Opened 5 years ago
Closed 5 years ago
#4438 closed defect (fixed)
meeting: self.room_to_scene is None
Reported by: | Owned by: | Tom Goddard | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | VR | 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: 1.2.dev202103310726 (2021-03-31 07:26:37 UTC) Description (Describe the actions that caused this problem to occur here) When Mike Schmid joined my apoferritin meeting I got this error. Log: UCSF ChimeraX version: 1.2.dev202103310726 (2021-03-31) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Unable to load numpy_formathandler accelerator from OpenGL_accelerate > open C:\Users\goddard\Desktop\apoferritin.cxs format session Opened emdb 22657 thresholded as #3, grid size 420,420,420, pixel 0.4, shown at level 0.018, step 1, values float32 Log from Tue Mar 30 18:57:35 2021UCSF ChimeraX version: 1.2.dev202103162155 (2021-03-16) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 2gbp 2gbp title: Sugar and signal-transducer binding sites of the escherichia coli galactose chemoreceptor protein [more info...] Chain information for 2gbp #1 --- Chain | Description A | D-galactose/D-glucose binding protein Non-standard residues in 2gbp #1 --- BGC — β-D-glucose CA — calcium ion > set bgColor white > graphics silhouettes true > molmap protein 8 gridSpacing 1 Opened 2gbp map 8 as #2, grid size 94,90,112, pixel 1, shown at level 0.0778, step 1, values float32 > transparency #2 70 > hide #!2 models > save /Users/goddard/Desktop/image1.png supersample 3 > hide #!1 models > show #!2 models > graphics silhouettes false > save /Users/goddard/Desktop/image2.png transparentBackground true > close > open 22658 fromDatabase emdb Summary of feedback from opening 22658 fetched from emdb --- note | Fetching compressed map 22658 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-22658/map/emd_22658.map.gz Opened emdb 22658 as #1, grid size 330,330,330, pixel 0.502, shown at level 0.08, step 2, values float32 > open 7k3v Summary of feedback from opening 7k3v fetched from pdb --- note | Fetching compressed mmCIF 7k3v from http://files.rcsb.org/download/7k3v.cif 7k3v title: Apoferritin structure at 1.34 angstrom resolution determined from a 300 kV Titan Krios G3i electron microscope with K3 detector [more info...] Chain information for 7k3v #2 --- Chain | Description A B C D E F G H I J K L M N O P Q R S T U V W X | Ferritin heavy chain Non-standard residues in 7k3v #2 --- NA — sodium ion ZN — zinc ion > style stick Changed 36918 atom styles > volume #1 level 0.03917 > ui tool show "Map Coordinates" > volume #1 level 0.027 > style sphere Changed 36918 atom styles > style stick Changed 36918 atom styles > fitmap #2 inMap #1 Fit molecule 7k3v (#2) to map emdb 22658 (#1) using 36918 atoms average map value = 0.01362, steps = 68 shifted from previous position = 0.0482 rotated from previous position = 1.56 degrees atoms outside contour = 30977, contour level = 0.026997 Position of 7k3v (#2) relative to emdb 22658 (#1) coordinates: Matrix rotation and translation 0.99975395 -0.01556557 0.01580326 -0.02687632 0.01581163 0.99975381 -0.01556648 -0.02836100 -0.01555707 0.01581252 0.99975394 -0.02828319 Axis 0.57747570 0.57713234 0.57744270 Axis point 0.00000000 0.02720432 -0.03457098 Rotation angle (degrees) 1.55686662 Shift along axis -0.04822039 > close #1 > close > open 22657 fromDatabase emdb Summary of feedback from opening 22657 fetched from emdb --- note | Fetching compressed map 22657 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-22657/map/emd_22657.map.gz Opened emdb 22657 as #1, grid size 420,420,420, pixel 0.4, shown at level 0.0273, step 2, values float32 > open 7k3v format mmcif fromDatabase pdb 7k3v title: Apoferritin structure at 1.34 angstrom resolution determined from a 300 kV Titan Krios G3i electron microscope with K3 detector [more info...] Chain information for 7k3v #2 --- Chain | Description A B C D E F G H I J K L M N O P Q R S T U V W X | Ferritin heavy chain Non-standard residues in 7k3v #2 --- NA — sodium ion ZN — zinc ion > style stick Changed 36918 atom styles > volume #1 level 0.01701 > lighting soft > volume #1 step 1 > volume #1 color #b2b2b2bf > volume #1 color #b2b2b2e7 > volume #1 color #b2b2b2 > volume showOutlineBox true > set bgColor black > volume #1 color #b2b2b2d2 > uage material Unknown command: uage material > usage material material [preset] [reflectivity a number] [specularReflectivity a number] [exponent a number] [ambientReflectivity a number] [transparentCastShadows true or false] [meshesCastShadows true or false] — report or alter material parameters preset: one of default, dull, or shiny > material meshcast true Expected one of 'default', 'dull', or 'shiny' or a keyword > material meshesCastShadows true > material transparentCastShadows true > volume #1 style mesh > set bgColor white > set bgColor black > volume #1 style surface > volume #1 step 2 > volume #1 level 0.01512 > volume #1 step 1 > close > open 22658 format ccp4 fromDatabase emdb Opened emdb 22658 as #1, grid size 330,330,330, pixel 0.502, shown at level 0.08, step 2, values float32 > volume #1 step 1 > volume #1 level 0.05226 > volume #1 level 0.0502 > volume showOutlineBox true > open 7k3w Summary of feedback from opening 7k3w fetched from pdb --- note | Fetching compressed mmCIF 7k3w from http://files.rcsb.org/download/7k3w.cif 7k3w title: Apoferritin structure at 1.36 angstrom resolution determined from a 300 kV Titan Krios G3i electron microscope with Falcon4 detector [more info...] Chain information for 7k3w #2 --- Chain | Description A B C D E F G H I J K L M N O P Q R S T U V W X | Ferritin heavy chain Non-standard residues in 7k3w #2 --- NA — sodium ion ZN — zinc ion > style stick Changed 36974 atom styles > color byhetero > volume #1 color #b2b2b2ae > usage volume thresh volume threshold volumes [minimum a number] [set a number] [maximum a number] [setMaximum a number] [subregion map region] [step map step] [modelId modelId] — Set map values below a threshold to zero modelId: a model id > volume #1 level 0.0202 > volume #1 level 0.0502 > volume threshold #1 minimum 0.02 Opened emdb 22658 thresholded as #3, grid size 330,330,330, pixel 0.502, shown at step 1, values float32 > close #1 > save /Users/goddard/Desktop/test.cxs includeMaps true > close > open 22657 format ccp4 fromDatabase emdb Opened emdb 22657 as #1, grid size 420,420,420, pixel 0.4, shown at level 0.0273, step 2, values float32 > open 7k3v format mmcif fromDatabase pdb 7k3v title: Apoferritin structure at 1.34 angstrom resolution determined from a 300 kV Titan Krios G3i electron microscope with K3 detector [more info...] Chain information for 7k3v #2 --- Chain | Description A B C D E F G H I J K L M N O P Q R S T U V W X | Ferritin heavy chain Non-standard residues in 7k3v #2 --- NA — sodium ion ZN — zinc ion > style stick Changed 36918 atom styles > style stick Changed 36918 atom styles > color byhetero > volume #1 level 0.01 > volume #1 level 0.02 > volume #1 step 1 > volume #1 level 0.01 > volume #1 level 0.02 > volume #1 level 0.015 > volume threshold #1 minimum 0.01 Opened emdb 22657 thresholded as #3, grid size 420,420,420, pixel 0.4, shown at step 1, values float32 > close #1 > volume #3 level 0.018 > volume #3 color #b2b2b2c2 > volume #3 color #b2b2b2a9 > volume #3 color #b2b2b275 > volume #3 color #b2b2b290 > volume #3 color #b2b2b2c1 > save /Users/goddard/Desktop/apoferritin.cxs includeMaps true ——— End of log from Tue Mar 30 18:57:35 2021 ——— opened ChimeraX session > ui tool show Meeting > meeting start tg Meeting "tg" started at chimeraxmeeting.net port 52199 Participants can join with command "meeting tg" 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 accepted from ::1 port 52912 Traceback (most recent call last): File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site- packages\chimerax\meeting\meeting.py", line 1242, in _data_available self._message_received_cb(msg, self) File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site- packages\chimerax\meeting\meeting.py", line 1138, in _message_received self._send_message(msg) File "C:\Program Files\ChimeraX-Mar-31-2021\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-Mar-31-2021\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-Mar-31-2021\bin\lib\site- packages\chimerax\meeting\meeting.py", line 927, in _message_received t.update_model(msg) File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site- packages\chimerax\meeting\meeting.py", line 1576, in update_model PointerModels.update_model(self, msg) File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site- packages\chimerax\meeting\meeting.py", line 1426, in update_model m.update_pointer(msg) File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site- packages\chimerax\meeting\meeting.py", line 1827, in update_pointer h.position = self.room_to_scene * rp TypeError: unsupported operand type(s) for *: 'NoneType' and 'Place' TypeError: unsupported operand type(s) for *: 'NoneType' and 'Place' File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site- packages\chimerax\meeting\meeting.py", line 1827, in update_pointer h.position = self.room_to_scene * rp See log for complete Python traceback. Traceback (most recent call last): File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site- packages\chimerax\meeting\meeting.py", line 1242, in _data_available self._message_received_cb(msg, self) File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site- packages\chimerax\meeting\meeting.py", line 1138, in _message_received self._send_message(msg) File "C:\Program Files\ChimeraX-Mar-31-2021\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-Mar-31-2021\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-Mar-31-2021\bin\lib\site- packages\chimerax\meeting\meeting.py", line 927, in _message_received t.update_model(msg) File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site- packages\chimerax\meeting\meeting.py", line 1576, in update_model