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Opened 15 hours ago
#19226 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: Linux-6.8.0-85-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /home/kimlab/Documents/124_PARP2mut_HPF1_EB47/EB47_final/124_P2mut_HPF1_EB47_Class_5a_isolde_v2_coot_v1_real_space_refined_009_B.pdb
Chain information for
124_P2mut_HPF1_EB47_Class_5a_isolde_v2_coot_v1_real_space_refined_009_B.pdb #1
---
Chain | Description
A B | No description available
C D | No description available
E F | No description available
G H | No description available
I J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
> open
> /home/kimlab/Documents/124_PARP2mut_HPF1_EB47/EB47_final/124_P2mut_HPF1_EB47_Class_5a_J151_flipped.mrc
Opened 124_P2mut_HPF1_EB47_Class_5a_J151_flipped.mrc as #2, grid size
400,400,400, pixel 0.828, shown at level 0.0367, step 2, values float32
> clipper associate #2 toModel #1
Opened 124_P2mut_HPF1_EB47_Class_5a_J151_flipped.mrc as #1.1.1.1, grid size
400,400,400, pixel 0.828, shown at level 0.238, step 1, values float32
Chain information for
124_P2mut_HPF1_EB47_Class_5a_isolde_v2_coot_v1_real_space_refined_009_B.pdb
---
Chain | Description
1.2/A 1.2/B | No description available
1.2/C 1.2/D | No description available
1.2/E 1.2/F | No description available
1.2/G 1.2/H | No description available
1.2/I 1.2/J | No description available
1.2/K | No description available
1.2/L | No description available
1.2/M | No description available
1.2/N | No description available
> set bgColor white
> addh
Summary of feedback from adding hydrogens to
124_P2mut_HPF1_EB47_Class_5a_isolde_v2_coot_v1_real_space_refined_009_B.pdb
#1.2
---
warnings | Not adding hydrogens to /K ARG 191 CB because it is missing heavy-atom bond partners
Not adding hydrogens to /L DA 6 P because it is missing heavy-atom bond
partners
Not adding hydrogens to /M DT 2 P because it is missing heavy-atom bond
partners
Not adding hydrogens to /N DG 1 P because it is missing heavy-atom bond
partners
notes | No usable SEQRES records for 124_P2mut_HPF1_EB47_Class_5a_isolde_v2_coot_v1_real_space_refined_009_B.pdb (#1.2) chain A; guessing termini instead
No usable SEQRES records for
124_P2mut_HPF1_EB47_Class_5a_isolde_v2_coot_v1_real_space_refined_009_B.pdb
(#1.2) chain B; guessing termini instead
No usable SEQRES records for
124_P2mut_HPF1_EB47_Class_5a_isolde_v2_coot_v1_real_space_refined_009_B.pdb
(#1.2) chain C; guessing termini instead
No usable SEQRES records for
124_P2mut_HPF1_EB47_Class_5a_isolde_v2_coot_v1_real_space_refined_009_B.pdb
(#1.2) chain D; guessing termini instead
No usable SEQRES records for
124_P2mut_HPF1_EB47_Class_5a_isolde_v2_coot_v1_real_space_refined_009_B.pdb
(#1.2) chain E; guessing termini instead
9 messages similar to the above omitted
Chain-initial residues that are actual N termini: /A LYS 13, /B LYS 13, /C LYS
27, /D LYS 27, /E LYS 38, /F LYS 38, /G LYS 21, /H LYS 21, /K LYS 91
Chain-initial residues that are not actual N termini: /I ALA 18, /I GLU 150,
/J ALA 18, /J GLU 150
Chain-final residues that are actual C termini: /A LYS 119, /B LYS 119, /C LYS
123, /D LYS 123, /E ARG 135, /F ARG 135, /G GLY 103, /H GLY 103, /I SER 269,
/J SER 269, /K TYR 208
Chain-final residues that are not actual C termini: /I ARG 127, /J ARG 127
1618 hydrogen bonds
1 hydrogens added
> isolde start
> set selectionWidth 4
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 152 residues in model #1.2 to IUPAC-IUB
standards.
