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#5902 closed defect (can't reproduce)

OpenMM: RuntimeError: Release Object

Reported by:	chimerax-bug-report@…	Owned by:	Tristan Croll
Priority:	normal	Milestone:
Component:	Third Party	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open "C:\Users\Andrew\Desktop\9H2 Project\VP1greydoneIsolde.cxs" format
> session

restore_snapshot for "RotamerRestraintMgr" returned None  

Log from Mon Jan 10 16:08:33 2022UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Users/Andrew/Desktop/9H2 Project/9H2-Purdue_PV1_cent.mrc"

Opened 9H2-Purdue_PV1_cent.mrc, grid size 2,2,2, pixel 1, shown at level
0.0002, step 1, values float32  

> show target m

> volume #1 level -0.08239

> open "C:/Users/Andrew/Desktop/9H2 Project/9H2-Purdue_PV2_cent.mrc"

Opened 9H2-Purdue_PV2_cent.mrc, grid size 560,560,560, pixel 1.1, shown at
level 1.35, step 4, values float32  

> volume #2 step 1

> close #1

> close #2

> open "C:/Users/Andrew/Desktop/9H2 Project/9H2-SIPV3_cent.mrc"
> "C:/Users/Andrew/Desktop/9H2 Project/SPV3.pdb"

Summary of feedback from opening C:/Users/Andrew/Desktop/9H2 Project/SPV3.pdb  
---  
warning | Ignored bad PDB record found on line 8109  
END  
  
SPV3.pdb title:  
Refinement of the sabin strain of type 3 poliovirus At 2.4 angstroms and the
crystal structures of its variants At 2.9 angstroms resolution [more info...]  
  
Chain information for SPV3.pdb #2  
---  
Chain | Description  
0 | poliovirus type 3, sabin strain  
1 | poliovirus type 3, sabin strain  
2 | poliovirus type 3, sabin strain  
3 | poliovirus type 3, sabin strain  
4 | poliovirus type 3, sabin strain  
  
Non-standard residues in SPV3.pdb #2  
---  
MYR — myristic acid  
SPH — sphingosine  
  
Opened 9H2-SIPV3_cent.mrc, grid size 560,560,560, pixel 1.14, shown at level
1.29, step 4, values float32  

> volume #1 step 1

Drag select of 7075 atoms, 2 pseudobonds, 64 bonds  

> style sel ball

Changed 7075 atom styles  

> style sel stick

Changed 7075 atom styles  

> show sel cartoons

> hide sel cartoons

> toolshed show

> ui tool show ISOLDE

> set selectionWidth 4

SPV3.pdb title:  
Refinement of the sabin strain of type 3 poliovirus At 2.4 angstroms and the
crystal structures of its variants At 2.9 angstroms resolution [more info...]  
  
Chain information for SPV3.pdb  
---  
Chain | Description  
2.2/0 | poliovirus type 3, sabin strain  
2.2/1 | poliovirus type 3, sabin strain  
2.2/2 | poliovirus type 3, sabin strain  
2.2/3 | poliovirus type 3, sabin strain  
2.2/4 | poliovirus type 3, sabin strain  
  
Non-standard residues in SPV3.pdb #2.2  
---  
MYR — myristic acid  
SPH — sphingosine  
  
Done loading forcefield  

> select up

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select up

27 atoms, 26 bonds, 3 residues, 1 model selected  

> select up

1931 atoms, 1857 bonds, 354 residues, 1 model selected  

> select up

7075 atoms, 6824 bonds, 1271 residues, 1 model selected  
Loading residue template for MYR from internal database  
Loading residue template for SPH from internal database  

> addh

Summary of feedback from adding hydrogens to SPV3.pdb #2.2  
---  
notes | Termini for SPV3.pdb (#2.2) chain 0 determined from SEQRES records  
Termini for SPV3.pdb (#2.2) chain 1 determined from SEQRES records  
Termini for SPV3.pdb (#2.2) chain 2 determined from SEQRES records  
Termini for SPV3.pdb (#2.2) chain 3 determined from SEQRES records  
Termini for SPV3.pdb (#2.2) chain 4 determined from SEQRES records  
Chain-initial residues that are actual N termini: /0 ILE 7, /3 GLY 1, /4 GLY 2  
Chain-initial residues that are not actual N termini: /1 GLN 24, /2 ALA 6, /4
SER 23  
Chain-final residues that are actual C termini: /0 VAL 10, /1 TYR 302, /2 GLN
271, /4 ASN 69  
Chain-final residues that are not actual C termini: /3 ALA 235, /4 SER 16  
Missing OXT added to C-terminal residue /0 VAL 10  
1991 hydrogen bonds  
Adding 'H' to /1 GLN 24  
Adding 'H' to /2 ALA 6  
Adding 'H' to /4 SER 23  
/3 ALA 235 is not terminus, removing H atom from 'C'  
7354 hydrogens added  
  