PointerModels.update_model(self, msg) File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site- packages\chimerax\meeting\meeting.py", line 1426, in update_model m.update_pointer(msg) File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site- packages\chimerax\meeting\meeting.py", line 1827, in update_pointer h.position = self.room_to_scene * rp TypeError: unsupported operand type(s) for *: 'NoneType' and 'Place' TypeError: unsupported operand type(s) for *: 'NoneType' and 'Place' File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site- packages\chimerax\meeting\meeting.py", line 1827, in update_pointer h.position = self.room_to_scene * rp See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 456.71 OpenGL renderer: GeForce GTX 1080 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Gigabyte Technology Co., Ltd. Model: Z270X-Gaming K7 OS: Microsoft Windows 10 Home (Build 19041) Memory: 17,129,693,184 MaxProcessMemory: 137,438,953,344 CPU: 8 Intel(R) Core(TM) i7-7700K CPU @ 4.20GHz OSLanguage: en-US Locale: ('en_US', 'cp1252') PyQt5 5.15.2, Qt 5.15.2 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: 1.4.1 chardet: 3.0.4 ChimeraX-AddCharge: 1.0 ChimeraX-AddH: 2.1.4 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.12 ChimeraX-AtomicLibrary: 3.0 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: 2.5.1 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-ColorKey: 1.2.1 ChimeraX-CommandLine: 1.1.3 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.2.dev202103310726 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.1 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: 1.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.1 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-Label: 1.0 ChimeraX-ListInfo: 1.1 ChimeraX-Log: 1.1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 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: 2.2 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.3 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.0 ChimeraX-ModelPanel: 1.0.1 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 ChimeraX-OpenCommand: 1.5 ChimeraX-PDB: 2.4 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.0.1 ChimeraX-ReadPbonds: 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: 1.4 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.3 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: 1.3 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: 1.0.1 ChimeraX-ToolshedUtils: 1.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.7.1 ChimeraX-uniprot: 2.1 ChimeraX-UnitCell: 1.0 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 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: 4.7.1 kiwisolver: 1.3.1 line-profiler: 2.1.2 lxml: 4.6.2 lz4: 3.1.0 MarkupSafe: 1.1.1 matplotlib: 3.3.2 msgpack: 1.0.0 netCDF4: 1.5.4 networkx: 2.5 numexpr: 2.7.3 numpy: 1.19.2 numpydoc: 1.1.0 openvr: 1.14.1501 packaging: 20.9 ParmEd: 3.2.0 parso: 0.7.1 pickleshare: 0.7.5 Pillow: 7.2.0 pip: 21.0.1 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.18 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 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.1 pytz: 2021.1 pywin32: 228 pyzmq: 22.0.3 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 six: 1.15.0 snowballstemmer: 2.1.0 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: 1.3.0 WMI: 1.5.1
Change History (4)
comment:1 by , 5 years ago
Component: | Unassigned → VR |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → meeting: self.room_to_scene is None |
comment:2 by , 5 years ago
comment:3 by , 5 years ago
This error is easily reproduced by starting a meeting without VR and another computer joining the meeting with VR already on.
comment:4 by , 5 years ago
Resolution: | → fixed |
---|---|
Status: | assigned → closed |
Fixed.
The problem is that when the joiner connects they do not send their VR room to scene transform because that would override other already joined VR users. But if they are the only VR users then the others don't get the room to scene transform at all so they can't position head and hands correctly in the scene until the VR users moves the scene causing the room to scene transform to be sent. The error happens because before that first move the room to scene transform is None. A simple solution is to set the initial room to scene transform to the identity. The head and hands will be mispositioned initially in the very rare case where a non-VR host is joined by a VR participant. It is tricky to do better. This solution seems adequate.
In other tries starting a meeting with Mike Schmid at SLAC with this same session minutes before this I did not get this error. It may be that the difference was that I had turned off VR before this attempt and loaded apoferritin.cxs but the VR had been on earlier so the SteamVR camera existed but was just not the current camera. Can't see this in the log because loading the apoferritin.cxs session cleared the log. Can see if the code fails to check if the SteamVR camera is active and can also just retest this scenario with my two VR machines.