Opened 4 years ago

Closed 4 years ago

#6324 closed defect (duplicate)

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

Reported by: chimerax-bug-report@… 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:        Linux-3.10.0-1160.6.1.el7.x86_64-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  

> open re-chained.pdb

Chain information for re-chained.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
H J | No description available  
K L | No description available  
  

> open 6hup

6hup title:  
CryoEM structure of human full-length alpha1beta3gamma2L GABA(A)R in complex
with diazepam (Valium), GABA and megabody Mb38. [more info...]  
  
Chain information for 6hup #2  
---  
Chain | Description  
A D | Gamma-aminobutyric acid receptor subunit alpha-1,Gamma-aminobutyric acid
receptor subunit alpha-1  
B E | Gamma-aminobutyric acid receptor subunit beta-3  
C | Gamma-aminobutyric acid receptor subunit gamma-2  
G | Megabody Mb38  
  
Non-standard residues in 6hup #2  
---  
ABU — γ-amino-butanoic acid (γ(amino)-butyric acid)  
BMA — beta-D-mannopyranose  
DZP — 7-chloro-1-methyl-5-phenyl-1,3-dihydro-2H-1,4-benzodiazepin-2-one  
MAN — alpha-D-mannopyranose  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
PIO —
[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-
cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (dioctanoyl l-alpha-
phosphatidyl-d-myo-inositol 4,5-diphosphate)  
  

> ui tool show Matchmaker

> matchmaker #!2 to #1 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 | 2  
  
Matchmaker re-chained.pdb, chain D (#1) with 6hup, chain D (#2), sequence
alignment score = 1676.5  
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: re-chained.pdb #1/D, 6hup #2/D  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 334 pruned atom pairs is 0.842 angstroms; (across all 343 pairs:
0.922)  
  

> show cartoons

> hide atoms

> select #2

15265 atoms, 15687 bonds, 6 pseudobonds, 1845 residues, 2 models selected  

> color (#!2 & sel) gray

> ~select #2

Nothing selected  

> open 6x3t

Summary of feedback from opening 6x3t fetched from pdb  
---  
notes | Fetching compressed mmCIF 6x3t from
http://files.rcsb.org/download/6x3t.cif  
Fetching CCD PFL from http://ligand-expo.rcsb.org/reports/P/PFL/PFL.cif  
  
6x3t title:  
Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus
propofol [more info...]  
  
Chain information for 6x3t #3  
---  
Chain | Description  
A C | Gamma-aminobutyric acid receptor subunit beta-2  
B D | Gamma-aminobutyric acid receptor subunit alpha-1  
E | Gamma-aminobutyric acid type A receptor subunit gamma-2  
I L | κ Fab Light Chain  
J K | IgG2b Fab Heavy Chain  
  
Non-standard residues in 6x3t #3  
---  
ABU — γ-amino-butanoic acid (γ(amino)-butyric acid)  
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)  
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
PFL — 2,6-bis(1-methylethyl)phenol (2,6-diisopropylphenol; propofol)  
  

> ui tool show Matchmaker

> matchmaker #3#!2 to #1 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 | 2  
  
Matchmaker re-chained.pdb, chain C (#1) with 6x3t, chain C (#3), sequence
alignment score = 1674.1  
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: re-chained.pdb #1/C, 6x3t #3/C  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2  
RMSD between 318 pruned atom pairs is 0.983 angstroms; (across all 332 pairs:
1.192)  
  
Matchmaker re-chained.pdb, chain D (#1) with 6hup, chain D (#2), sequence
alignment score = 1676.5  
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: re-chained.pdb #1/D, 6hup #2/D  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3  
RMSD between 334 pruned atom pairs is 0.842 angstroms; (across all 343 pairs:
0.922)  
  

