Opened 4 years ago

Closed 4 years ago

#5119 closed defect (can't reproduce)

Matchmaker: 'NoneType' object has no attribute 'setChecked'

Reported by: jonathan.sheehan@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Comparison Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19042
ChimeraX Version: 1.3.dev202108260719 (2021-08-26 07:19:00 UTC)
Description
Restrict to selection checkbox in MatchMaker dialog.

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.3.dev202108260719 (2021-08-26)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> "C:/Users/jonathan.sheehan/Box/projects/vanderbilt/mbgd/mukhtar_macara_exocyst_complex/Yeast
> PDB/5yfp.cif"

5yfp.cif title:  
Cryo-EM Structure of the Exocyst Complex [more info...]  
  
Chain information for 5yfp.cif #1  
---  
Chain | Description | UniProt  
A | Exocyst complex component SEC3 | SEC3_YEAST  
B | Exocyst complex component SEC5 | SEC5_YEAST  
C | Exocyst complex component SEC6 | SEC6_YEAST  
D | Exocyst complex component SEC8 | SEC8_YEAST  
E | Exocyst complex component SEC10 | SEC10_YEAST  
F | Exocyst complex component SEC15 | SEC15_YEAST  
G | Exocyst complex component EXO70 | EXO70_YEAST  
H | Exocyst complex component EXO84 | EXO84_YEAST  
  

> open
> "C:/Users/jonathan.sheehan/Box/projects/vanderbilt/mbgd/mukhtar_macara_exocyst_complex/Human
> Deepmind/Exoc1_Sec3/AF-Q9NV70-F1-model_v1.cif"

Chain information for AF-Q9NV70-F1-model_v1.cif #2  
---  
Chain | Description | UniProt  
A | Exocyst complex component 1 | EXOC1_HUMAN  
  

> select clear

[Repeated 1 time(s)]

> view

> ui tool show Matchmaker

> matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 5yfp.cif, chain C (#1) with AF-Q9NV70-F1-model_v1.cif, chain A
(#2), sequence alignment score = 460.9  
RMSD between 22 pruned atom pairs is 1.013 angstroms; (across all 629 pairs:
55.920)  
  

> view

> open
> "C:/Users/jonathan.sheehan/Box/projects/vanderbilt/mbgd/mukhtar_macara_exocyst_complex/Human
> Deepmind/Exoc2_Sec5/AF-Q96KP1-F1-model_v1.cif"

Chain information for AF-Q96KP1-F1-model_v1.cif #3  
---  
Chain | Description | UniProt  
A | Exocyst complex component 2 | EXOC2_HUMAN  
  

> ui tool show Matchmaker

> matchmaker #3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 5yfp.cif, chain B (#1) with AF-Q96KP1-F1-model_v1.cif, chain A
(#3), sequence alignment score = 787.6  
RMSD between 25 pruned atom pairs is 1.406 angstroms; (across all 769 pairs:
22.221)  
  

> hide #!1 models

> show #!1 models

> open
> "C:/Users/jonathan.sheehan/Box/projects/vanderbilt/mbgd/mukhtar_macara_exocyst_complex/Human
> Deepmind/Exoc3_Sec6/AF-O60645-F1-model_v1.cif"

Chain information for AF-O60645-F1-model_v1.cif #4  
---  
Chain | Description | UniProt  
A | Exocyst complex component 3 | EXOC3_HUMAN  
  

> ui tool show Matchmaker

> matchmaker #4 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 5yfp.cif, chain C (#1) with AF-O60645-F1-model_v1.cif, chain A
(#4), sequence alignment score = 750.4  
RMSD between 66 pruned atom pairs is 1.247 angstroms; (across all 692 pairs:
19.833)  
  

> save
> C:/Users/jonathan.sheehan/Box/projects/vanderbilt/mbgd/mukhtar_macara_exocyst_complex/test/overlaid_first_3.cxs

> close session

> open
> "C:/Users/jonathan.sheehan/Box/projects/vanderbilt/mbgd/mukhtar_macara_exocyst_complex/Yeast
> PDB/5yfp.cif"

5yfp.cif title:  
Cryo-EM Structure of the Exocyst Complex [more info...]  
  
