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Opened 12 days ago
Closed 4 days ago
#20435 closed defect (fixed)
Minimize 6i4q: KeyError: 'N'
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Editing | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-6.17.0-29-generic-x86_64-with-glibc2.39
ChimeraX Version: 1.12rc202606020412 (2026-06-02 04:12:41 UTC)
Description
1. Fetch PDB 6i4q
2. del :btb :so4 :hoh
3. Tools > Structure Editing > Minimize Structure
Possibly related to (though the error trace is different):
https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/19923
Thanks for making ChimeraX!
Log:
Startup Messages
---
warning | No presets found in custom preset folder /home/paul/config/chimerax
> alias cls close session
UCSF ChimeraX version: 1.12rc202606020412 (2026-06-02)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 6i4q format mmcif fromDatabase pdbe_bio
Summary of feedback from opening 6i4q fetched from pdbe_bio
---
warnings | Missing or incorrect sequence information. Inferred polymer connectivity.
Atom H is not in the residue template for VAL /B:-6
6i4q bioassembly 1 title:
Crystal structure of the human dihydrolipoamide dehydrogenase at 1.75 Angstrom
resolution [more info...]
Chain information for 6i4q bioassembly 1 #1
---
Chain | Description
A | Dihydrolipoyl dehydrogenase, mitochondrial
B | Dihydrolipoyl dehydrogenase, mitochondrial
Non-standard residues in 6i4q bioassembly 1 #1
---
BTB — (BTB)
FAD — (FAD)
SO4 — (SO4)
249 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Computing secondary structure
Opened 1 biological assemblies for 6i4q
> delete :btb
> delete :so4
> delete :hoh
> ui tool show "Minimize Structure"
> minimize #1 logEnergy true
Starting dock prep
Deleting solvent
Deleting non-metal-complex ions
Deleting non-current alt locs
Deleting residues with incomplete backbones
Summary of feedback from adding hydrogens to 6i4q bioassembly 1 #1
---
notes | No usable SEQRES records for 6i4q bioassembly 1 (#1) chain A; guessing termini instead
No usable SEQRES records for 6i4q bioassembly 1 (#1) chain B; guessing termini
instead
Chain-initial residues that are actual N termini: /A GLN 3
Chain-initial residues that are not actual N termini: /B VAL -6
Chain-final residues that are actual C termini: /A PHE 474, /B PHE 474
Chain-final residues that are not actual C termini:
905 hydrogen bonds
5 hydrogens added
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue FAD (net charge -1) with am1-bcc method
Running ANTECHAMBER command: /usr/lib/ucsf-
chimerax/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
/tmp/tmp4jydjonb/ante.in.mol2 -fi mol2 -o /tmp/tmp4jydjonb/ante.out.mol2 -fo
mol2 -c bcc -nc -1 -j 5 -s 2 -dr n
(FAD) ``
(FAD) `Welcome to antechamber 20.0: molecular input file processor.`
(FAD) ``
(FAD) `Info: Finished reading file (/tmp/tmp4jydjonb/ante.in.mol2); atoms read
(85), bonds read (90).`
(FAD) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(FAD) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(FAD) ``
(FAD) ``
(FAD) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(FAD) `Info: Total number of electrons: 408; net charge: -1`
(FAD) ``
(FAD) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out`
(FAD) ``
(FAD) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /usr/lib/ucsf-
chimerax/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1`
(FAD) ``
(FAD) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(FAD) ``
Charges for residue FAD determined
Dock prep finished
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/minimize/tool.py", line 116, in minimize
run(self.session, cmd)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/minimize/cmd.py", line 43, in cmd_minimize
dock_prep_caller(session, [structure], memorize_name="minimization",
nogui=True,
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 146, in dock_prep_caller
run_steps(session, state, structures)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 161, in run_steps
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/dock_prep/prep.py", line 132, in prep
callback(session, state, structures)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 161, in run_steps
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/addh/dock_prep.py", line 56, in run_for_dock_prep
callback(session, state, structures)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 161, in run_steps
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/add_charge/dock_prep.py", line 58, in run_for_dock_prep
callback(session, state, structures)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 156, in run_steps
callback()
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/dock_prep/prep.py", line 131, in <lambda>
state['callback'] = lambda cb=cb, ps=postscript: (ps(), cb())
^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/minimize/cmd.py", line 45, in <lambda>
steps=max_steps: _minimize(ses, struct, updates, log, steps), **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/minimize/cmd.py", line 232, in _minimize
system = forcefield.createSystem(top, nonbondedCutoff=1*nanometer,
constraints=HBonds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/openmm/app/forcefield.py", line 1279, in createSystem
data.setAtomClasses(self)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/openmm/app/forcefield.py", line 683, in setAtomClasses
self.atomClasses = [classNameForType[self.atomType[atom]] for atom in
self.atoms]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/openmm/app/forcefield.py", line 683, in <listcomp>
self.atomClasses = [classNameForType[self.atomType[atom]] for atom in
self.atoms]
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^
KeyError: 'N'
KeyError: 'N'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/openmm/app/forcefield.py", line 683, in
self.atomClasses = [classNameForType[self.atomType[atom]] for atom in
self.atoms]
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.6 (Core Profile) Mesa 25.2.8-0ubuntu0.24.04.1
OpenGL renderer: Mesa Intel(R) HD Graphics 630 (KBL GT2)
OpenGL vendor: Intel
Python: 3.11.13
Locale: en_US.UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.2
Qt platform: xcb
XDG_SESSION_TYPE=wayland
DESKTOP_SESSION=ubuntu-wayland
XDG_SESSION_DESKTOP=ubuntu-wayland
XDG_CURRENT_DESKTOP=ubuntu:GNOME
WAYLAND_DISPLAY=wayland-0
GNOME_SETUP_DISPLAY=:2
DISPLAY=:1
Manufacturer: Dell Inc.