Done loading forcefield
> isolde set simFidelityMode Highest/Slowest
ISOLDE: setting sim fidelity mode to Highest/Slowest
nonbonded_cutoff_distance = 1.700000
use_gbsa = True
gbsa_cutoff = 2.000000
> select /L:84-95
384 atoms, 413 bonds, 12 residues, 1 model selected
> isolde sim start /L:84-95
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /L:81-96
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select /L:14-25
383 atoms, 412 bonds, 12 residues, 1 model selected
> isolde sim start /L:14-25
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save
> /home/kimlab/Documents/124_PARP2mut_HPF1_EB47/EB47_final/124_P2mut_HPF1_EB47_Class_5a_isolde_v3_coot_v1_real_space_refined_009_B.pdb
> isolde sim start /L:11-26
ISOLDE: started sim
> volume #1.1.1.1 level 0.1361
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save
> /home/kimlab/Documents/124_PARP2mut_HPF1_EB47/EB47_final/124_P2mut_HPF1_EB47_Class_5a_isolde_v3_coot_v1_real_space_refined_009_B.pdb
> isolde sim start /L:8-29
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde restrain basepairs sel
> hbonds
1620 hydrogen bonds found
> isolde sim start /L:6-32
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Build Structure"
> select clear
[Repeated 1 time(s)]
> ~bond sel
[Repeated 2 time(s)]
> isolde sim start /L:6/N:18
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /L:6-9/N:15-18
ISOLDE: started sim
> ~bond sel
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/kimlab/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 770, in _sim_end_cb
self._starting_checkpoint.revert()
File "/home/kimlab/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/checkpoint.py", line 64, in revert
rm.restore_checkpoint(data)
File "/home/kimlab/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/molobject.py", line 3634, in restore_checkpoint
_RestraintMgr.restore_checkpoint(self, data)
File "/home/kimlab/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/molobject.py", line 1940, in restore_checkpoint
setattr(restraints, key, vals)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 226, in set_prop
raise ValueError('Values array length %d does not match objects array length
%d'
ValueError: Values array length 48 does not match objects array length 6
Error processing trigger "sim terminated":
ValueError: Values array length 48 does not match objects array length 6
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 226, in set_prop
raise ValueError('Values array length %d does not match objects array length
%d'
See log for complete Python traceback.
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
OpenGL version: 3.3.0 NVIDIA 550.163.01
OpenGL renderer: NVIDIA GeForce RTX 4070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Dell Inc.
Model: XPS 8960
OS: Ubuntu 22.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 32 13th Gen Intel(R) Core(TM) i9-13900
Cache Size: 36864 KB
Memory:
total used free shared buff/cache available
Mem: 29Gi 11Gi 10Gi 1.1Gi 6.9Gi 15Gi
Swap: 2.0Gi 769Mi 1.2Gi
Graphics:
0000:00:02.0 VGA compatible controller [0300]: Intel Corporation Device [8086:a780] (rev 04)
DeviceName: Onboard - Video
Subsystem: Dell Device [1028:0bc0]
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.6.1
build: 1.2.2.post1
certifi: 2025.7.14
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.19
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: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-Clipper: 0.25.1
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.1
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: 1.1.4
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: 2.5.1
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-ISOLDE: 1.10.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-LinuxSupport: 1.0.1
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
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
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: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
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: 1.1.3
ChimeraX-ProfileGrids: 1.1.3
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
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: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
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-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
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: 2.5.2
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: 1.45.2
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: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.10.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.15
decorator: 5.2.1
distro: 1.9.0
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.59.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.3.2
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
nvidia-nvjitlink-cu12: 12.9.86
OpenMM: 8.2.0
OpenMM-CUDA-12: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
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: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.1
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
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