Chain information for 5yfp.cif #1  
---  
Chain | Description | UniProt  
A | Exocyst complex component SEC3 | SEC3_YEAST  
B | Exocyst complex component SEC5 | SEC5_YEAST  
C | Exocyst complex component SEC6 | SEC6_YEAST  
D | Exocyst complex component SEC8 | SEC8_YEAST  
E | Exocyst complex component SEC10 | SEC10_YEAST  
F | Exocyst complex component SEC15 | SEC15_YEAST  
G | Exocyst complex component EXO70 | EXO70_YEAST  
H | Exocyst complex component EXO84 | EXO84_YEAST  
  

> log metadata #1

Metadata for 5yfp.cif #1  
---  
Title | Cryo-EM Structure of the Exocyst Complex  
Citation | Mei, K., Li, Y., Wang, S., Shao, G., Wang, J., Ding, Y., Luo, G.,
Yue, P., Liu, J.J., Wang, X., Dong, M.Q., Wang, H.W., Guo, W. (2018). Cryo-EM
structure of the exocyst complex. Nat. Struct. Mol. Biol., 25, 139-146. PMID:
29335562. DOI: 10.1038/s41594-017-0016-2  
Source (natural) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
(baker's yeast)  
Experimental method | Electron microscopy  
Resolution | 4.40Å  
  
> open
> "C:/Users/jonathan.sheehan/Box/projects/vanderbilt/mbgd/mukhtar_macara_exocyst_complex/Human
> Deepmind/Exoc1_Sec3/AF-Q9NV70-F1-model_v1.cif"

Chain information for AF-Q9NV70-F1-model_v1.cif #2  
---  
Chain | Description | UniProt  
A | Exocyst complex component 1 | EXOC1_HUMAN  
  

> ui tool show Matchmaker

> matchmaker #2 to #1 cutoffDistance 5.0 showAlignment true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 5  
  
Matchmaker 5yfp.cif, chain C (#1) with AF-Q9NV70-F1-model_v1.cif, chain A
(#2), sequence alignment score = 460.9  
Alignment identifier is 1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: 5yfp.cif #1/C,
AF-Q9NV70-F1-model_v1.cif #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 40 pruned atom pairs is 2.865 angstroms; (across all 629 pairs:
57.417)  
  

> view

> select clear

> select

40253 atoms, 40483 bonds, 25 pseudobonds, 6876 residues, 3 models selected  

> style sel sphere

Changed 40253 atom styles  

> style sel sphere

Changed 40253 atom styles  

> show sel cartoons

> hide (#2#!1 & sel) target a

> select clear

> select #1

33096 atoms, 33209 bonds, 25 pseudobonds, 5982 residues, 2 models selected  

> color (#!1 & sel) red

> select clear

> open
> "C:/Users/jonathan.sheehan/Box/projects/vanderbilt/mbgd/mukhtar_macara_exocyst_complex/Human
> Deepmind/Exoc2_Sec5/AF-Q96KP1-F1-model_v1.cif"

Chain information for AF-Q96KP1-F1-model_v1.cif #3  
---  
Chain | Description | UniProt  
A | Exocyst complex component 2 | EXOC2_HUMAN  
  

> ui tool show Matchmaker

> matchmaker #3 to #1 cutoffDistance 5.0 showAlignment true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 5  
  
Matchmaker 5yfp.cif, chain B (#1) with AF-Q96KP1-F1-model_v1.cif, chain A
(#3), sequence alignment score = 787.6  
Alignment identifier is 2  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2  
Hiding conservation header for alignment 2  
Chains used in RMSD evaluation for alignment 2: 5yfp.cif #1/B,
AF-Q96KP1-F1-model_v1.cif #3/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2  
RMSD between 157 pruned atom pairs is 3.511 angstroms; (across all 769 pairs:
21.970)  
  

> ui tool show Matchmaker

[Repeated 1 time(s)]

> open
> "C:/Users/jonathan.sheehan/Box/projects/vanderbilt/mbgd/mukhtar_macara_exocyst_complex/Human
> Deepmind/Exoc3_Sec6/AF-O60645-F1-model_v1.cif"

