The following bug report has been submitted:
Platform: macOS-14.3-arm64-arm-64bit
ChimeraX Version: 1.12rc202605142114 (2026-05-14 21:14:16 UTC)
Description
I get an error when i try to go back to previous colorings and the structure turns all white
Log:
UCSF ChimeraX version: 1.12rc202605142114 (2026-05-14)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 8hnh
8hnh title:
Cryo-EM structure of human OATP1B1 in complex with simeprevir [more info...]
Chain information for 8hnh #1
---
Chain | Description | UniProt
A | Solute carrier organic anion transporter family member 1B1 | SO1B1_HUMAN 1-691
Non-standard residues in 8hnh #1
---
30B —
(2R,3aR,10Z,11aS,12aR,14aR)-N-(cyclopropylsulfonyl)-2-({7-methoxy-8-methyl-2-[4-(1-methylethyl)-1,3-thiazol-2-yl]quinolin-4-yl}oxy)-5-methyl-4,14-dioxo-2,3,3a,4,5,6,7,8,9,11a,12,13,14,14a-tetradecahydrocyclopenta[c]cyclopropa[g][1,6]diazacyclotetradecine-12a(1H)-carboxamide
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> label delete
> select protein
4142 atoms, 4250 bonds, 3 pseudobonds, 563 residues, 2 models selected
> hide sel atoms
> color (#!1 & sel) light gray
> graphics silhouettes true
> lighting soft
> select celar
Expected an objects specifier or a keyword
> select clear
> open /Users/everodonnell/Documents/slco1b1DMS2024March.csv chains /A
Summary of feedback from opening
/Users/everodonnell/Documents/slco1b1DMS2024March.csv
---
notes | Ignored 2710 variants: 785 deletions p.(A112_L113del), p.(A13del), p.(A200_K201del) ..., 1925 insertions p.(A11_E12insG), p.(A11_E12insGS), p.(A11_E12insGSG) ...
Associated 1 chain to mutation set slco1b1DMS2024March.
Associated chain /A with 0 mismatches.
Opened deep mutational scan data for 13465 mutations of 676 residues with
score names len, lfsr_ros, mean_ros, pos, score_GFP, score_MTX. Assigned
scores to 549 of 563 residues of chain #1/A. Found scores for 127 residues not
present in structures #1/A.
Color the structure first, then you can adjust colors
> mutationscores define mutation_score fromScoreName score_GFP combine mean
Defined score mutation_score having range -2.5 to 0.96 for 676 residues using
13450 mutations
Set attribute mutation_score for 549 residues of chain #1/A
> color byattribute r:mutation_score #1/A palette
> -1.25,blue:-0.391,white:0.465,white:1.32,red noValueColor white
4208 atoms, 565 residues, atom mutation_score range -2.5 to 0.96
> ui tool show "Render/Select by Attribute"
Desktop color scheme is light
> mutationscores scatterplot len lfsr_ros
Plotted 13435 mutations with len on x-axis and lfsr_ros on y-axis
> mutationscores scatterplot len lfsr_ros
Plotted 13435 mutations with len on x-axis and lfsr_ros on y-axis
> set bgColor white
Drag select of 16 atoms, 16 bonds
> select clear
> select :NAG
42 atoms, 43 bonds, 3 residues, 1 model selected
> hide sel atoms
> select ::name="30B"
52 atoms, 58 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel forest green
> color sel hot pink
> color sel yellow
> color sel orange
> color sel byhetero
> select clear
> mutationscores define mutation_score fromScoreName score_GFP combine count
Defined score mutation_score having range 13 to 20 for 676 residues using
13450 mutations
Re-registration of attr 'mutation_score' with Residue by Deep Mutational Scan
changes type information
Set attribute mutation_score for 549 residues of chain #1/A
> color byattribute r:mutation_score #1/A palette
> 19,blue:19.6,white:20.2,white:20.8,red noValueColor white
4208 atoms, 565 residues, atom mutation_score range 13 to 20
> ui tool show "Render/Select by Attribute"
> help help:user/tools/mutationscores.html#coloring
> color byattribute r:raw_gfp #1/A palette
> -1.25,blue:-0.391,white:0.465,white:1.32,red noValueColor white
All 'raw_gfp' values are None
> color byattribute r:raw_gfp #1/A palette
> -1.25,blue:-0.391,white:0.465,white:1.32,red noValueColor white
All 'raw_gfp' values are None
> color byattribute r:raw_gfp #1/A palette
> -1.25,blue:-0.391,white:0.465,white:1.32,red noValueColor white
All 'raw_gfp' values are None
> ui tool show "Render/Select by Attribute"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_color_history.py", line 964, in
_adjust_colors
_show_render_by_attribute_panel(self.session, mset, options['attribute_name'],
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_color_history.py", line 338, in
_show_render_by_attribute_panel
rba_gui.configure(models = models, target = 'residues', tab = 'render',
attr_name = attribute_name,
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/render_by_attr/tool.py", line 476, in configure
marker = markers.append(arg)
^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/histogram.py", line 944, in append
self.histogram._ensure_range(marker.xy)
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/histogram.py", line 515, in _ensure_range
if x < self._min_val and (self._draw_min is None or x < self._draw_min):
^^^^^^^^^^^^^
AttributeError: 'MarkedHistogram' object has no attribute '_min_val'
AttributeError: 'MarkedHistogram' object has no attribute '_min_val'
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/histogram.py", line 515, in _ensure_range
if x < self._min_val and (self._draw_min is None or x < self._draw_min):
^^^^^^^^^^^^^
See log for complete Python traceback.