> addh

Summary of feedback from adding hydrogens to SPV3.pdb #2.2  
---  
notes | Termini for SPV3.pdb (#2.2) chain 0 determined from SEQRES records  
Termini for SPV3.pdb (#2.2) chain 1 determined from SEQRES records  
Termini for SPV3.pdb (#2.2) chain 2 determined from SEQRES records  
Termini for SPV3.pdb (#2.2) chain 3 determined from SEQRES records  
Termini for SPV3.pdb (#2.2) chain 4 determined from SEQRES records  
Chain-initial residues that are actual N termini: /0 ILE 7, /3 GLY 1, /4 GLY 2  
Chain-initial residues that are not actual N termini: /1 GLN 24, /2 ALA 6, /4
SER 23  
Chain-final residues that are actual C termini: /0 VAL 10, /1 TYR 302, /2 GLN
271, /4 ASN 69  
Chain-final residues that are not actual C termini: /3 ALA 235, /4 SER 16  
1390 hydrogen bonds  
/3 ALA 235 is not terminus, removing H atom from 'C'  
0 hydrogens added  
  

> hide HC

Fetching CCD MYR from http://ligand-expo.rcsb.org/reports/M/MYR/MYR.cif  
Fetching CCD GLY_LL from http://ligand-
expo.rcsb.org/reports/G/GLY_LL/GLY_LL.cif  
Fetching CCD GLY_LFZW from http://ligand-
expo.rcsb.org/reports/G/GLY_LFZW/GLY_LFZW.cif  
Deleted the following atoms from residue GLY 42: H2, H3  

> select clear

reverting to start  

> select up

91 atoms, 90 bonds, 6 residues, 1 model selected  

> select up

3962 atoms, 3888 bonds, 354 residues, 1 model selected  

> select up

14430 atoms, 14179 bonds, 1271 residues, 1 model selected  

> select up

14430 atoms, 14179 bonds, 1271 residues, 3 models selected  

> select clear

> volume #2.1.1.1 level 0.6268

> volume #2.1.1.1 level 2.435

> volume #2.1.1.1 level 1.879

> select up

12 atoms, 11 bonds, 1 residue, 1 model selected  

> select up

83 atoms, 83 bonds, 5 residues, 1 model selected  

> select up

4854 atoms, 4774 bonds, 423 residues, 1 model selected  

> select up

14430 atoms, 14179 bonds, 1271 residues, 1 model selected  

> select up

14430 atoms, 14179 bonds, 1271 residues, 3 models selected  

> select up

14430 atoms, 14179 bonds, 1271 residues, 4 models selected  

> select up

14430 atoms, 14179 bonds, 1271 residues, 4 models selected  

> select up

14430 atoms, 14179 bonds, 1271 residues, 4 models selected  

> h2o

Unknown command: rm h2o  

> $ delete solvent

Unknown command: $ delete solvent  

> delete solvent

> delete solvent

> select clear

No rotamer preview selected! Ignoring command.  

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> save "C:/Users/Andrew/Desktop/9H2 Project/VP1greydoneIsolde.cxs"

Taking snapshot of stepper: SPV3.pdb  
Restoring stepper: SPV3.pdb  
opened ChimeraX session  

> ui tool show ISOLDE

> set selectionWidth 4

Done loading forcefield  

> select up

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select up

161 atoms, 164 bonds, 10 residues, 1 model selected  

> select up

4097 atoms, 4155 bonds, 266 residues, 1 model selected  

> select up

13161 atoms, 13333 bonds, 848 residues, 1 model selected  

> select up

13161 atoms, 13333 bonds, 848 residues, 3 models selected  

> select up

13161 atoms, 13333 bonds, 848 residues, 4 models selected  

> select up

13161 atoms, 13333 bonds, 848 residues, 4 models selected  

> select clear

> select up

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select up

171 atoms, 172 bonds, 10 residues, 1 model selected  

> select up

4097 atoms, 4155 bonds, 266 residues, 1 model selected  

> select up

13161 atoms, 13333 bonds, 848 residues, 1 model selected  

> select down

4097 atoms, 4155 bonds, 266 residues, 1 model selected  
Loading residue template for SPH from internal database  