Model: XPS 15 9560
OS: Ubuntu 24.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 8 Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz
Cache Size: 6144 KB
Memory:
total used free shared buff/cache available
Mem: 31Gi 7.9Gi 11Gi 1.9Gi 12Gi 23Gi
Swap: 8.0Gi 4.0Ki 8.0Gi
Graphics:
00:02.0 VGA compatible controller [0300]: Intel Corporation HD Graphics 630 [8086:591b] (rev 04)
DeviceName: Onboard IGD
Subsystem: Dell HD Graphics 630 [1028:07be]
Installed Packages:
accessible-pygments: 0.0.5
aiohappyeyeballs: 2.6.2
aiohttp: 3.13.4
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.13.0
appdirs: 1.4.4
asttokens: 3.0.1
attrs: 26.1.0
babel: 2.18.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 4.3.3
bs4: 0.0.2
build: 1.3.0
certifi: 2026.5.20
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: 1.12rc202606020412
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-LinuxSupport: 1.0.1
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
ChimeraX-MatchMaker: 2.4.1
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.2.0
ChimeraX-MDcrds: 2.19
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.9
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: 1.50.7
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: 8.4.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.14.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.2.4
debugpy: 1.8.21
decorator: 5.3.1
distro: 1.9.0
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: 3.17
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: 2.22.0
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: 2.4.6
numpy: 1.26.4
nvidia-nvjitlink-cu12: 12.9.86
OpenMM: 8.4.0
OpenMM-CUDA-12: 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: 4.10.0
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: 0.18.0
pydicom: 2.4.4
Pygments: 2.18.0
pyKVFinder: 0.9.2
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: 6.10.2
PyQt6-Qt6: 6.10.2
PyQt6-WebEngine: 6.10.0
PyQt6-WebEngine-Qt6: 6.10.2
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: 0.0.30
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: 2026.5.1
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.1.0
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: 3.4.4
stack-data: 0.6.3
starlette: 1.2.1
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
tomlkit: 0.15.0
tornado: 6.5.6
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: 0.48.0
wcwidth: 0.7.0
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
yarl: 1.24.2
Attachments (8)
Change History (16)
comment:1 by , 12 days ago
| Component: | Unassigned → Structure Editing |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Minimize 6i4q: KeyError: 'N' |
comment:2 by , 12 days ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
comment:3 by , 11 days ago
Hi Eric,
Thank you for you continued support, and your quick replies.
I will try again with the new daily build once it is available.
However, I do want to mention that I originally ran into the problem while processing a sanitized version of the structure with altlocs removed (I used an unmodified structure to keep the bug report simple and easily reproducible).
Specifically, the error also occurs, if I first set all altlocs to A, remove all other altlocs, and then run minimize (log attached).
On another note: I have taken up a quite a bit of your time. Normally, I would try to address one or two open issues on the github tracker in return, but you don't have any. Anything else I can help out with? I write decent python, without any AI slop: https://github.com/paulbrodersen
All the best,
Paul
________________________________
Paul J. N. Brodersen, DPhil
Postdoctoral Researcher
Department of Pharmacology
University of Oxford
Tel: +44 (0)1865 281113
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 02 June 2026 20:05
To: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Paul Brodersen <paul.brodersen@pharm.ox.ac.uk>
Subject: Re: [ChimeraX] #20435: Minimize 6i4q: KeyError: 'N'
#20435: Minimize 6i4q: KeyError: 'N'
----------------------------------------+----------------------------
Reporter: paul.brodersen@… | Owner: Eric Pettersen
Type: defect | Status: closed
Priority: normal | Milestone:
Component: Structure Editing | Version:
Resolution: fixed | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
----------------------------------------+----------------------------
Changes (by Eric Pettersen):
* resolution: => fixed
* status: accepted => closed
Comment:
Hi Paul,
Thanks for reporting this problem. The issue was that in some alt
locs a disulphide bond was present, but in other alt locs there was no
bond and the sulphurs were protonated. Now the minimization preparation
steps chooses one or the other based on the sulphur-sulphur distance.
