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#7800 closed defect (can't reproduce)

Tool instance→windows map out of date

Reported by:	chimerax-bug-report@…	Owned by:	Eric Pettersen
Priority:	normal	Milestone:
Component:	UI	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Linux-3.10.0-862.el7.x86_64-x86_64-with-glibc2.17
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)

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 Relion.mrc

Opened Relion.mrc as #1, grid size 256,256,256, pixel 1.08, shown at level
0.0212, step 1, values float32  

> view orient

> turn x 90

> turn x -90

[Repeated 1 time(s)]

> turn y 30

> turn y -30

[Repeated 1 time(s)]

> turn y 10

> turn y -5

> volume #1 level 0.01758

> volume #1 level 0.015

> open
> /sailab4/sailab/sai/figures/figure2021-1220-cov2_Delta/spa_model/model_20220601.pdb

Summary of feedback from opening
/sailab4/sailab/sai/figures/figure2021-1220-cov2_Delta/spa_model/model_20220601.pdb  
---  
warnings | Ignored bad PDB record found on line 16171  
  
  
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  
16163 messages similar to the above omitted  
Ignored bad PDB record found on line 32341  
  
  
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  
16163 messages similar to the above omitted  
Ignored bad PDB record found on line 48511  
  
  
Ignored bad PDB record found on line 48512  
  
Chain information for model_20220601.pdb #2  
---  
Chain | Description  
A B C | No description available  
  

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> ui tool show "Volume Viewer"

> ui tool show "Hide Dust"

> surface dust #1 size 18.75

> transparency 50

> volume #1 level 0.016

> ui tool show "Color Actions"

> color bychain

> ui tool show "Segment Map"

> ui tool show "Surface Color"

> ui tool show "Color Zone"

Need to color zone map before it can be split  

> color zone #1 near #2 distance 6.49

> volume splitbyzone #1

Opened Relion.mrc 0 as #3.1, grid size 256,256,256, pixel 1.08, shown at level
0.016, step 1, values float32  
Opened Relion.mrc 1 as #3.2, grid size 256,256,256, pixel 1.08, shown at level
0.016, step 1, values float32  
Opened Relion.mrc 2 as #3.3, grid size 256,256,256, pixel 1.08, shown at level
0.016, step 1, values float32  
Opened Relion.mrc 3 as #3.4, grid size 256,256,256, pixel 1.08, shown at level
0.016, step 1, values float32  

> hide #!3 models

> show #!3 models

> hide #!3.1 models

> hide #!3.2 models

> show #!3.2 models

> hide #!3.3 models

> hide #!3.4 models

> show #!3.4 models

> hide #!3.4 models

> show #!3.4 models

> color #3.3 #b2b2b2 models transparency 0

> color #3.4 #b2b2b2 models transparency 0

> color #3.2 #b2b2b2 models transparency 0

> hide #!3 models

> show #!3 models

> show #!3.1 models

> hide #!3.1 models

> show #!3.1 models

> hide #!3.1 models

> show #!3.3 models

> hide #!3.3 models

> show #!3.3 models

> hide #!3.3 models

> hide #!3.2 models

> show #!3.2 models

> hide #!3.4 models

> show #!3.4 models

> transparency #3.2.1#3.4.1 50

> transparency #

Missing or invalid "percent" argument: Expected a number  

> transparency #3

Missing or invalid "percent" argument: Expected a number  

> transparency #3 0

> transparency #3.1 50

> hide #!3.4 models

> show #!3.4 models

> transparency #3.4 50

> select clear

> hide #!3.4 models

> show #!3.4 models

> color #3.4 white models transparency 0

> transparency #3.4 50

> select clear

> hide #!3 models

> hide #!2 models

> show #!2 models

> show #!1 models

> hide #!1 models

> show #!1 models

> color single #1

> hide #!1 models

> show #!3 models

> show #!1 models

> hide #!1 models

> close #3

> show #!1 models

> color zone #1 near #2 distance 6.49

> volume splitbyzone #1

Opened Relion.mrc 0 as #3.1, grid size 256,256,256, pixel 1.08, shown at level
0.016, step 1, values float32  
Opened Relion.mrc 1 as #3.2, grid size 256,256,256, pixel 1.08, shown at level
0.016, step 1, values float32  
Opened Relion.mrc 2 as #3.3, grid size 256,256,256, pixel 1.08, shown at level
0.016, step 1, values float32  
Opened Relion.mrc 3 as #3.4, grid size 256,256,256, pixel 1.08, shown at level
0.016, step 1, values float32  