Chain information for AF-O60645-F1-model_v1.cif #4  
---  
Chain | Description | UniProt  
A | Exocyst complex component 3 | EXOC3_HUMAN  
  

> matchmaker #4 to #1 cutoffDistance 5.0 showAlignment true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 5  
  
Matchmaker 5yfp.cif, chain C (#1) with AF-O60645-F1-model_v1.cif, chain A
(#4), sequence alignment score = 750.4  
Alignment identifier is 3  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3  
Hiding conservation header for alignment 3  
Chains used in RMSD evaluation for alignment 3: 5yfp.cif #1/C,
AF-O60645-F1-model_v1.cif #4/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3  
RMSD between 232 pruned atom pairs is 3.087 angstroms; (across all 692 pairs:
18.179)  
  

> select /A:611-1332

9179 atoms, 9277 bonds, 4 pseudobonds, 1405 residues, 5 models selected  

> hide #2 models

> hide #3 models

> hide #4 models

> show #3 models

> show #4 models

> show #2 models

> select clear

> ui tool show Matchmaker

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3.dev202108260719\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.3.dev202108260719\bin\lib\site-
packages\chimerax\ui\options\options.py", line 50, in <lambda>  
data[0] == pself.attr_name and setattr(pself, "value", pself.get_attribute()))  
File "C:\Program Files\ChimeraX 1.3.dev202108260719\bin\lib\site-
packages\chimerax\ui\options\options.py", line 339, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "C:\Program Files\ChimeraX 1.3.dev202108260719\bin\lib\site-
packages\chimerax\ui\options\options.py", line 339, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3.dev202108260719\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.3.dev202108260719\bin\lib\site-
packages\chimerax\ui\options\options.py", line 50, in <lambda>  
data[0] == pself.attr_name and setattr(pself, "value", pself.get_attribute()))  
File "C:\Program Files\ChimeraX 1.3.dev202108260719\bin\lib\site-
packages\chimerax\ui\options\options.py", line 339, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "C:\Program Files\ChimeraX 1.3.dev202108260719\bin\lib\site-
packages\chimerax\ui\options\options.py", line 339, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 24.20.100.6286
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel
Manufacturer: Dell Inc.
Model: Latitude 7490
OS: Microsoft Windows 10 Enterprise (Build 19042)
Memory: 34,233,217,024
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-8650U CPU @ 1.90GHz
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: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.0
    chardet: 4.0.0
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.29
    ChimeraX-AtomicLibrary: 4.1.3
    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: 2.5.3
    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: 1.4
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202108260719
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.4
    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: 2.1.1
    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-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
    ChimeraX-MDcrds: 2.5
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.1
    ChimeraX-ModelPanel: 1.1
    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
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
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    ChimeraX-PubChem: 2.1
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    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: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.2
    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
    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: 1.11.1
    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
    comtypes: 1.1.10
    cxservices: 1.0.1
    cycler: 0.10.0
    Cython: 0.29.23
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.4.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.20
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 2.11.3
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    kiwisolver: 1.3.1
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 1.1.1
    matplotlib: 3.4.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.2
    netCDF4: 1.5.6
    networkx: 2.6.2
    numexpr: 2.7.3
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    openvr: 1.16.801
    packaging: 21.0
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    parso: 0.8.2
    pickleshare: 0.7.5
    Pillow: 8.2.0
    pip: 21.1.1
    pkginfo: 1.7.0
    prompt-toolkit: 3.0.20
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.9.0
    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: 22.2.1
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    QtPy: 1.10.0
    RandomWords: 0.3.0
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    scipy: 1.6.3
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    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.2
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (3)

in reply to:  1 ; comment:1 by jonathan.sheehan@…, 4 years ago 

Aaah- sorry- I made a mistake in my report. That error message occurred after I selected the button to "Specify a chain to match on" ... NOT "Restrict to selection" as I typed above.