The fix will be tomorrow's daily build and 1.12 release candidate.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
Fix:
https://github.com/RBVI/ChimeraX/commit/8d8818e6dc2f091ca70dc0ed25cb2ff9fd20fad9
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/20435#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
comment:4 by , 11 days ago
Hi Paul,
With the fix I made yesterday, if I set all altlocs to A and then minimize, it works. If it doesn't for you, let me know.
Your offer for help is very kind, but it is my job to ensure that things in ChimeraX work correctly, and though this altloc issue is on the rare side I nonetheless imagine it does not impact just you alone, so the fix will be of benefit to others as well. Do not hesitate to report these kinds of issues, and have a great day!
--Eric
comment:5 by , 10 days ago
Hi Eric,
I downloaded the daily build this morning (10 am BST), but unfortunately, it didn't solve the issue for me, with or without specifying the altlocs (log(s) attached).
Furthermore, I have found several other structures for which minimize fails with the same error:
- 7wgr (log also attached)
- 6sy1
- 2bff
All of them have disulfide bonds, but 7wgr, for example, doesn't have any altlocs.
Any further ideas? I am definitely running the daily (/usr/bin/chimerax-daily), and the release date under Help>About says Jun 3.
I can only offer.
All the best,
Paul
________________________________
Paul J. N. Brodersen, DPhil
Postdoctoral Researcher
Department of Pharmacology
University of Oxford
Tel: +44 (0)1865 281113
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 03 June 2026 17:59
To: Paul Brodersen <paul.brodersen@pharm.ox.ac.uk>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #20435: Minimize 6i4q: KeyError: 'N'
#20435: Minimize 6i4q: KeyError: 'N'
----------------------------------------+----------------------------
Reporter: paul.brodersen@… | Owner: Eric Pettersen
Type: defect | Status: closed
Priority: normal | Milestone:
Component: Structure Editing | Version:
Resolution: fixed | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
----------------------------------------+----------------------------
Comment (by Eric Pettersen):
Hi Paul,
With the fix I made yesterday, if I set all altlocs to A and then
minimize, it works. If it doesn't for you, let me know.
Your offer for help is very kind, but it is my job to ensure that
things in ChimeraX work correctly, and though this altloc issue is on the
rare side I nonetheless imagine it does not impact just you alone, so the
fix will be of benefit to others as well. Do not hesitate to report these
kinds of issues, and have a great day!
--Eric
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/20435#comment:4>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
comment:6 by , 10 days ago
| Resolution: | fixed |
|---|---|
| Status: | closed → reopened |
I see. It seems to be because these structures are coming from pdbe_bio. If I get just the "normal" versions of these files, minimization works for all of them. I'll have to look into what the difference/issue is.
--Eric
comment:7 by , 9 days ago
Great catch.
That works for me as well, and is a more than good enough workaround.
Much obliged,
Paul
________________________________
Paul J. N. Brodersen, DPhil
Postdoctoral Researcher
Department of Pharmacology
University of Oxford
Tel: +44 (0)1865 281113
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 04 June 2026 22:14
To: Paul Brodersen <paul.brodersen@pharm.ox.ac.uk>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #20435: Minimize 6i4q: KeyError: 'N'
#20435: Minimize 6i4q: KeyError: 'N'
----------------------------------------+----------------------------
Reporter: paul.brodersen@… | Owner: Eric Pettersen
Type: defect | Status: reopened
Priority: normal | Milestone:
Component: Structure Editing | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
----------------------------------------+----------------------------
Changes (by Eric Pettersen):
* resolution: fixed =>
* status: closed => reopened
Comment:
I see. It seems to be because these structures are coming from pdbe_bio.
If I get just the "normal" versions of these files, minimization works for
all of them. I'll have to look into what the difference/issue is.
--Eric
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/20435#comment:6>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
comment:8 by , 4 days ago
| Resolution: | → fixed |
|---|---|
| Status: | reopened → closed |
The pdbe_bio files were not supplying the full sequence information, and the minimization code did not correctly handle that case. Now it does (fix in tomorrow's daily build).
Fix: https://github.com/RBVI/ChimeraX/commit/c80862d7b2dbf500dc5a0a475c75845e9da04f4a
Note:
See TracTickets
for help on using tickets.
Hi Paul,
--Eric
Fix: https://github.com/RBVI/ChimeraX/commit/8d8818e6dc2f091ca70dc0ed25cb2ff9fd20fad9