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#5343 assigned defect

Session tries to restore non-StateManager as StateManager

Reported by:	chimerax-bug-report@…	Owned by:	Greg Couch
Priority:	normal	Milestone:
Component:	Sessions	Version:
Keywords:		Cc:	pett
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Linux-4.4.0-210-generic-x86_64-with-glibc2.14
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 567, resource id:
11846866, major code: 40 (TranslateCoords), minor code: 0  

> open /scratch2/jrai/90s_realspace/Bfr2/bfr2_lcp5_aplhafold_v8_edited.pdb

Summary of feedback from opening
/scratch2/jrai/90s_realspace/Bfr2/bfr2_lcp5_aplhafold_v8_edited.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
1120 messages similar to the above omitted  
  
Chain information for bfr2_lcp5_aplhafold_v8_edited.pdb #1  
---  
Chain | Description  
5 | No description available  
6 | No description available  
  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 4686, resource id:
11847680, major code: 40 (TranslateCoords), minor code: 0  

> open /scratch2/jrai/90s_realspace/densities/job206_pp.mrc

Opened job206_pp.mrc as #2, grid size 432,432,432, pixel 1.07, shown at level
0.00899, step 2, values float32  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 6204, resource id:
11848519, major code: 40 (TranslateCoords), minor code: 0  

> volume #2 step 1

> set bgColor white

> volume #2 level 0.007863

> select #1 /6 :3300-3310

Nothing selected  

> select #1 /6 :3300-3310

Nothing selected  

> select #1 /6

3386 atoms, 3413 bonds, 1 pseudobond, 277 residues, 2 models selected  

> volume zone #2 nearAtoms sel range

Missing "range" keyword's argument  

> volume zone #2 nearAtoms sel range 3

> color sel red

> color sel cyan

> volume #2 level 0.005159

> volume #2 level 0.004859

> transparency #1 90

> transparency #1290

Missing or invalid "percent" argument: Expected a number  

> transparency #2 90

> lighting soft

> lighting simple

> graphics silhouettes true

> transparency #2 80

> transparency #2 50

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows true

> lighting flat

> lighting full

> lighting shadows false

> volume zone #2 nearAtoms sel range 2

> volume #2 level 0.004107

> volume zone #2 nearAtoms sel range 5

> volume #2 level 0.005384

> lighting soft

> graphics silhouettes false

> graphics silhouettes true width 0.01 depthJump 0.1 color black

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows true intensity 0.5

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> lighting flat

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> select #2

2 models selected  

> select clear

> graphics silhouettes true

> lighting shadows true intensity 0.5

> lighting flat

> lighting full

> lighting soft

> lighting simple

> graphics silhouettes false

> graphics silhouettes true width 0.01 depthJump 0.102 color black

> volume zone #2 nearAtoms sel range 3

no atoms specified for zone  

> select #1 /6

3386 atoms, 3413 bonds, 1 pseudobond, 277 residues, 2 models selected  

> select #1 /6

3386 atoms, 3413 bonds, 1 pseudobond, 277 residues, 2 models selected  

> volume #2 level 0.005535

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes true width 6 depthJump 0.2 color black

> graphics silhouettes true width 5 depthJump 0.2 color black

> graphics silhouettes true width 1 depthJump 0.2 color black

> graphics silhouettes true width 2 depthJump 0.2 color black

> select #2

2 models selected  

> select #1

7472 atoms, 7532 bonds, 2 pseudobonds, 573 residues, 2 models selected  

> ~select #1

Nothing selected  

> select #2

2 models selected  

> color sel cyan

> transparency #2 90

> select clear

> open /disks/li/d1/Jay/90S/Mapstich_toppartonly.mrc

Opened Mapstich_toppartonly.mrc as #3, grid size 432,432,432, pixel 1.07,
shown at level 0.0103, step 2, values float32  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 56459, resource id:
11857241, major code: 40 (TranslateCoords), minor code: 0  

> volume #3 step 1

> hide #!2 models

> select #1 /6

3386 atoms, 3413 bonds, 1 pseudobond, 277 residues, 2 models selected  

> volume zone #3 nearAtoms sel range 3

> volume #3 level 0.007714

> volume #3 level 0.005769

> volume #3 level 0.006588

> select #3

2 models selected  

> color sel cyan

> transparency #3 90

> select clear

> select #1 /6

3386 atoms, 3413 bonds, 1 pseudobond, 277 residues, 2 models selected  

> volume zone #3 nearAtoms sel range 2

> volume zone #3 nearAtoms sel range 4

> volume zone #3 nearAtoms sel range 5

> volume #3 level 0.01119

> volume #3 level 0.008635

> volume zone #3 nearAtoms sel range 3

> volume #3 level 0.0071

> lighting soft

> lighting full

> lighting shadows false

> graphics silhouettes false

> lighting shadows true

> lighting soft

> graphics silhouettes true

> graphics silhouettes true width 2 depthJump 0.1 color black

> graphics silhouettes true width 2 depthJump 0.01 color black

> graphics silhouettes true width 1 depthJump 0.01 color black

> lighting shadows true intensity 0.5

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes true width 12 depthJump 0.01 color black