And then the MatchMaker operation seemed to go ahead fine, anyway. So no worries.  :-)

Thanks,
-Jonathan

______________________________________________________________
Jonathan Sheehan PhD (he,him) | Assoc. Prof. | Div. Infectious Diseases​
660 South Euclid | Campus Box 8051 | St. Louis, MO 63110​
10621 BJCIH bldg. | (314) 273-8368 | https://sheehanlab.wustl.edu/​
Personalized Structural Biology​
Washington University School of Medicine, St. Louis

________________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Friday, August 27, 2021 3:30 PM
To: Sheehan, Jonathan
Subject: [ChimeraX] #5119: ChimeraX bug report submission

* External Email - Caution *

#5119: ChimeraX bug report submission
--------------------------------+-----------------------------
 Reporter:  jonathan.sheehan@…  |                Type:  defect
   Status:  new                 |            Priority:  normal
Component:  Unassigned          |          Blocked By:
 Blocking:                      |  Notify when closed:
--------------------------------+-----------------------------
 {{{
 The following bug report has been submitted:
 Platform:        Windows-10-10.0.19042
 ChimeraX Version: 1.3.dev202108260719 (2021-08-26 07:19:00 UTC)
 Description
 Restrict to selection checkbox in MatchMaker dialog.

 Log:
 Startup Messages
 ---
 note | available bundle cache has not been initialized yet

 UCSF ChimeraX version: 1.3.dev202108260719 (2021-08-26)
 © 2016-2021 Regents of the University of California. All rights reserved.
 How to cite UCSF ChimeraX

 > open
 >
 "C:/Users/jonathan.sheehan/Box/projects/vanderbilt/mbgd/mukhtar_macara_exocyst_complex/Yeast
 > PDB/5yfp.cif"

 5yfp.cif title:
 Cryo-EM Structure of the Exocyst Complex [more info...]

 Chain information for 5yfp.cif #1
 ---
 Chain | Description | UniProt
 A | Exocyst complex component SEC3 | SEC3_YEAST
 B | Exocyst complex component SEC5 | SEC5_YEAST
 C | Exocyst complex component SEC6 | SEC6_YEAST
 D | Exocyst complex component SEC8 | SEC8_YEAST
 E | Exocyst complex component SEC10 | SEC10_YEAST
 F | Exocyst complex component SEC15 | SEC15_YEAST
 G | Exocyst complex component EXO70 | EXO70_YEAST
 H | Exocyst complex component EXO84 | EXO84_YEAST


 > open
 >
 "C:/Users/jonathan.sheehan/Box/projects/vanderbilt/mbgd/mukhtar_macara_exocyst_complex/Human
 > Deepmind/Exoc1_Sec3/AF-Q9NV70-F1-model_v1.cif"

 Chain information for AF-Q9NV70-F1-model_v1.cif #2
 ---
 Chain | Description | UniProt
 A | Exocyst complex component 1 | EXOC1_HUMAN


 > select clear

 [Repeated 1 time(s)]

 > view

 > ui tool show Matchmaker

 > matchmaker #2 to #1

 Parameters
 ---
 Chain pairing | bb
 Alignment algorithm | Needleman-Wunsch
 Similarity matrix | BLOSUM-62
 SS fraction | 0.3
 Gap open (HH/SS/other) | 18/18/6
 Gap extend | 1
 SS matrix |  |  | H | S | O
 ---|---|---|---
 H | 6 | -9 | -6
 S |  | 6 | -6
 O |  |  | 4
 Iteration cutoff | 2

 Matchmaker 5yfp.cif, chain C (#1) with AF-Q9NV70-F1-model_v1.cif, chain A
 (#2), sequence alignment score = 460.9
 RMSD between 22 pruned atom pairs is 1.013 angstroms; (across all 629
 pairs:
 55.920)


 > view

 > open
 >
 "C:/Users/jonathan.sheehan/Box/projects/vanderbilt/mbgd/mukhtar_macara_exocyst_complex/Human
 > Deepmind/Exoc2_Sec5/AF-Q96KP1-F1-model_v1.cif"

 Chain information for AF-Q96KP1-F1-model_v1.cif #3
 ---
 Chain | Description | UniProt
 A | Exocyst complex component 2 | EXOC2_HUMAN


