Opened 2 years ago

Closed 2 years ago

Last modified 2 years ago

#9379 closed defect (fixed)

ViewDockX data not in session

Reported by: sabrinamoffit@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Sessions Version:
Keywords: Cc: Greg Couch
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-5.13.0-051300-generic-x86_64-with-glibc2.27
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)

I'm unable to open the saved ChimeraX session ( .cxs)

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/sabrina/Desktop/DOCKIT_SABBY/vina_results/3r2u_dockview_n_activesite.cxs

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 725, in restore  
obj = sm.restore_snapshot(self, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/viewdockx/tool.py", line 287, in restore_snapshot  
inst.setup(structures, data.get(cls.html_state, None))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/viewdockx/tool.py", line 23, in setup  
self._setup(structures)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/viewdockx/tool.py", line 55, in _setup  
raise UserError("No suitable models found for ViewDockX")  
chimerax.core.errors.UserError: No suitable models found for ViewDockX  
  
opened ChimeraX session  

> open
> /home/sabrina/Desktop/DOCKIT_SABBY/vina_results/3r2u_dockview_n_activesite.cxs
> format session

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 725, in restore  
obj = sm.restore_snapshot(self, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/viewdockx/tool.py", line 287, in restore_snapshot  
inst.setup(structures, data.get(cls.html_state, None))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/viewdockx/tool.py", line 23, in setup  
self._setup(structures)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/viewdockx/tool.py", line 55, in _setup  
raise UserError("No suitable models found for ViewDockX")  
chimerax.core.errors.UserError: No suitable models found for ViewDockX  
  
opened ChimeraX session  

QXcbConnection: XCB error: 8 (BadMatch), sequence: 4093, resource id:
77594668, major code: 42 (SetInputFocus), minor code: 0  




OpenGL version: 4.6 (Core Profile) Mesa 20.0.8
OpenGL renderer: Mesa DRI Intel(R) UHD Graphics 630 (CFL GT2)
OpenGL vendor: Intel Open Source Technology Center
Manufacturer: Intel(R) Client Systems
Model: LAPQC71C
OS: Ubuntu 18.04 bionic
Architecture: 64bit ELF
Virutal Machine: none
CPU: 12 Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz
Cache Size: 12288 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            15G        4.2G        7.4G        799M        3.9G         10G
	Swap:          2.0G          0B        2.0G

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation Device [8086:3e9b]	
	Subsystem: Intel Corporation Device [8086:3011]	
	Kernel driver in use: i915
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    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: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    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: 1.0
    ChimeraX-DistMonitor: 1.1.5
    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: 1.1
    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
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    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: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    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: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    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
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    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: 1.6.1
    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: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    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: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
File attachment: 3r2u_dockview_n_activesite.cxs

3r2u_dockview_n_activesite.cxs​

Attachments (1)

3r2u_dockview_n_activesite.cxs​ (1.2 MB ) - added by sabrinamoffit@… 2 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (9)

by sabrinamoffit@…, 2 years ago

Attachment: 3r2u_dockview_n_activesite.cxs​ added

Added by email2trac

comment:1 by Eric Pettersen, 2 years ago

Component: Unassigned → Sessions
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → ViewDockX data not in session

comment:2 by Eric Pettersen, 2 years ago

Status: accepted → feedback

Hi Sabrina,

Thanks for reporting this problem. Somehow, the docking-specific data for your ligands did not get saved in the session. I tried some things but could not reproduce this, so it's a mystery to me how it happened. If it is of any use to you, I could send you a session that has everything except for the ViewDockX tool in it (the structures, surface, etc.) Let me know.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:3 by Eric Pettersen, 2 years ago

Resolution: → fixed
Status: feedback → closed

Hi Sabrina,

With further investigation I have determined that this is a problem specifically with saving AutoDock Vina data in sessions in ChimeraX 1.3. It was fixed by 1.5. So if you upgrade to the current version of ChimeraX you won't run into this problem again.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:4 by sabrinamoffit@…, 2 years ago 

Hi Eric,

I will upgrade to ChimeraX 1.5 then. Thank you so much for your help.


On Tue, 18 Jul 2023 at 4:48 AM, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>
>
>
>
>
>

comment:5 by Eric Pettersen, 2 years ago

Thanks for providing the session file. Sorry I wasn't able to "rescue" the data (since it was missing) but the file provided a lot of clues about what the problem was.

--Eric

comment:6 by sabrinamoffit@…, 2 years ago 

Hi Eric,

I tried installing versions 1.5 and 1.6 but I got this error: ./ChimeraX:
/lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.28' not found (required
by /home/sabrina/Downloads/chimerax-1.5/bin/../lib/libpython3.9.so.1.0).
I'm trying to find which release of ChimeraX1.5 or 1.6 is compatible with
my Ubuntu 18.04 running GLIBC 2.27 on the Download page, but couldn't find
this info. Could you please advise?

Thank you.

On Tue, Jul 18, 2023 at 9:02 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>
>
>

comment:7 by Eric Pettersen, 2 years ago

Cc: Greg Couch added

Greg, could you advise Sabrina on how to get the latest ChimeraX working on her Ubuntu 18.04 system? Thanks!

--Eric

comment:8 by Greg Couch, 2 years ago

Ubuntu 18.04 stopped getting updates on May 31, 2023, so you want to upgrade your system ASAP. And once you upgrade your system, ChimeraX will work on it.

See ​https://ubuntu.com/tutorials/upgrading-ubuntu-desktop for the basic instructions. Specific instructions are at ​https://ubuntu.com/blog/how-to-upgrade-from-ubuntu-18-04-lts-to-20-04-lts-today. You want to end up with Ubuntu 22.04, but you might need to upgrade to 20.04 first, and then upgrade to 22.04.

Note: See TracTickets for help on using tickets.