> show cartoons

> hide atoms

> select #3

17415 atoms, 17881 bonds, 2148 residues, 1 model selected  

> color sel white

> ~select #3

Nothing selected  

> hide #!1 models

> hide #!2 models

> show #!1 models

> select #3:A-E

3760 atoms, 3412 bonds, 479 residues, 1 model selected  

> save /home/sunch/Phenix/Test/RealSpaceRefine_61/6x3t_gabaar-only.pdb models
> #3 selectedOnly true relModel #1

> select #2:A-E

3493 atoms, 3174 bonds, 1 pseudobond, 428 residues, 2 models selected  

> hide #3 models

> show #!2 models

> save /home/sunch/Phenix/Test/RealSpaceRefine_61/6hup_gabaar-only.pdb models
> #2 selectedOnly true relModel #1

> select #1:A-E

7546 atoms, 7179 bonds, 482 residues, 1 model selected  

> hide #!2 models

> hide #!1 models

> show #!1 models

> select #1:A-E

7546 atoms, 7179 bonds, 482 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> hide sel atoms

> hide sel atoms

> hide sel atoms

> select #1

36428 atoms, 36818 bonds, 5 pseudobonds, 2179 residues, 2 models selected  

> hide #!1 models

> ~select #1

Nothing selected  

> show #!2 models

> select #2:A-E

3493 atoms, 3174 bonds, 1 pseudobond, 428 residues, 2 models selected  

> select #2/A-E

13952 atoms, 14323 bonds, 5 pseudobonds, 1694 residues, 2 models selected  

> save /home/sunch/Phenix/Test/RealSpaceRefine_61/6hup_gabaar-only.pdb
> selectedOnly true relModel #1

> hide #!2 models

> select #2

15265 atoms, 15687 bonds, 6 pseudobonds, 1845 residues, 2 models selected  

> ~select #2

Nothing selected  

> show #3 models

> select #3/A-E

13720 atoms, 14083 bonds, 1683 residues, 1 model selected  
No model chosen to save relative to  

> save /home/sunch/Phenix/Test/RealSpaceRefine_61/6x3t_gabaar-only.pdb
> selectedOnly true relModel #1

> hide #3 models

> select #3

17415 atoms, 17881 bonds, 2148 residues, 1 model selected  

> ~select #3

Nothing selected  

> show #!1 models

> select #1

36428 atoms, 36818 bonds, 5 pseudobonds, 2179 residues, 2 models selected  

> select #1/A-E

27332 atoms, 27688 bonds, 5 pseudobonds, 1679 residues, 2 models selected  

> save /home/sunch/Phenix/Test/RealSpaceRefine_61/re-chained_gabaar-only.pdb
> selectedOnly true relModel #1

> hide #!1 models

> select #1

36428 atoms, 36818 bonds, 5 pseudobonds, 2179 residues, 2 models selected  

> show #!1 models

> ~select #1

Nothing selected  

> show #!2 models

> ui tool show Matchmaker

> select #1/B:222-415

2129 atoms, 2159 bonds, 1 pseudobond, 131 residues, 2 models selected  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>  
data[0] == pself.attr_name and setattr(pself, "value", pself.get_attribute()))  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/ui/options/options.py", line 277, 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 "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/ui/options/options.py", line 277, 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 "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>  
data[0] == pself.attr_name and setattr(pself, "value", pself.get_attribute()))  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/ui/options/options.py", line 277, 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 "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/ui/options/options.py", line 277, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 440.64
OpenGL renderer: GeForce GTX 1070 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Gigabyte Technology Co., Ltd.
Model: Z390 I AORUS PRO WIFI
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         22G        318M        683M        8.0G        7.2G
	Swap:           15G        143M         15G

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104 [GeForce GTX 1070 Ti] [10de:1b82] (rev a1)	
	Subsystem: eVga.com. Corp. Device [3842:5671]	
	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-Clipper: 0.16.0
    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-ISOLDE: 1.2.2
    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 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:2 by Eric Pettersen, 4 years ago

Resolution: → duplicate
Status: accepted → closed

Duplicate of #5207

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