 > ui tool show Matchmaker

 > matchmaker #3 to #1

 Parameters
 ---
 Chain pairing | bb
 Alignment algorithm | Needleman-Wunsch
 Similarity matrix | BLOSUM-62
 SS fraction | 0.3
 Gap open (HH/SS/other) | 18/18/6
 Gap extend | 1
 SS matrix |  |  | H | S | O
 ---|---|---|---
 H | 6 | -9 | -6
 S |  | 6 | -6
 O |  |  | 4
 Iteration cutoff | 2

 Matchmaker 5yfp.cif, chain B (#1) with AF-Q96KP1-F1-model_v1.cif, chain A
 (#3), sequence alignment score = 787.6
 RMSD between 25 pruned atom pairs is 1.406 angstroms; (across all 769
 pairs:
 22.221)


 > hide #!1 models

 > show #!1 models

 > open
 >
 "C:/Users/jonathan.sheehan/Box/projects/vanderbilt/mbgd/mukhtar_macara_exocyst_complex/Human
 > Deepmind/Exoc3_Sec6/AF-O60645-F1-model_v1.cif"

 Chain information for AF-O60645-F1-model_v1.cif #4
 ---
 Chain | Description | UniProt
 A | Exocyst complex component 3 | EXOC3_HUMAN


 > ui tool show Matchmaker

 > matchmaker #4 to #1

 Parameters
 ---
 Chain pairing | bb
 Alignment algorithm | Needleman-Wunsch
 Similarity matrix | BLOSUM-62
 SS fraction | 0.3
 Gap open (HH/SS/other) | 18/18/6
 Gap extend | 1
 SS matrix |  |  | H | S | O
 ---|---|---|---
 H | 6 | -9 | -6
 S |  | 6 | -6
 O |  |  | 4
 Iteration cutoff | 2

 Matchmaker 5yfp.cif, chain C (#1) with AF-O60645-F1-model_v1.cif, chain A
 (#4), sequence alignment score = 750.4
 RMSD between 66 pruned atom pairs is 1.247 angstroms; (across all 692
 pairs:
 19.833)


 > save
 >
 C:/Users/jonathan.sheehan/Box/projects/vanderbilt/mbgd/mukhtar_macara_exocyst_complex/test/overlaid_first_3.cxs

 > close session

 > open
 >
 "C:/Users/jonathan.sheehan/Box/projects/vanderbilt/mbgd/mukhtar_macara_exocyst_complex/Yeast
 > PDB/5yfp.cif"

 5yfp.cif title:
 Cryo-EM Structure of the Exocyst Complex [more info...]

 Chain information for 5yfp.cif #1
 ---
 Chain | Description | UniProt
 A | Exocyst complex component SEC3 | SEC3_YEAST
 B | Exocyst complex component SEC5 | SEC5_YEAST
 C | Exocyst complex component SEC6 | SEC6_YEAST
 D | Exocyst complex component SEC8 | SEC8_YEAST
 E | Exocyst complex component SEC10 | SEC10_YEAST
 F | Exocyst complex component SEC15 | SEC15_YEAST
 G | Exocyst complex component EXO70 | EXO70_YEAST
 H | Exocyst complex component EXO84 | EXO84_YEAST


 > log metadata #1

 Metadata for 5yfp.cif #1
 ---
 Title | Cryo-EM Structure of the Exocyst Complex
 Citation | Mei, K., Li, Y., Wang, S., Shao, G., Wang, J., Ding, Y., Luo,
 G.,
 Yue, P., Liu, J.J., Wang, X., Dong, M.Q., Wang, H.W., Guo, W. (2018).
 Cryo-EM
 structure of the exocyst complex. Nat. Struct. Mol. Biol., 25, 139-146.
 PMID:
 29335562. DOI: 10.1038/s41594-017-0016-2
 Source (natural) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
 (baker's yeast)
 Experimental method | Electron microscopy
 Resolution | 4.40Å

 > open
 >
 "C:/Users/jonathan.sheehan/Box/projects/vanderbilt/mbgd/mukhtar_macara_exocyst_complex/Human
 > Deepmind/Exoc1_Sec3/AF-Q9NV70-F1-model_v1.cif"

 Chain information for AF-Q9NV70-F1-model_v1.cif #2
 ---
 Chain | Description | UniProt
 A | Exocyst complex component 1 | EXOC1_HUMAN


