Opened 5 years ago

Closed 5 years ago

#3808 closed defect (fixed)

Meeting command should not clear the log

Reported by: goddard@… 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.dev202009250143 (2020-09-25 01:43:07 UTC)
Description
Joining meeting clears the log when the new session is loaded.  This made debugging a previous meeting bug very confusing (I never figured it out).

It is not clear whether the log should be cleared when a session file is opened.  Need to check if it clears the log during a normal session open, not from the meeting command.

Log:
UCSF ChimeraX version: 1.2.dev202009250143 (2020-09-25)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> meeting 192.168.0.2 faceImage C:\Users\goddard/Desktop/greta.jpg

Log from Tue Oct 6 18:44:30 2020UCSF ChimeraX version: 1.2.dev202010010012
(2020-10-01)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open C:\cygwin64\home\goddard\ucsf\data\sars-cov-2-pore\sars-pores3.cxs
> format session

Log from Wed Sep 30 19:47:59 2020UCSF ChimeraX version: 1.2.dev202009300503
(2020-09-30)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open /Users/goddard/ucsf/data/sars-cov-2-pore/sars-pores2.cxs format session

Log from Wed Sep 30 17:54:31 2020UCSF ChimeraX version: 1.2.dev202009300503
(2020-09-30)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open /Users/goddard/ucsf/data/sars-cov-2-pore/sars-pores.cxs format session

Log from Fri Sep 18 10:47:56 2020UCSF ChimeraX version: 1.2.dev202009020044
(2020-09-02)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/goddard/ucsf/data/sars-cov-2-pore/emd_11514.map

Opened emd_11514.map, grid size 96,96,96, pixel 7.02, shown at level 3.21,
step 1, values float32  

> volume #1 level 2.022

> open /Users/goddard/ucsf/data/sars-cov-2-pore/models/QHD43415_3.pdb

Chain information for QHD43415_3.pdb #2  
---  
Chain | Description  
| No description available  
  

> rainbow #2

Drag select of 287 residues  

> ui mousemode right translate

> ui mousemode right "translate selected models"

> select clear

> open /Users/goddard/ucsf/data/sars-cov-2-pore/F1.large.png

Opened multi-channel map F1.large.png, 3 channels, grid size 1280,639,1, pixel
1, shown at step 1, values uint8  

> volume #3.1 level 105,0 level 120,0.8 level 255,1

> volume #3.1 level 120,0.8 level 255,1 color red color red

> volume #3.1 level 0.4713,0 level 255,1

> volume #3.2 level 107,0 level 121.8,0.8 level 255,1

> volume #3.2 level 107,0 level 255,1 color lime color lime

> volume #3.2 level 0,0 level 255,1

> volume #3.3 level 86.99,0 level 103.8,0.8 level 255,1

> volume #3.3 level 86.99,0 level 255,1 color blue color blue

> volume #3.3 level 0,0 level 255,1

> select #3

7 models selected  

> select clear

> lighting full

> save sars-pores.cxs

opened ChimeraX session  

> close #3

> open /Users/goddard/ucsf/data/sars-cov-2-pore/F1.large.jpg

Opened image F1.large.jpg  

> ui mousemode right "move picked models"

> view matrix models #3,1,0,0,-66.333,0,1,0,-644.48,0,0,1,343.15

> view matrix models
> #3,0.9918,-0.12365,0.032338,-66.333,-0.067921,-0.29559,0.9529,-644.48,-0.10826,-0.94728,-0.30156,343.15

> view matrix models
> #3,0.9853,-0.044457,0.16497,-66.333,-0.15335,0.19566,0.96861,-644.48,-0.07534,-0.97966,0.18597,343.15

> view matrix models
> #3,0.9611,-0.13297,0.2421,-66.333,-0.2303,0.098158,0.96816,-644.48,-0.1525,-0.98625,0.063716,343.15

> view matrix models
> #3,-0.95885,-0.090898,0.26896,-66.333,0.28389,-0.29665,0.91181,-644.48,-0.0030938,0.95065,0.31025,343.15

> open /Users/goddard/ucsf/data/sars-cov-2-pore/F2.large.jpg

Opened image F2.large.jpg  

> close #4

> open /Users/goddard/ucsf/data/sars-cov-2-pore/F2.large.jpg format photo

Opened image F2.large.jpg  

> view matrix models #4,1,0,0,-904.05,0,1,0,61.98,0,0,1,150.79

> view matrix models #4,1,0,0,-979.47,0,1,0,123.66,0,0,1,56.087

> view matrix models
> #4,-0.79402,0.52269,-0.31036,-979.47,-0.53392,-0.35559,0.76713,123.66,0.29061,0.77482,0.56142,56.087