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> save "C:/Users/Andrew/Desktop/9H2 Project/VP1VP2doneIsoldeSIPV3.cxs"

Taking snapshot of stepper: SPV3.pdb  

> select clear

> select clear

> select up

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select up

74 atoms, 73 bonds, 5 residues, 1 model selected  

> select up

3605 atoms, 3650 bonds, 235 residues, 1 model selected  

> select up

13161 atoms, 13333 bonds, 848 residues, 1 model selected  

> select down

3605 atoms, 3650 bonds, 235 residues, 1 model selected  
Loading residue template for MYR from internal database  

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> save "C:/Users/Andrew/Desktop/9H2 Project/VP1VP2VP3doneIsoldeSIPV3.cxs"

Taking snapshot of stepper: SPV3.pdb  

> select clear

> select clear

> select up

1075 atoms, 1092 bonds, 65 residues, 1 model selected  

> select up

5067 atoms, 5132 bonds, 329 residues, 1 model selected  

> select down

1075 atoms, 1092 bonds, 65 residues, 1 model selected  

> select down

287 atoms, 17 residues, 1 model selected  

> select down

287 atoms, 17 residues, 1 model selected  

> select clear

> select up

96 atoms, 97 bonds, 6 residues, 1 model selected  

> select up

970 atoms, 977 bonds, 63 residues, 1 model selected  

> select up

13161 atoms, 13333 bonds, 848 residues, 1 model selected  

> select down

970 atoms, 977 bonds, 63 residues, 1 model selected  

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> save "C:/Users/Andrew/Desktop/9H2 Project/VP1VP2VP3VP4doneIsoldeSIPV3.cxs"

Taking snapshot of stepper: SPV3.pdb  

> select clear

> select up

43 atoms, 42 bonds, 3 residues, 1 model selected  

> select up

64 atoms, 63 bonds, 4 residues, 1 model selected  

> select up

13161 atoms, 13333 bonds, 848 residues, 1 model selected  

> select down

64 atoms, 63 bonds, 4 residues, 1 model selected  

> select up

128 atoms, 128 bonds, 8 residues, 1 model selected  

> select up

4425 atoms, 4488 bonds, 280 residues, 1 model selected  

> select up

13161 atoms, 13333 bonds, 848 residues, 1 model selected  

> select up

13161 atoms, 13333 bonds, 848 residues, 3 models selected  

> select up

13161 atoms, 13333 bonds, 848 residues, 4 models selected  

> select clear

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Users\Andrew\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\delayed_reaction.py", line 80, in callback  
self.ff(*self.ff_args)  
File "C:\Users\Andrew\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1673, in
_update_coordinates_and_repeat  
self.atoms.coords = th.coords  
File "C:\Users\Andrew\AppData\Local\UCSF\ChimeraX\1.1\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 "C:\Users\Andrew\AppData\Local\UCSF\ChimeraX\1.1\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.  
  




OpenGL version: 3.3.0 NVIDIA 456.71
OpenGL renderer: GeForce GTX 1060 3GB/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: To be filled by O.E.M.
Model: To be filled by O.E.M.
OS: Microsoft Windows 10 Pro (Build 19043)
Memory: 8,247,136,256
MaxProcessMemory: 137,438,953,344
CPU: 8 AMD FX(tm)-8320 Eight-Core Processor           "
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-Clipper: 0.15.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    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: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-ISOLDE: 1.1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    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: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    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
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    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: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    gdcm: 2.8.8
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5+mkl
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pywin32: 228
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Component:	Unassigned → Third Party
Owner:	set to Tristan Croll
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → OpenMM: RuntimeError: Release Object

Maybe the user needs a newer version...

comment:2 by Tristan Croll, 4 years ago

Resolution:	→ can't reproduce
Status:	assigned → closed

Yeah... chances are this is already fixed, but if not will have to wait until it crops up in a more modern version.

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