 > ui tool show Matchmaker

 > matchmaker #2 to #1 cutoffDistance 5.0 showAlignment true

 Parameters
 ---
 Chain pairing | bb
 Alignment algorithm | Needleman-Wunsch
 Similarity matrix | BLOSUM-62
 SS fraction | 0.3
 Gap open (HH/SS/other) | 18/18/6
 Gap extend | 1
 SS matrix |  |  | H | S | O
 ---|---|---|---
 H | 6 | -9 | -6
 S |  | 6 | -6
 O |  |  | 4
 Iteration cutoff | 5

 Matchmaker 5yfp.cif, chain C (#1) with AF-Q9NV70-F1-model_v1.cif, chain A
 (#2), sequence alignment score = 460.9
 Alignment identifier is 1
 Showing conservation header ("seq_conservation" residue attribute) for
 alignment 1
 Hiding conservation header for alignment 1
 Chains used in RMSD evaluation for alignment 1: 5yfp.cif #1/C,
 AF-Q9NV70-F1-model_v1.cif #2/A
 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
 RMSD between 40 pruned atom pairs is 2.865 angstroms; (across all 629
 pairs:
 57.417)


 > view

 > select clear

 > select

 40253 atoms, 40483 bonds, 25 pseudobonds, 6876 residues, 3 models selected

 > style sel sphere

 Changed 40253 atom styles

 > style sel sphere

 Changed 40253 atom styles

 > show sel cartoons

 > hide (#2#!1 & sel) target a

 > select clear

 > select #1

 33096 atoms, 33209 bonds, 25 pseudobonds, 5982 residues, 2 models selected

 > color (#!1 & sel) red

 > select clear

 > open
 >
 "C:/Users/jonathan.sheehan/Box/projects/vanderbilt/mbgd/mukhtar_macara_exocyst_complex/Human
 > Deepmind/Exoc2_Sec5/AF-Q96KP1-F1-model_v1.cif"

 Chain information for AF-Q96KP1-F1-model_v1.cif #3
 ---
 Chain | Description | UniProt
 A | Exocyst complex component 2 | EXOC2_HUMAN


 > ui tool show Matchmaker

 > matchmaker #3 to #1 cutoffDistance 5.0 showAlignment true

 Parameters
 ---
 Chain pairing | bb
 Alignment algorithm | Needleman-Wunsch
 Similarity matrix | BLOSUM-62
 SS fraction | 0.3
 Gap open (HH/SS/other) | 18/18/6
 Gap extend | 1
 SS matrix |  |  | H | S | O
 ---|---|---|---
 H | 6 | -9 | -6
 S |  | 6 | -6
 O |  |  | 4
 Iteration cutoff | 5

 Matchmaker 5yfp.cif, chain B (#1) with AF-Q96KP1-F1-model_v1.cif, chain A
 (#3), sequence alignment score = 787.6
 Alignment identifier is 2
 Showing conservation header ("seq_conservation" residue attribute) for
 alignment 2
 Hiding conservation header for alignment 2
 Chains used in RMSD evaluation for alignment 2: 5yfp.cif #1/B,
 AF-Q96KP1-F1-model_v1.cif #3/A
 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
 RMSD between 157 pruned atom pairs is 3.511 angstroms; (across all 769
 pairs:
 21.970)


 > ui tool show Matchmaker

 [Repeated 1 time(s)]

 > open
 >
 "C:/Users/jonathan.sheehan/Box/projects/vanderbilt/mbgd/mukhtar_macara_exocyst_complex/Human
 > Deepmind/Exoc3_Sec6/AF-O60645-F1-model_v1.cif"

 Chain information for AF-O60645-F1-model_v1.cif #4
 ---
 Chain | Description | UniProt
 A | Exocyst complex component 3 | EXOC3_HUMAN


 > matchmaker #4 to #1 cutoffDistance 5.0 showAlignment true

 Parameters
 ---
 Chain pairing | bb
 Alignment algorithm | Needleman-Wunsch
 Similarity matrix | BLOSUM-62
 SS fraction | 0.3
 Gap open (HH/SS/other) | 18/18/6
 Gap extend | 1
 SS matrix |  |  | H | S | O
 ---|---|---|---
 H | 6 | -9 | -6
 S |  | 6 | -6
 O |  |  | 4
 Iteration cutoff | 5

