.
I uninstalled matplotlib 3.10 and installed 3.9 using ChimeraX commands
pip uninstall matplotlib
pip install matplotlib==3.9
then restarted ChimeraX to use the new matplotlib.
comment:7 by , 5 months ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Fixed in ChimeraX 1.10 release candidates and daily builds dated May 28, 2025 or newer.
Matplotlib 3.10 made a breaking change compared to 3.9 where removing an "artist" (ie any drawn element) from a plot that has already been cleared now raises an error. I added code to avoid removing the artist if the plot has been cleared.
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Hi Ever,
The error comes from matplotlib, the plotting package that is trying to draw the scatter plot. Could you try this with the ChimeraX 1.10 release candidate?