id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7750 Tug: All atoms within a residue must be contiguous eackad@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Linux-5.15.0-48-generic-x86_64-with-glibc2.35 ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC) Description I wanted to move a water mol out of the way since it was inside a ligand so I tried the tug mode. Log: UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /home/eddie/shareddata/namdoutput/p450/p450_pgm_allo_C1/p450_pgm_allo_level2_chimera_hy36.pdb > format pdb Chain information for p450_pgm_allo_level2_chimera_hy36.pdb #1 --- Chain | Description P | No description available > select all 146509 atoms, 113354 bonds, 33755 residues, 1 model selected > hide sel atoms > select :TRA 39 atoms, 42 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 39 atom styles > show sel atoms > select zone :TRA 5 Selected 236 atoms > select zone :TRA 4 Selected 144 atoms > show sel atoms > style sel stick Changed 144 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > nucleotides sel fill > style nucleic & sel stick Changed 0 atom styles > nucleotides sel tube/slab shape box > nucleotides sel ladder > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > style sel stick Changed 144 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > style sel stick Changed 144 atom styles > style sel ball Changed 144 atom styles > style sel stick Changed 144 atom styles > select zone /O:53,142 4 Selected 28 atoms > show sel atoms [Repeated 1 time(s)] > select zone /O:53,142 4 Selected 28 atoms > show sel atoms > select zone /O:53 4 Selected 28 atoms > show sel atoms > style sel stick Changed 28 atom styles > select /O:53 1 atom, 1 residue, 1 model selected > show sel atoms > select all 146509 atoms, 113354 bonds, 33755 residues, 1 model selected > hide sel atoms > select :TRA 39 atoms, 42 bonds, 1 residue, 1 model selected > show sel atoms > select zone :TRA 4 Selected 144 atoms > show sel atoms > select zone /CO:53,142 4 Selected 483 atoms > select /CO:53,142 4 Expected a keyword > select /CO:53,142 268 atoms, 266 bonds, 2 residues, 1 model selected > show sel atoms > close session > open > /home/eddie/shareddata/namdoutput/p450/p450_pgm_allo_C1/p450_pgm_allo_level3_hy36.pdb Chain information for p450_pgm_allo_level3_hy36.pdb #1 --- Chain | Description P | No description available > select all 146510 atoms, 113360 bonds, 33754 residues, 1 model selected > hide sel atoms > select :TRA 39 atoms, 42 bonds, 1 residue, 1 model selected > select add zone :TRA 4 ; show sel atoms ; Expected an objects specifier or a keyword > hide sel atoms > select :TRA 39 atoms, 42 bonds, 1 residue, 1 model selected > show sel atoms > select zone :TRA 4 Selected 178 atoms > show sel atoms > select zone /CO:53,142 4 show sel atoms ;sel /CO:53,142 4 ; show sel atoms Expected an objects specifier or a keyword > hide sel atoms > select :TRA 39 atoms, 42 bonds, 1 residue, 1 model selected > show sel atoms > select zone :TRA 4 Selected 178 atoms > show sel atoms > select zone /CO:53,142 4 No atoms or surfaces specified > select zone /CO:53,142 4 No atoms or surfaces specified > hide sel atoms > select :TRA 39 atoms, 42 bonds, 1 residue, 1 model selected > show sel atoms > select zone :TRA 4 Selected 178 atoms > show sel atoms > select zone /O:53,142 4 Selected 506 atoms > show sel atoms > select /O:53,142 4 ; show sel atoms Expected a keyword > style sel stick Changed 506 atom styles > hide sel atoms > select :TRA 39 atoms, 42 bonds, 1 residue, 1 model selected > show sel atoms > select zone :TRA 4 Selected 178 atoms > show sel atoms > select zone /O:53,142 4 Selected 506 atoms > show sel atoms > select /O:53,142 269 atoms, 266 bonds, 3 residues, 1 model selected > show sel atoms > vr true started SteamVR rendering VR mode select [Repeated 1 time(s)]VR mode translate selected models > view matrix models > #1,0.99985,-0.017483,0.00088293,-0.17722,0.017489,0.99982,-0.0076857,0.31484,-0.00074836,0.0077,0.99997,0.057937 > view matrix models > #1,0.99995,-0.0016497,0.0096747,0.020316,0.0016951,0.99999,-0.0046812,0.106,-0.0096669,0.0046974,0.99994,-0.076068 > view matrix models > #1,0.99922,0.03815,0.010375,0.33932,-0.038704,0.99746,0.059842,-0.19892,-0.0080658,-0.060196,0.99815,-0.60397 > view matrix models > #1,0.99882,0.03844,0.029816,0.38248,-0.040742,0.99589,0.080894,-0.090432,-0.026584,-0.082013,0.99628,-1.0687 VR mode move picked models > view matrix models > #1,0.99957,0.025299,0.015126,0.19637,-0.026903,0.99271,0.11748,0.17181,-0.012044,-0.11784,0.99296,-0.91153 VR mode move scene VR mode translate selected atoms VR mode select > select @@serial_number=84181 1 atom, 1 residue, 1 model selected VR mode translate selected atoms VR mode select > select clear > select @@serial_number=84182 1 atom, 1 residue, 1 model selected > select @@serial_number=84181 1 atom, 1 residue, 1 model selected > select clear [Repeated 3 time(s)] > select @@serial_number=84182 1 atom, 1 residue, 1 model selected > select up 3 atoms, 2 bonds, 1 residue, 1 model selected > select clear [Repeated 1 time(s)] > select up Nothing selected > select clear > select up Nothing selected > select /P:211@HD11 1 atom, 1 residue, 1 model selected > select @@serial_number=84182 1 atom, 1 residue, 1 model selected > select up 3 atoms, 2 bonds, 1 residue, 1 model selected VR mode translate selected models > view matrix models > #1,0.99957,0.025299,0.015126,0.19637,-0.026903,0.99271,0.11748,0.17181,-0.012044,-0.11784,0.99296,-0.91153 > view matrix models > #1,0.99979,0.013343,0.015631,0.092361,-0.015081,0.99302,0.11697,0.42637,-0.013961,-0.11719,0.99301,-0.88157 VR mode translate selected atoms VR mode select > select @@serial_number=65475 1 atom, 1 residue, 1 model selected > select @@serial_number=65476 1 atom, 1 residue, 1 model selected > select @@serial_number=65474 1 atom, 1 residue, 1 model selected > select @@serial_number=65476 1 atom, 1 residue, 1 model selected VR mode tug 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 ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/vive/vr.py"", line 802, in _next_frame self.process_controller_events() File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/vive/vr.py"", line 830, in process_controller_events self.process_controller_buttons() File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/vive/vr.py"", line 857, in process_controller_buttons hc.process_event(e) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/vive/vr.py"", line 2691, in process_event self._dispatch_event(m, event) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/vive/vr.py"", line 2695, in _dispatch_event mode.pressed(hand_event) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/vive/vr.py"", line 3536, in pressed self._click(hand_button_event) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/vive/vr.py"", line 3545, in _click m.vr_press(e) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/tug/tugatoms.py"", line 161, in vr_press self._pick_atom(pick) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/tug/tugatoms.py"", line 86, in _pick_atom self._tugger = st = StructureTugger(a.structure) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/tug/tugatoms.py"", line 248, in __init__ self._create_openmm_system() File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/tug/tugatoms.py"", line 420, in _create_openmm_system self._topology = openmm_topology(atoms, bonds) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/tug/tugatoms.py"", line 589, in openmm_topology atoms[i] = top.addAtom(aname[i], element, rmap[rid]) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/openmm/app/topology.py"", line 190, in addAtom raise ValueError('All atoms within a residue must be contiguous') ValueError: All atoms within a residue must be contiguous Error processing trigger ""new frame"": ValueError: All atoms within a residue must be contiguous File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/openmm/app/topology.py"", line 190, in addAtom raise ValueError('All atoms within a residue must be contiguous') See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 515.76 OpenGL renderer: NVIDIA GeForce RTX 2080 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.9.11 Locale: en_US.UTF-8 Qt version: PyQt6 6.3.0, Qt 6.3.0 Qt runtime version: 6.3.0 Qt platform: xcb XDG_SESSION_TYPE=x11 DESKTOP_SESSION=ubuntu XDG_SESSION_DESKTOP=ubuntu XDG_CURRENT_DESKTOP=ubuntu:GNOME DISPLAY=:1 Manufacturer: System manufacturer Model: System Product Name OS: Ubuntu 22.04 jammy Architecture: 64bit ELF Virtual Machine: none CPU: 8 Intel(R) Core(TM) i7-7700K CPU @ 4.20GHz Cache Size: 8192 KB Memory: total used free shared buff/cache available Mem: 62Gi 7.8Gi 30Gi 272Mi 24Gi 53Gi Swap: 31Gi 0B 31Gi Graphics: 03:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU102 [GeForce RTX 2080 Ti] [10de:1e04] (rev a1) Subsystem: PNY TU102 [GeForce RTX 2080 Ti] [196e:12af] Kernel driver in use: nvidia Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.10.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2022.5.18.1 cftime: 1.6.0 charset-normalizer: 2.0.12 ChimeraX-AddCharge: 1.2.3 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.4.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.39.1 ChimeraX-AtomicLibrary: 7.0 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.7 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: 2.2.4 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.1 ChimeraX-CommandLine: 1.2.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4 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: 1.1 ChimeraX-DistMonitor: 1.1.5 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.2 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-ItemsInspection: 1.0 ChimeraX-Label: 1.1.1 ChimeraX-LinuxSupport: 1.0 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 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: 2.0.6 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.7 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.5 ChimeraX-ModelPanel: 1.3.2 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: 1.9 ChimeraX-PDB: 2.6.6 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 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: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.6 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: 1.8 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.0.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.18.3 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.1.2 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: 1.1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.6.0 decorator: 5.1.1 distro: 1.6.0 docutils: 0.17.1 entrypoints: 0.4 filelock: 3.4.2 fonttools: 4.33.3 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.27 imagecodecs: 2021.11.20 imagesize: 1.3.0 ipykernel: 6.6.1 ipython: 7.31.1 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.0.3 jupyter-client: 7.1.0 jupyter-core: 4.10.0 kiwisolver: 1.4.2 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.1.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 msgpack: 1.0.3 nest-asyncio: 1.5.5 netCDF4: 1.5.8 networkx: 2.6.3 numexpr: 2.8.1 numpy: 1.22.1 openvr: 1.16.802 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.0.1 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.29 psutil: 5.9.0 ptyprocess: 0.7.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.0 PyQt6-Qt6: 6.3.0 PyQt6-sip: 13.3.1 PyQt6-WebEngine-commercial: 6.3.0 PyQt6-WebEngine-Qt6: 6.3.0 python-dateutil: 2.8.2 pytz: 2022.1 pyzmq: 23.1.0 qtconsole: 5.3.0 QtPy: 2.1.0 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 setuptools: 59.8.0 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.3.2 sphinx-autodoc-typehints: 1.15.2 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 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-community: 1.0.0 tables: 3.7.0 tifffile: 2021.11.2 tinyarray: 1.2.4 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.9 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 }}} " defect closed normal Structure Editing not a bug all ChimeraX