> graphics silhouettes true width 2 depthJump 0.01 color black

> graphics silhouettes true width 0.5 depthJump 0.01 color black

> graphics silhouettes true width 1 depthJump 0.01 color black

> graphics silhouettes true width 1.5 depthJump 0.01 color black

> graphics silhouettes true width 1 depthJump 0.01 color black

> select clear

> graphics silhouettes depthJump 0.8

> graphics silhouettes true width 0.01 depthJump 0.1 color black

> graphics silhouettes true width 6 depthJump 0.2 color black

> graphics silhouettes true width 2 depthJump 0.2 color black

> graphics silhouettes true width 1 depthJump 0.2 color black

> open /disks/li/d1/Jay/90S/Mapstich_vopmax.mrc

Opened Mapstich_vopmax.mrc as #4, grid size 432,432,432, pixel 1.07, shown at
level 0.0146, step 2, values float32  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 37647, resource id:
11865104, major code: 40 (TranslateCoords), minor code: 0  

> volume #4 step 1

> select #1 /6

3386 atoms, 3413 bonds, 1 pseudobond, 277 residues, 2 models selected  

> volume zone #4 nearAtoms sel range 3

> open /disks/li/d1/Jay/90S/Brf2models/brf2_alpghafold_truncatged.pdb

Summary of feedback from opening
/disks/li/d1/Jay/90S/Brf2models/brf2_alpghafold_truncatged.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 LEU A 5
ILE A 14 1 10  
Start residue of secondary structure not found: HELIX 2 2 ALA A 29 LEU A 31 1
3  
Start residue of secondary structure not found: HELIX 3 3 GLU A 52 LYS A 56 1
5  
Start residue of secondary structure not found: HELIX 4 4 LYS A 66 GLU A 70 1
5  
Start residue of secondary structure not found: HELIX 5 5 ARG A 87 GLU A 92 1
6  
1 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 20 20 THR A 456 SER A 459
1 4  
Start residue of secondary structure not found: HELIX 21 21 ASP A 487 LEU A
497 1 11  
  
Chain information for brf2_alpghafold_truncatged.pdb #5  
---  
Chain | Description  
A | No description available  
  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 46763, resource id:
11866741, major code: 40 (TranslateCoords), minor code: 0  

> ui tool show "Model Panel"

> close #5

QXcbConnection: XCB error: 3 (BadWindow), sequence: 54000, resource id:
11867617, major code: 40 (TranslateCoords), minor code: 0  

> open /scratch2/jrai/90s_realspace/fig1.cxs

Opened Mapstich_toppartonly.mrc as #2, grid size 432,432,432, pixel 1.07,
shown at step 1, values float32  
Opened Mapstich_vopmax.mrc as #4, grid size 432,432,432, pixel 1.07, shown at
level 0.013, step 2, values float32  
Opened Mapstich_toppartonly.mrc zone as #5, grid size 432,432,432, pixel 1.07,
shown at level 0.0103, step 1, values float32  
Opened Mapstich_toppartonly.mrc zone as #3, grid size 432,432,432, pixel 1.07,
shown at level 0.00723, step 1, values float32  
Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "/scratch/users/Jay/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-
packages/chimerax/core/session.py", line 694, in restore  
self.add_state_manager(name, data)  
File "/scratch/users/Jay/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-
packages/chimerax/core/session.py", line 546, in add_state_manager  
raise ValueError('container "%s" of type "%s" does not have snapshot methods
and does not have clear method' % (tag, str(type(container))))  
ValueError: container "presets" of type "<class
'chimerax.preset_mgr.manager.PresetsManager'>" does not have snapshot methods
and does not have clear method  
  
opened ChimeraX session  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 55237, resource id:
11869163, major code: 40 (TranslateCoords), minor code: 0  




OpenGL version: 3.3.0 NVIDIA 460.32.03
OpenGL renderer: GeForce GTX 1080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: ASUS
Model: All Series
OS: Ubuntu 16.04 xenial
Architecture: 64bit ELF
Virutal Machine: none
CPU: 16 Intel(R) Core(TM) i7-6900K CPU @ 3.20GHz
Cache Size: 20480 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            62G         19G         14G        464M         28G         41G
	Swap:           15G        3.6G         12G

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:1b80] (rev a1)	
	Subsystem: ASUSTeK Computer Inc. Device [1043:859b]	
	Kernel driver in use: nvidia
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: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    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: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    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: 2.5.2
    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-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    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-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    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: 1.2.1
    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: 1.0.1
    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: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    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: 1.3.1
    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: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    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: 5.0.9
    distlib: 0.3.1
    distro: 1.5.0
    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: 2.0.1
    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
    pexpect: 4.8.0
    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
    ptyprocess: 0.7.0
    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
    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: 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: 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

Change History (2)

comment:1 by pett, 4 years ago

Cc:	pett added
Component:	Unassigned → Sessions
Owner:	set to Greg Couch
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Session tries to restore non-StateManager as StateManager

Seeming duplicate of #3757, and apparently not "fixed by a daily build" of 1.2.

comment:2 by pett, 4 years ago

Will likely have to close as unable to reproduce though.

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