id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6240 OpenMM runtime error: Release Object chimerax-bug-report@… Tristan Croll "The following bug report has been submitted: Platform: Linux-5.11.0-46-generic-x86_64-with-glibc2.31 ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX open /home/cryosparc2/Documents/Rana/Lemon_del_H_38_coot_10.pdb format pdb Chain information for Lemon_del_H_38_coot_10.pdb #1 --- Chain | Description A | No description available B | No description available C E | No description available D | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available a | No description available b | No description available c | No description available d | No description available e | No description available g l | No description available h j k m n | No description available i | No description available o | No description available r | No description available open /home/cryosparc2/Documents/Rana/State2ConsensusTrimmed.mrc Opened State2ConsensusTrimmed.mrc as #2, grid size 140,140,200, pixel 1.62,1.62,1.62, shown at level 1.36, step 1, values float32 style stick Changed 46163 atom styles set bgColor white select clear [Repeated 1 time(s)] select /O:255@CA 1 atom, 1 residue, 1 model selected select up 5 atoms, 4 bonds, 1 residue, 1 model selected select up 115 atoms, 114 bonds, 23 residues, 1 model selected select up 1571 atoms, 1578 bonds, 311 residues, 1 model selected isolde start sel Expected fewer arguments isolde start sel Expected fewer arguments isolde sim start sel set selectionWidth 4 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 146 residues in model #1 to IUPAC-IUB standards. Chain information for Lemon_del_H_38_coot_10.pdb --- Chain | Description 1.2/A | No description available 1.2/B | No description available 1.2/C 1.2/E | No description available 1.2/D | No description available 1.2/F | No description available 1.2/G | No description available 1.2/H | No description available 1.2/I | No description available 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 1.2/O | No description available 1.2/P | No description available 1.2/a | No description available 1.2/b | No description available 1.2/c | No description available 1.2/d | No description available 1.2/e | No description available 1.2/g 1.2/l | No description available 1.2/h 1.2/j 1.2/k 1.2/m 1.2/n | No description available 1.2/i | No description available 1.2/o | No description available 1.2/r | No description available ISOLDE: stopped sim Done loading forcefield addh Summary of feedback from adding hydrogens to Lemon_del_H_38_coot_10.pdb #1.2 --- warnings | Not adding hydrogens to /M ARG 28 CB because it is missing heavy- atom bond partners Not adding hydrogens to /M LYS 34 CB because it is missing heavy-atom bond partners Not adding hydrogens to /M LYS 35 CB because it is missing heavy-atom bond partners Not adding hydrogens to /M ASP 38 CB because it is missing heavy-atom bond partners Not adding hydrogens to /M GLN 43 CB because it is missing heavy-atom bond partners 3518 messages similar to the above omitted notes | No usable SEQRES records for Lemon_del_H_38_coot_10.pdb (#1.2) chain A; guessing termini instead No usable SEQRES records for Lemon_del_H_38_coot_10.pdb (#1.2) chain B; guessing termini instead No usable SEQRES records for Lemon_del_H_38_coot_10.pdb (#1.2) chain C; guessing termini instead No usable SEQRES records for Lemon_del_H_38_coot_10.pdb (#1.2) chain D; guessing termini instead No usable SEQRES records for Lemon_del_H_38_coot_10.pdb (#1.2) chain E; guessing termini instead 26 messages similar to the above omitted Chain-initial residues that are actual N termini: /A TYR 21, /B LEU 15, /C TYR 21, /D GLU 12, /E TYR 21, /F GLU 12, /G GLN 12, /H LEU 14, /I MET 13, /J LEU 14, /K ASN 2, /L GLY 9, /M VAL 9, /N SER 12, /O ALA 2, /P ASP 2, /a PRO 23, /b GLU 273, /c SER 11, /d ALA 6, /e ASN 32, /g GLU 8, /h GLU 8, /i GLU 8, /j GLU 8, /k GLU 8, /l GLU 8, /m GLU 8, /n GLU 8, /o ALA 9, /r VAL 332 Chain-initial residues that are not actual N termini: /A ILE 569, /B ASP 203, /D ASP 199, /F GLY 200, /G HIS 178, /I LEU 172, /K PRO 176, /O LEU 181, /O THR 204, /O LEU 223, /P LEU 32, /P LYS 90, /P ILE 158, /a ASP 107, /a LYS 193, /a HIS 710, /d THR 69, /d PRO 92, /d ARG 120, /d MET 147, /d LEU 247, /d GLY 284, /e PRO 60 Chain-final residues that are actual C termini: /E ARG 623 Chain-final residues that are not actual C termini: /A GLU 619, /A VAL 558, /B ARG 484, /B LYS 192, /C ARG 623, /D ARG 484, /D LYS 192, /F ARG 484, /F ARG 189, /G SER 226, /G VAL 166, /H ASN 110, /I SER 226, /I ILE 164, /J LYS 109, /K SER 226, /K ASP 167, /L LYS 109, /M SER 221, /N ASN 118, /O GLY 339, /O LYS 171, /O PRO 189, /O ASP 218, /P ILE 327, /P PRO 17, /P MET 84, /P ARG 135, /a