id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4060 VR meeting: LZ4F_decompress failed with code: ERROR_frameSize_wrong phil.cruz@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.18362 ChimeraX Version: 1.2.dev202012100409 (2020-12-10 04:09:15 UTC) Description (Describe the actions that caused this problem to occur here) Log: Startup Messages --- warning | Unable to load numpy_formathandler accelerator from OpenGL_accelerate notes | OpenGL_accelerate module loaded Using accelerated ArrayDatatype UCSF ChimeraX version: 1.2.dev202012100409 (2020-12-10) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 1d8v format mmcif fromDatabase pdb Summary of feedback from opening 1d8v fetched from pdb --- note | Fetching compressed mmCIF 1d8v from http://files.rcsb.org/download/1d8v.cif 1d8v title: The restrained and minimized average NMR structure of MAP30. [more info...] Chain information for 1d8v #1 --- Chain | Description A | ANTI-hiv and ANTI-tumor protein MAP30 > close session > open 6xra Summary of feedback from opening 6xra fetched from pdb --- notes | Fetching compressed mmCIF 6xra from http://files.rcsb.org/download/6xra.cif Fetching CCD NAG from http://ligand-expo.rcsb.org/reports/N/NAG/NAG.cif Fetching CCD MAN from http://ligand-expo.rcsb.org/reports/M/MAN/MAN.cif 6xra title: Distinct conformational states of SARS-CoV-2 spike protein [more info...] Chain information for 6xra #1 --- Chain | Description A B C | Spike glycoprotein Non-standard residues in 6xra #1 --- MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 6vsb Summary of feedback from opening 6vsb fetched from pdb --- note | Fetching compressed mmCIF 6vsb from http://files.rcsb.org/download/6vsb.cif 6vsb title: Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain up [more info...] Chain information for 6vsb #2 --- Chain | Description A B C | SARS-CoV-2 spike glycoprotein Non-standard residues in 6vsb #2 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose > select #2 22854 atoms, 23418 bonds, 39 pseudobonds, 2966 residues, 2 models selected > ui mousemode right ""move picked models"" > view matrix models #2,1,0,0,45.756,0,1,0,36.483,0,0,1,-2.8973 > ui mousemode right select > select clear > ui tool show Meeting > ui tool show Meeting > meeting start pc Meeting ""pc"" started at chimeraxmeeting.net port 52201 Participants can join with command ""meeting pc"" The ChimeraX meeting command message protocol was changed December 9, 2020 in order to reduce the network bandwidth (4 - 10 times reduction), and to block participants that do not provide the meeting name for better security. All participants must use ChimeraX newer than December 9, 2020, or all must use an older version because the old protocol is not compatible with the new one. Connection from ::1 port 58179 refused because meeting name mismatch ""PC"" != ""pc"" Connection from ::1 port 58181 refused because meeting name mismatch ""PC"" != ""pc"" Connection from ::1 port 58182 refused because meeting name mismatch ""PC"" != ""pc"" Connection accepted from ::1 port 58183 Connection accepted from ::1 port 58185 > vr true started SteamVR rendering Connection accepted from ::1 port 58211 Disconnected from ::1 port 58211 Connection accepted from ::1 port 58213 Disconnected from ::1 port 58213 Connection accepted from ::1 port 58218 VR mode tape measure > marker segment #3 position 307.7,266.2,162.2 toPosition 307.1,275.5,179.4 > color yellow radius 0.4525 label 19.5 labelHeight 1.95 labelColor yellow > adjust #3:1,2 Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.dev202012100409\bin\lib\site- packages\chimerax\meeting\meeting.py"", line 1242, in _data_available self._message_received_cb(msg, self) File ""C:\Program Files\ChimeraX 1.2.dev202012100409\bin\lib\site- packages\chimerax\meeting\meeting.py"", line 1138, in _message_received self._send_message(msg) File ""C:\Program Files\ChimeraX 1.2.dev202012100409\bin\lib\site- packages\chimerax\meeting\meeting.py"", line 1157, in _send_message msg_stream.send_message_bytes(msg_bytes) File ""C:\Program Files\ChimeraX 1.2.dev202012100409\bin\lib\site- packages\chimerax\meeting\meeting.py"", line 1386, in send_message_bytes self._send_message_cb(msg, self) File ""C:\Program Files\ChimeraX 1.2.dev202012100409\bin\lib\site- packages\chimerax\meeting\meeting.py"", line 