 Matchmaker 5yfp.cif, chain C (#1) with AF-O60645-F1-model_v1.cif, chain A
 (#4), sequence alignment score = 750.4
 Alignment identifier is 3
 Showing conservation header ("seq_conservation" residue attribute) for
 alignment 3
 Hiding conservation header for alignment 3
 Chains used in RMSD evaluation for alignment 3: 5yfp.cif #1/C,
 AF-O60645-F1-model_v1.cif #4/A
 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3
 RMSD between 232 pruned atom pairs is 3.087 angstroms; (across all 692
 pairs:
 18.179)


 > select /A:611-1332

 9179 atoms, 9277 bonds, 4 pseudobonds, 1405 residues, 5 models selected

 > hide #2 models

 > hide #3 models

 > hide #4 models

 > show #3 models

 > show #4 models

 > show #2 models

 > select clear

 > ui tool show Matchmaker

 Traceback (most recent call last):
 File "C:\Program Files\ChimeraX 1.3.dev202108260719\bin\lib\site-
 packages\chimerax\core\triggerset.py", line 134, in invoke
 return self._func(self._name, data)
 File "C:\Program Files\ChimeraX 1.3.dev202108260719\bin\lib\site-
 packages\chimerax\ui\options\options.py", line 50, in <lambda>
 data[0] == pself.attr_name and setattr(pself, "value",
 pself.get_attribute()))
 File "C:\Program Files\ChimeraX 1.3.dev202108260719\bin\lib\site-
 packages\chimerax\ui\options\options.py", line 339, in set_value
 self.__button_group.button(self.values.index(value)).setChecked(True)
 AttributeError: 'NoneType' object has no attribute 'setChecked'

 Error processing trigger "setting changed":
 AttributeError: 'NoneType' object has no attribute 'setChecked'

 File "C:\Program Files\ChimeraX 1.3.dev202108260719\bin\lib\site-
 packages\chimerax\ui\options\options.py", line 339, in set_value
 self.__button_group.button(self.values.index(value)).setChecked(True)

 See log for complete Python traceback.

 Traceback (most recent call last):
 File "C:\Program Files\ChimeraX 1.3.dev202108260719\bin\lib\site-
 packages\chimerax\core\triggerset.py", line 134, in invoke
 return self._func(self._name, data)
 File "C:\Program Files\ChimeraX 1.3.dev202108260719\bin\lib\site-
 packages\chimerax\ui\options\options.py", line 50, in <lambda>
 data[0] == pself.attr_name and setattr(pself, "value",
 pself.get_attribute()))
 File "C:\Program Files\ChimeraX 1.3.dev202108260719\bin\lib\site-
 packages\chimerax\ui\options\options.py", line 339, in set_value
 self.__button_group.button(self.values.index(value)).setChecked(True)
 AttributeError: 'NoneType' object has no attribute 'setChecked'

 Error processing trigger "setting changed":
 AttributeError: 'NoneType' object has no attribute 'setChecked'

 File "C:\Program Files\ChimeraX 1.3.dev202108260719\bin\lib\site-
 packages\chimerax\ui\options\options.py", line 339, in set_value
 self.__button_group.button(self.values.index(value)).setChecked(True)

 See log for complete Python traceback.