> hide #!3 models

> show #!3 models

> hide #!3.1 models

> hide #!3.2 models

> show #!3.2 models

> hide #!3.3 models

> transparency #3.4 50

> transparency #3.3 50

> transparency #3.2 50

> hide #!3.2 models

> color #2@a yellow

> color #2/A yellow

> color #2/A Dodger blue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color #2/A Dodger Blue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color #2/A 'Dodger Blue'

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color #2/A#2E86C1

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color #2/A #2E86C1

> select clear

> color #2/A #F7DC6F

> color zone #1 near #2 distance 6.49

> show #!1 models

> hide #!3 models

> show #!3 models

> hide #!2 models

> hide #!1 models

> hide #2.1 models

> hide #!3 models

> hide #!3.4 models

> show #!2 models

> color #2/C #2E86C1

> select clear

> show #!1 models

> color zone #1 near #2 distance 6.49

> color #2/C #AED6F1

> hide #!1 models

> color #2/C #5DADE2

> select clear

> color zone #1 near #2 distance 6.49

> show #!1 models

> color #2/C #2874A6

> color zone #1 near #2 distance 6.49

> select clear

> color #2/C #5499C7

> color zone #1 near #2 distance 6.49

> select clear

> hide #!1 models

> show #!1 models

> color zone #1 near #2 distance 67.75

[Repeated 5 time(s)]Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 2251, in <lambda>  
dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 648, in close_request  
all_windows = self.tool_instance_to_windows[tool_instance]  
KeyError: <chimerax.help_viewer.tool.HelpUI object at 0x7fcc22275670>  
  
KeyError:  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 648, in close_request  
all_windows = self.tool_instance_to_windows[tool_instance]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 2251, in <lambda>  
dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 648, in close_request  
all_windows = self.tool_instance_to_windows[tool_instance]  
KeyError: <chimerax.help_viewer.tool.HelpUI object at 0x7fcc22275670>  
  
KeyError:  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 648, in close_request  
all_windows = self.tool_instance_to_windows[tool_instance]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 2251, in <lambda>  
dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 648, in close_request  
all_windows = self.tool_instance_to_windows[tool_instance]  
KeyError: <chimerax.help_viewer.tool.HelpUI object at 0x7fcc22275670>  
  
KeyError:  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 648, in close_request  
all_windows = self.tool_instance_to_windows[tool_instance]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 2251, in <lambda>  
dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 648, in close_request  
all_windows = self.tool_instance_to_windows[tool_instance]  
KeyError: <chimerax.help_viewer.tool.HelpUI object at 0x7fcc22275670>  
  
KeyError:  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 648, in close_request  
all_windows = self.tool_instance_to_windows[tool_instance]  
  
See log for complete Python traceback.  
  

QMainWindowLayout::tabPosition called with out-of-bounds value '0'  

> save /sailab4/sailab/songyt/figure/Delta/spa_map/20221015_spa.cxs
> includeMaps true

> show #!3.2 models

> hide #!1 models

> show #!3.3 models

> show #!3.4 models

> hide #!3.4 models

> show #!3.4 models

> hide #!3.3 models

> hide #!3.4 models

> show #!3.4 models

> hide #!3 models

> show #!3 models

> color #2 #ef2929 transparency 0

> color #2 #c4a000 transparency 0

> hide #!3.2 models

> color #3.2 #b2b2b280 models

> show #!3.2 models

> show #!3.3 models

> color #3.3 #babdb6 models transparency 0

[Repeated 1 time(s)]

> color #3.4 #b2b2b280 models

> color #3.2 #d3d7cf models transparency 0

> color #3.2 #babdb6 models transparency 0

[Repeated 1 time(s)]

> hide #!3.4 models

> color #3.2 #babdb6 models transparency 0

[Repeated 1 time(s)]

> color #3.3 #b2b2b280 models




OpenGL version: 3.3.0 NVIDIA 450.80.02
OpenGL renderer: GeForce RTX 2080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision 3630 Tower
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 8 Intel(R) Core(TM) i7-9700K CPU @ 3.60GHz
Cache Size: 12288 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            31G        2.5G         24G         16M        3.6G         28G
	Swap:          124G          0B        124G

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU104 [GeForce RTX 2080] [10de:1e82] (rev a1)	
	Subsystem: Device [7377:0000]	
	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: 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

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Component:	Unassigned → UI
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → Tool instance→windows map out of date

comment:2 by Eric Pettersen, 3 years ago

Resolution:	→ can't reproduce
Status:	accepted → closed

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