Opened 5 years ago

Closed 5 years ago

#4600 closed defect (duplicate)

MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ChainMenuButton has been deleted

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-3.10.0-1062.1.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /mnt/lab-microe20/xhan/Downloads/ResolveCryoEM_9/denmod_map_job240.ccp4
> format ccp4

Opened denmod_map_job240.ccp4, grid size 139,135,129, pixel 1.09, shown at
level 0.324, step 1, values float32  

> open "/home/CICBIOGUNE/xhan/Downloads/model from galaxy.pdb" format pdb

Chain information for model from galaxy.pdb #2  
---  
Chain | Description  
A | No description available  
  

> open /home/CICBIOGUNE/xhan/Downloads/symmetry_from_map_octomater.pdb format
> pdb

Chain information for symmetry_from_map_octomater.pdb #3  
---  
Chain | Description  
A B C D E F G H | No description available  
  

> ui tool show Matchmaker

> matchmaker #2/A to #3/A pairing ss

Parameters  
---  
Chain pairing | ss  
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 symmetry_from_map_octomater.pdb, chain A (#3) with model from
galaxy.pdb, chain A (#2), sequence alignment score = 2561.8  
RMSD between 490 pruned atom pairs is 0.882 angstroms; (across all 514 pairs:
1.038)  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> hide #3 models

> ui tool show "Fit in Map"

Fit molecule model from galaxy.pdb (#2) to map denmod_map_job240.ccp4 (#1)
using 4962 atoms  
average map value = 0.09531, steps = 112  
shifted from previous position = 0.656  
rotated from previous position = 1.69 degrees  
atoms outside contour = 4409, contour level = 0.32418  
  
Position of model from galaxy.pdb (#2) relative to denmod_map_job240.ccp4 (#1)
coordinates:  
Matrix rotation and translation  
-0.26666287 -0.02821675 -0.96337673 102.51173725  
0.34359595 -0.93667616 -0.06767273 156.46453738  
-0.90046251 -0.34905815 0.25947191 271.05371789  
Axis -0.59804213 -0.13371465 0.79023161  
Axis point 140.67890466 114.86029716 0.00000000  
Rotation angle (degrees) 166.39331466  
Shift along axis 131.96727805  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> show #3 models

> hide #3 models

> close #3

Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> isolde start

> set selectionWidth 4

Chain information for model from galaxy.pdb  
---  
Chain | Description  
2.2/A | No description available  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Done loading forcefield  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 418.87.00
OpenGL renderer: Quadro K4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Hewlett-Packard
Model: HP Z420 Workstation
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 8 Intel(R) Xeon(R) CPU E5-1620 v2 @ 3.70GHz
Cache Size: 10240 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            31G         18G        4.9G        188M        7.3G         11G
	Swap:           15G        3.8M         15G

Graphics:
	05:00.0 VGA compatible controller [0300]: NVIDIA Corporation GK106GL [Quadro K4000] [10de:11fa] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:097c]	
	Kernel driver in use: nvidia
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-Clipper: 0.15.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    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: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-ISOLDE: 1.1.0
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    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: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    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
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    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: 0.29.20
    decorator: 4.4.2
    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: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

Change History (2)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Structure Comparison
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ChainMenuButton has been deleted

comment:2 by Eric Pettersen, 5 years ago

Resolution: → duplicate
Status: accepted → closed
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