Update coordinates: OpenMM: RuntimeError: Release Object

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-5.4.0-90-generic-x86_64-with-glibc2.14
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /data/Cryosparc/D2A2+CitronylcoA_16721/J373/cryosparc_P59_J373_009_volume_map.mrc

Opened cryosparc_P59_J373_009_volume_map.mrc as #1, grid size 480,480,480,
pixel 0.87, shown at level 0.0828, step 2, values float32  

> open /data/Cryosparc/D2A2+CitronylcoA_16721/J373/J373-coot-1.pdb

Chain information for J373-coot-1.pdb #2  
---  
Chain | Description  
1 3 A C | No description available  
2 4 6 B F | No description available  
5 E | No description available  
7 9 | No description available  
D | No description available  
  

> volume #1 step 1

> volume #1 level 0.1124

> ui tool show ISOLDE

> set selectionWidth 4

Chain information for J373-coot-1.pdb  
---  
Chain | Description  
2.2/1 2.2/3 2.2/A 2.2/C | No description available  
2.2/2 2.2/4 2.2/6 2.2/B 2.2/F | No description available  
2.2/5 2.2/E | No description available  
2.2/7 2.2/9 | No description available  
2.2/D | No description available  
  
Done loading forcefield  

> addh hbond

Missing "hbond" keyword's argument  

> addh

Summary of feedback from adding hydrogens to J373-coot-1.pdb #2.2  
---  
notes | No usable SEQRES records for J373-coot-1.pdb (#2.2) chain 1; guessing
termini instead  
No usable SEQRES records for J373-coot-1.pdb (#2.2) chain 2; guessing termini
instead  
No usable SEQRES records for J373-coot-1.pdb (#2.2) chain 3; guessing termini
instead  
No usable SEQRES records for J373-coot-1.pdb (#2.2) chain 4; guessing termini
instead  
No usable SEQRES records for J373-coot-1.pdb (#2.2) chain 5; guessing termini
instead  
9 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /1 GLY 2, /2 MET 0, /3 GLY
2, /4 MET 0, /5 GLY 2, /6 MET 0, /7 PRO 580, /9 PRO 580, /A GLY 2, /B MET 0,
/C GLY 2, /D MET 0, /E GLY 2, /F MET 0  
Chain-initial residues that are not actual N termini: /5 MET 157, /E MET 157  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /1 GLU 579, /2 MET 529, /3
GLU 579, /4 MET 529, /5 GLU 579, /5 ALA 150, /6 MET 529, /7 VAL 584, /9 VAL
584, /A GLU 579, /B MET 529, /C GLU 579, /D MET 529, /E GLU 579, /E ALA 150,
/F MET 529  
4235 hydrogen bonds  
Adding 'H' to /5 MET 157  
Adding 'H' to /E MET 157  
/1 GLU 579 is not terminus, removing H atom from 'C'  
/2 MET 529 is not terminus, removing H atom from 'C'  
/3 GLU 579 is not terminus, removing H atom from 'C'  
/4 MET 529 is not terminus, removing H atom from 'C'  
/5 GLU 579 is not terminus, removing H atom from 'C'  
9 messages similar to the above omitted  
49384 hydrogens added  
  
Opened cryosparc_P59_J373_009_volume_map.mrc as #2.1.1.1, grid size
480,480,480, pixel 0.87, shown at step 1, values float32  

> volume #2.1.1.1 level 0.2068

ISOLDE: started sim  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/edu/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/delayed_reaction.py", line 81, in callback  
self.ff(*self.ff_args)  
File "/home/edu/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1673, in
_update_coordinates_and_repeat  
self.atoms.coords = th.coords  
File "/home/edu/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 305, in coords  
f(self._c_pointer, n, pointer(coords))  
RuntimeError: Release Object  
  
Error processing trigger "new frame":  
RuntimeError: Release Object  
  
File "/home/edu/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 305, in coords  
f(self._c_pointer, n, pointer(coords))  
  
See log for complete Python traceback.  
  
ISOLDE: resumed sim  
Traceback (most recent call last):  
File "/home/edu/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2728, in _start_sim_or_toggle_pause  
self.pause_sim_toggle()  
File "/home/edu/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2991, in pause_sim_toggle  
self.sim_manager.toggle_pause()  
File "/home/edu/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 720, in
toggle_pause  
self.pause = not self.pause  
File "/home/edu/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 699, in pause  
self.sim_handler.pause = flag  
File "/home/edu/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1772, in pause  
self._resume()  
File "/home/edu/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1663, in _resume  
self._repeat_step()  
File "/home/edu/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1653, in
_repeat_step  
self._delayed_reaction_handler = delayed_reaction(self.session.triggers, 'new
frame', f, f_args,  
File "/home/edu/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/delayed_reaction.py", line 71, in delayed_reaction  
initiator_func(*initiator_args)  
File "/home/edu/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 165, in step  
f(self._c_pointer, steps, self._smoothing)  
RuntimeError: Release Object  
  
RuntimeError: Release Object  
  
File "/home/edu/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 165, in step  
f(self._c_pointer, steps, self._smoothing)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 470.82.00
OpenGL renderer: Quadro P1000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision 5530
OS: Ubuntu 18.04 bionic
Architecture: 64bit ELF
Virutal Machine: none
CPU: 12 Intel(R) Core(TM) i7-8850H CPU @ 2.60GHz
Cache Size: 9216 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            30G        3.9G         22G        431M        4.4G         26G
	Swap:          975M          0B        975M

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation Device [8086:3e9b]	
	Subsystem: Dell Device [1028:087d]	
	Kernel driver in use: i915
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-Clipper: 0.16.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.2.2
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
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    Sphinx: 3.2.1
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    sphinxcontrib-blockdiag: 2.0.0
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    tables: 3.6.1
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    tinyarray: 1.2.3
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    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.2.0

[Tristan Croll]

Huh. That’s a new one.