ASP 819, /a SER 93, /a GLN 161, /a HIS 669, /b GLY 304, /c PRO 178, /d CYS 334, /d LEU 28, /d LEU 86, /d GLY 115, /d ILE 138, /d SER 242, /d SER 282, /e GLU 68, /e ALA 56, /g GLN 160, /h ARG 162, /i ALA 163, /j ARG 162, /k ARG 162, /l GLN 160, /m ARG 162, /n ARG 162, /o ALA 160, /r ILE 355 5473 hydrogen bonds Adding 'H' to /A ILE 569 Adding 'H' to /B ASP 203 Adding 'H' to /D ASP 199 Adding 'H' to /F GLY 200 Adding 'H' to /G HIS 178 15 messages similar to the above omitted /A GLU 619 is not terminus, removing H atom from 'C' /B ARG 484 is not terminus, removing H atom from 'C' /C ARG 623 is not terminus, removing H atom from 'C' /D ARG 484 is not terminus, removing H atom from 'C' /F ARG 484 is not terminus, removing H atom from 'C' 25 messages similar to the above omitted 36388 hydrogens added ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim Opened State2ConsensusTrimmed.mrc as #1.1.1.1, grid size 140,140,200, pixel 1.62,1.62,1.62, shown at step 1, values float32 ISOLDE: started sim Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/core/triggerset.py"", line 134, in invoke return self._func(self._name, data) File ""/home/cryosparc2/.local/share/ChimeraX/1.3/site- packages/chimerax/isolde/delayed_reaction.py"", line 81, in callback self.ff(*self.ff_args) File ""/home/cryosparc2/.local/share/ChimeraX/1.3/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1687, in _update_coordinates_and_repeat self.atoms.coords = th.coords File ""/home/cryosparc2/.local/share/ChimeraX/1.3/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/cryosparc2/.local/share/ChimeraX/1.3/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: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim ISOLDE: started sim Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/core/triggerset.py"", line 134, in invoke return self._func(self._name, data) File ""/home/cryosparc2/.local/share/ChimeraX/1.3/site- packages/chimerax/isolde/delayed_reaction.py"", line 81, in callback self.ff(*self.ff_args) File ""/home/cryosparc2/.local/share/ChimeraX/1.3/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1687, in _update_coordinates_and_repeat self.atoms.coords = th.coords File ""/home/cryosparc2/.local/share/ChimeraX/1.3/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/cryosparc2/.local/share/ChimeraX/1.3/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 470.86 OpenGL renderer: NVIDIA GeForce GTX 750 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: ASUS Model: All Series OS: Ubuntu 20.04 focal Architecture: 64bit ELF Virutal Machine: none CPU: 12 Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz Cache Size: 15360 KB Memory: total used free shared buff/cache available Mem: 31Gi 4.2Gi 19Gi 37Mi 7.4Gi 26Gi Swap: 2.0Gi 0B 2.0Gi Graphics: 03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GM107 [GeForce GTX 750 Ti] [10de:1380] (rev a2) Subsystem: eVga.com. Corp. GM107 [GeForce GTX 750 Ti] [3842:3751] Kernel driver in use: nvidia Locale: ('en_CA', '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: 2021.10.8 cftime: 1.5.1.1 charset-normalizer: 2.0.9 ChimeraX-AddCharge: 1.2.2 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.31 ChimeraX-AtomicLibrary: 4.2 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.2 ChimeraX-Clipper: 0.17.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 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: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.3 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1 ChimeraX-LinuxSupport: 1.0 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.4 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2.6 ChimeraX-ModelPanel: 1.2.1 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: 2.0.2 ChimeraX-OpenCommand: 1.7 ChimeraX-PDB: 2.6.5 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.6.1 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: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.13.7 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 ChimeraX-VIPERdb: 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: 0.4.4 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.24 decorator: 5.1.0 distro: 1.6.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.3.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.9.1 kiwisolver: 1.3.2 line-profiler: 3.3.0 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.8.0 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.3 ParmEd: 3.2.0 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.23 psutil: 5.8.0 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.6 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.3 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0" defect assigned moderate Third Party Tom Goddard all ChimeraX