 OpenGL version: 3.3.0 - Build 24.20.100.6286
 OpenGL renderer: Intel(R) UHD Graphics 620
 OpenGL vendor: Intel
 Manufacturer: Dell Inc.
 Model: Latitude 7490
 OS: Microsoft Windows 10 Enterprise (Build 19042)
 Memory: 34,233,217,024
 MaxProcessMemory: 137,438,953,344
 CPU: 8 Intel(R) Core(TM) i7-8650U CPU @ 1.90GHz
 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: 2.9.1
     backcall: 0.2.0
     blockdiag: 2.0.1
     certifi: 2021.5.30
     cftime: 1.5.0
     chardet: 4.0.0
     ChimeraX-AddCharge: 1.1.4
     ChimeraX-AddH: 2.1.10
     ChimeraX-AlignmentAlgorithms: 2.0
     ChimeraX-AlignmentHdrs: 3.2
     ChimeraX-AlignmentMatrices: 2.0
     ChimeraX-Alignments: 2.2.2
     ChimeraX-AlphaFold: 1.0
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     ChimeraX-AtomicLibrary: 4.1.3
     ChimeraX-AtomSearch: 2.0
     ChimeraX-AtomSearchLibrary: 1.0
     ChimeraX-AxesPlanes: 2.0
     ChimeraX-BasicActions: 1.1
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     ChimeraX-CageBuilder: 1.0
     ChimeraX-CellPack: 1.0
     ChimeraX-Centroids: 1.1
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     ChimeraX-Clashes: 2.1
     ChimeraX-ColorActions: 1.0
     ChimeraX-ColorGlobe: 1.0
     ChimeraX-ColorKey: 1.4
     ChimeraX-CommandLine: 1.1.5
     ChimeraX-ConnectStructure: 2.0
     ChimeraX-Contacts: 1.0
     ChimeraX-Core: 1.3.dev202108260719
     ChimeraX-CoreFormats: 1.1
     ChimeraX-coulombic: 1.3
     ChimeraX-Crosslinks: 1.0
     ChimeraX-Crystal: 1.0
     ChimeraX-CrystalContacts: 1.0
     ChimeraX-DataFormats: 1.2.1
     ChimeraX-Dicom: 1.0
     ChimeraX-DistMonitor: 1.1.4
     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: 2.1.1
     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-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
     ChimeraX-MDcrds: 2.5
     ChimeraX-MedicalToolbar: 1.0.1
     ChimeraX-Meeting: 1.0
     ChimeraX-MLP: 1.1
     ChimeraX-mmCIF: 2.4
     ChimeraX-MMTF: 2.1
     ChimeraX-Modeller: 1.1
     ChimeraX-ModelPanel: 1.1
     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
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     ChimeraX-PDBLibrary: 1.0.1
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     ChimeraX-RotamerLibsDunbrack: 2.0
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     ChimeraX-RotamerLibsRichardson: 2.0
     ChimeraX-SaveCommand: 1.5
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     ChimeraX-SDF: 2.0
     ChimeraX-Segger: 1.0
     ChimeraX-Segment: 1.0
     ChimeraX-SelInspector: 1.0
     ChimeraX-SeqView: 2.4.2
     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
     ChimeraX-STL: 1.0
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     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: 1.11.1
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     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
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     cycler: 0.10.0
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     decorator: 5.0.9
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     funcparserlib: 0.3.6
     grako: 3.16.5
     h5py: 3.4.0
     html2text: 2020.1.16
     idna: 2.10
     ihm: 0.20
     imagecodecs: 2021.4.28
     imagesize: 1.2.0
     ipykernel: 5.5.5
     ipython: 7.23.1
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     Jinja2: 2.11.3
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     lxml: 4.6.3
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     netCDF4: 1.5.6
     networkx: 2.6.2
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     PyQt5-commercial: 5.15.2
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     PyQtWebEngine-commercial: 5.15.2
     python-dateutil: 2.8.1
     pytz: 2021.1
     pywin32: 228
     pyzmq: 22.2.1
     qtconsole: 5.1.0
     QtPy: 1.10.0
     RandomWords: 0.3.0
     requests: 2.25.1
     scipy: 1.6.3
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     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: 5.0.5
     urllib3: 1.26.6
     wcwidth: 0.2.5
     webcolors: 1.11.1
     wheel: 0.36.2
     wheel-filename: 1.3.0
     WMI: 1.5.1

 }}}

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5119>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

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comment:2 by Eric Pettersen, 4 years ago

Component: Unassigned → Structure Comparison
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Matchmaker: 'NoneType' object has no attribute 'setChecked'

comment:3 by Eric Pettersen, 4 years ago

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

Hi Jonathan,

Thanks for reporting this problem. I have tried various things and have been unable to reproduce it. Given that it seems otherwise harmless, I guess I will close this ticket. Please feel free to report it if it happens again though.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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