927, in _message_received t.update_model(msg) File ""C:\Program Files\ChimeraX 1.2.dev202012100409\bin\lib\site- packages\chimerax\meeting\meeting.py"", line 1576, in update_model PointerModels.update_model(self, msg) File ""C:\Program Files\ChimeraX 1.2.dev202012100409\bin\lib\site- packages\chimerax\meeting\meeting.py"", line 1426, in update_model m.update_pointer(msg) File ""C:\Program Files\ChimeraX 1.2.dev202012100409\bin\lib\site- packages\chimerax\meeting\meeting.py"", line 1852, in update_pointer self._gui_panel.update_panel(pchanges) File ""C:\Program Files\ChimeraX 1.2.dev202012100409\bin\lib\site- packages\chimerax\meeting\meeting.py"", line 1943, in update_panel p.update_image(panel_changes['image'], self.session) File ""C:\Program Files\ChimeraX 1.2.dev202012100409\bin\lib\site- packages\chimerax\meeting\meeting.py"", line 1962, in update_image rgba = _decode_numpy_array(encoded_rgba) File ""C:\Program Files\ChimeraX 1.2.dev202012100409\bin\lib\site- packages\chimerax\meeting\meeting.py"", line 2045, in _decode_numpy_array bytes = decompress(array_data['data']) RuntimeError: LZ4F_decompress failed with code: ERROR_frameSize_wrong RuntimeError: LZ4F_decompress failed with code: ERROR_frameSize_wrong File ""C:\Program Files\ChimeraX 1.2.dev202012100409\bin\lib\site- packages\chimerax\meeting\meeting.py"", line 2045, in _decode_numpy_array bytes = decompress(array_data['data']) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 441.20 OpenGL renderer: GeForce GTX 1080/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Notebook Model: P870KM_KM1 OS: Microsoft Windows 10 Pro (Build 18363) Memory: 34,306,633,728 MaxProcessMemory: 137,438,953,344 CPU: 8 Intel(R) Core(TM) i7-7700K CPU @ 4.20GHz OSLanguage: en-US Locale: ('en_US', 'cp1252') PySide2 version: 5.15.1 Qt version: 5.15.1 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.9.0 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.12.5 cftime: 1.3.0 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: 1.9.6 ChimeraX-AtomicLibrary: 1.1 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: 2.2 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-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-CommandLine: 1.1.3 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.2.dev202012100409 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.0.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-DataFormats: 1.0.1 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: 2.1 ChimeraX-Help: 1.0 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.1 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0 ChimeraX-Label: 1.0 ChimeraX-ListInfo: 1.1 ChimeraX-Log: 1.1.1 ChimeraX-LookingGlass: 1.1 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: 1.1 ChimeraX-MDcrds: 2.1 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: 1.3.1 ChimeraX-PDB: 2.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.0.1 ChimeraX-Read-Pbonds: 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: 1.2.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.2.1 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: 1.2.2 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: 1.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.3.1 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: 0.29.21 decorator: 4.4.2 distlib: 0.3.1 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 imagecodecs-lite: 2020.1.31 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: 4.7.0 kiwisolver: 1.3.1 line-profiler: 2.1.2 lxml: 4.5.2 lz4: 3.1.0 MarkupSafe: 1.1.1 matplotlib: 3.3.2 msgpack: 1.0.0 netCDF4: 1.5.4 networkx: 2.5 numexpr: 2.7.1 numpy: 1.19.2 numpydoc: 1.1.0 openvr: 1.14.1501 packaging: 20.7 parso: 0.7.1 pickleshare: 0.7.5 Pillow: 7.2.0 pip: 20.3.1 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.8 psutil: 5.7.2 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 PySide2: 5.15.1 python-dateutil: 2.8.1 pytz: 2020.4 pywin32: 228 pyzmq: 20.0.0 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 shiboken2: 5.15.1 six: 1.15.0 snowballstemmer: 2.0.0 sortedcontainers: 2.2.2 Sphinx: 3.2.1 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: 2020.9.3 tinyarray: 1.2.3 tornado: 6.1 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 WMI: 1.5.1 }}} " defect closed normal VR can't reproduce all ChimeraX