id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3694 Crash adding then deleting residue Tristan Croll Eric Pettersen "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-1127.19.1.el7.x86_64-x86_64-with-centos-7.8.2003-Core ChimeraX Version: 1.1rc202009022202 (2020-09-02 22:02:29 UTC) Description Adding a residue to the N-terminus of a chain and then deleting it causes a segmentation fault in _make_ribbon_graphics() (possibly at other positions in the chain as well - haven't tried). Looks like somehow the deleted residue is still being queried? (command line) open 3fhr sel /A:33 (shell) m = session.models.list()[0] from chimerax.isolde.atomic.building.build_utils import add_amino_acid_residue from chimerax.atomic import selected_residues add_amino_acid_residue(m, 'PRO', next_res=selected_residues(session)[0]) (command line) del /A:32 Current thread 0x00007f55055c9740 (most recent call first): File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/molc.py"", line 195 in get_prop File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/ribbon.py"", line 96 in _make_ribbon_graphics File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/ribbon.py"", line 588 in compute_ribbons File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/structure.py"", line 559 in _create_ribbon_graphics File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/structure.py"", line 302 in update_graphics_if_needed File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/structure.py"", line 1567 in _update_graphics_if_needed File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/triggerset.py"", line 130 in invoke File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/triggerset.py"", line 213 in _activate File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/triggerset.py"", line 182 in activate File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/triggerset.py"", line 350 in activate_trigger File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/graphics/view.py"", line 269 in check_for_drawing_change File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/updateloop.py"", line 65 in draw_new_frame File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/updateloop.py"", line 138 in _redraw_timer_callback File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/ui/gui.py"", line 269 in event_loop File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/ChimeraX_main.py"", line 772 in init File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/ChimeraX_main.py"", line 919 in File ""/opt/UCSF/ChimeraX/lib/python3.7/runpy.py"", line 85 in _run_code File ""/opt/UCSF/ChimeraX/lib/python3.7/runpy.py"", line 193 in _run_module_as_main Program received signal SIGSEGV, Segmentation fault. 0x00007fffb072b55a in residue_secondary_structure_id () from /opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/libmolc.so Missing separate debuginfos, use: debuginfo-install ucsf-chimerax-1.1-0.2020.09.02.el7.x86_64 (gdb) bt #0 0x00007fffb072b55a in residue_secondary_structure_id () at /opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/libmolc.so #1 0x00007fffe760de2c in ffi_call_unix64 () at /lib64/libffi.so.6 #2 0x00007fffe760d755 in ffi_call () at /lib64/libffi.so.6 #3 0x00007fffe78221fa in _ctypes_callproc (argcount=3, resmem=0x7fffffffa6d0, restype=, atypes=, avalues=0x7fffffffa6a0, pProc=0x7fffb072b240 , flags=4357) at ./tmp/Python-3.7.8/Modules/_ctypes/callproc.c:829 #4 0x00007fffe78221fa in _ctypes_callproc (pProc=pProc@entry=0x7fffb072b240 , argtuple=argtuple@entry=0x7ffe9110cb40, Log: UCSF ChimeraX version: 1.1rc202009022202 (2020-09-02) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 3.3.0 NVIDIA 450.51.06 OpenGL renderer: TITAN Xp/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Dell Inc. Model: Precision T5600 OS: CentOS Linux 7 Core Architecture: 64bit ELF CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz Cache Size: 20480 KB Memory: total used free shared buff/cache available Mem: 62G 4.9G 48G 255M 9.7G 57G Swap: 4.9G 0B 4.9G Graphics: 03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1) Subsystem: NVIDIA Corporation Device [10de:11df] Kernel driver in use: nvidia 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: 2.1.1 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: 1.1rc202009022202 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: 1.0 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.0 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0 ChimeraX-ISOLDE: 1.0.2 ChimeraX-Label: 1.0 ChimeraX-LinuxSupport: 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-Phenix: 0.1 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 distro: 1.5.0 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 graphviz: 0.14.1 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 numpydoc: 1.0.0 objgraph: 3.4.1 openvr: 1.12.501 packaging: 20.4 parso: 0.7.1 pexpect: 4.8.0 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 ptyprocess: 0.6.0 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 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: 5.0.2 urllib3: 1.25.10 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.34.2 }}} " defect closed normal Core fixed Tom Goddard all ChimeraX