> ui tool show "Render/Select by Attribute"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_color_history.py", line 964, in
_adjust_colors
_show_render_by_attribute_panel(self.session, mset, options['attribute_name'],
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_color_history.py", line 338, in
_show_render_by_attribute_panel
rba_gui.configure(models = models, target = 'residues', tab = 'render',
attr_name = attribute_name,
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/render_by_attr/tool.py", line 476, in configure
marker = markers.append(arg)
^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/histogram.py", line 944, in append
self.histogram._ensure_range(marker.xy)
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/histogram.py", line 515, in _ensure_range
if x < self._min_val and (self._draw_min is None or x < self._draw_min):
^^^^^^^^^^^^^
AttributeError: 'MarkedHistogram' object has no attribute '_min_val'
AttributeError: 'MarkedHistogram' object has no attribute '_min_val'
File
"/Applications/ChimeraX-1.12-rc2026.05.18.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/histogram.py", line 515, in _ensure_range
if x < self._min_val and (self._draw_min is None or x < self._draw_min):
^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.9
Locale: UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.1
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 hour, 30 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:
accessible-pygments: 0.0.5
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.13.0
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: 4.2.0
bs4: 0.0.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.7
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.2
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.2
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: 1.67.1
ChimeraX-AtomicLibrary: 14.4
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: 1.12rc202605142114
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.2.1
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: 2.5.3
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: 1.8.2
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: 1.1
ChimeraX-MatchMaker: 2.4
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.2.0
ChimeraX-MDcrds: 2.19
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.8
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.23
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-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.4
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: 1.6
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: 2.18
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: 1.19.3
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: 1.50.6
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.6.2
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: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.4.0
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.14.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.2.4
debugpy: 1.8.20
decorator: 5.3.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
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: 3.15
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 2.0.0
iniconfig: 2.3.0
ipykernel: 7.1.0
ipython: 9.9.0
ipython_pygments_lexers: 1.1.1
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.8.0
jupyter_core: 5.9.1
kiwisolver: 1.5.0
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.2
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.1
narwhals: 2.21.2
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
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: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.9.6
plotly: 6.7.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.5.2
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: 2.14.1
pydantic_core: 2.46.4
pydata-sphinx-theme: 0.17.1
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.5.1
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.10.2
PyQt6-Qt6: 6.10.1
PyQt6-WebEngine-commercial: 6.10.0
PyQt6-WebEngine-Qt6: 6.10.1
PyQt6_sip: 13.10.3
pytest: 9.0.3
pytest-cov: 7.1.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.2
python-multipart: 0.0.29
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
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: 3.4.4
stack-data: 0.6.3
starlette: 1.0.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 3.2.1
threadpoolctl: 3.6.0
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.5
tqdm: 4.67.3
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
Unidecode: 1.4.0
urllib3: 2.7.0
uvicorn: 0.47.0
wcwidth: 0.7.0
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
yarl: 1.23.0
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Tom, I can only seem to reproduce this if I use configure() with 'level_info' but with no valid target/attr_name given (or currently active). Do you have code that does this, or is there some other way to reproduce it?
--Eric