> view matrix models
> #4,-0.97197,-0.21499,-0.095174,-979.47,0.0020878,-0.41268,0.91087,123.66,-0.2351,0.88514,0.40156,56.087

> view matrix models
> #4,-0.13764,0.28993,0.9471,-979.47,0.89258,-0.3782,0.24549,123.66,0.42937,0.87915,-0.20673,56.087

> view matrix models
> #4,-0.23117,-0.20228,0.95165,-1051.1,0.84163,-0.53228,0.09131,-2.5657,0.48808,0.82205,0.29329,564.7

> view matrix models
> #3,-0.95578,-0.11723,0.26969,-66.333,0.29382,-0.41838,0.85944,-644.48,0.012082,0.90068,0.43432,343.15

> save sars-pores2.cxs

opened ChimeraX session  

> usage rename

rename models [name] [id id]  
— rename a model or change its id number  
name: a text string  
id: a model id  

> open /Users/goddard/ucsf/data/sars-cov-2-pore/models/QHD43415_4.pdb

Chain information for QHD43415_4.pdb #5  
---  
Chain | Description  
| No description available  
  

> hide #5 models

> show #5 models

> hide #4 models

> hide #2 models

> hide #3 models

> show #2 models

> show #3 models

> hide #2 models

> show #4 models

> hide #4 models

> hide #3 models

> hide #!1 models

> open /Users/goddard/ucsf/data/sars-cov-2-pore/models/QHD43415_6.pdb

Chain information for QHD43415_6.pdb #6  
---  
Chain | Description  
| No description available  
  

> show #!1 models

> show #2 models

> hide #!1 models

> ui mousemode right "move picked models"

> view matrix models #5,1,0,0,46.693,0,1,0,215.51,0,0,1,83.347

> view matrix models #6,1,0,0,70.795,0,1,0,73.781,0,0,1,-79.717

> view matrix models #5,1,0,0,124.63,0,1,0,161.13,0,0,1,144.79

> view matrix models #6,1,0,0,143.28,0,1,0,22.959,0,0,1,-34.14

> show #!1 models

> hide #!1 models

> view matrix models #6,1,0,0,181.33,0,1,0,59.891,0,0,1,105.96

> show #!1 models

> hide #2 models

> hide #5-6 cartoons

> show #5-6 atoms

> style #5-6 sphere

Changed 12595 atom styles  

> show #2 models

> show #3 models

> show #4 models

> save /Users/goddard/ucsf/data/sars-cov-2-pore/sars-pores3.cxs

opened ChimeraX session  

> vr true

> lighting simple

started SteamVR rendering  

> meeting start

Meeting at DESKTOP-J8FC2Q4 or 192.168.0.2 port 52194  

=== End of log from Tue Oct 6 18:44:30 2020 ===

started SteamVR rendering  




OpenGL version: 3.3.0 NVIDIA 398.35
OpenGL renderer: GeForce GTX 1070 with Max-Q Design/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Micro-Star International Co., Ltd.
Model: GS65 Stealth Thin 8RF
OS: Microsoft Windows 10 Pro (Build 19041)
Memory: 34,195,668,992
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-8750H CPU @ 2.20GHz"
PyQt version: 5.15.1
Compiled Qt version: 5.15.1
Runtime Qt version: 5.15.1
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
    cftime: 1.2.1
    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: 1.8.2
    ChimeraX-AtomicLibrary: 1.0
    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: 2.2
    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: 2.1
    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.dev202009250143
    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: 2.1
    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-Label: 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: 2.1
    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: 1.2.1
    ChimeraX-PDB: 2.1.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0.1
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    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: 2.2.1
    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: 1.1
    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: 1.3.1
    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: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.2
    MarkupSafe: 1.1.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    netifaces: 0.10.9
    networkx: 2.5
    numexpr: 2.7.1
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.4
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 20.2.3
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    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: 5.15.1
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pywin32: 228
    pyzmq: 19.0.2
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.0
    sfftk-rw: 0.6.6.dev0
    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: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2
    WMI: 1.5.1

Change History (2)

comment:1 by Tom Goddard, 5 years ago

Component: Unassigned → VR
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Meeting command should not clear the log

When opening a session file the log is currently cleared and there is a preference setting to preserve the log. For meetings the session restore is just an implementation detail for syncing and should not clear the log.

comment:2 by Tom Goddard, 5 years ago

Resolution: → fixed
Status: assigned → closed

Fixed.

Added clear_log option to Session.restore().

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