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

[stefan.knight@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3.dev202104230049 (2021-04-23 00:49:01 UTC)
Description
Runnin matchmaker

Log:
UCSF ChimeraX version: 1.3.dev202104230049 (2021-04-23)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/stefan/Dropbox/MdTMPK/Refine_209/MdTMPK_refine_209.pdb format
> pdb

Summary of feedback from opening
/Users/stefan/Dropbox/MdTMPK/Refine_209/MdTMPK_refine_209.pdb  
---  
warning | Ignored bad PDB record found on line 61  
  
Chain information for MdTMPK_refine_209.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  

> preset cartoons/nucleotides cylinders/stubs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> select add /B

3011 atoms, 3035 bonds, 2 pseudobonds, 199 residues, 2 models selected  

> select add /D

4801 atoms, 4835 bonds, 10 pseudobonds, 319 residues, 2 models selected  

> hide sel cartoons

Drag select of 21 atoms, 22 bonds  

> hide sel atoms

> ui mousemode right zoom

> interfaces sel & ~solvent

0 buried areas:  
Drag select of 21 atoms, 379 residues, 10 pseudobonds, 22 bonds  

> interfaces sel & ~solvent

2 buried areas: A C 632, A X 315  

> show sel atoms

> hide sel atoms

> select clear

Drag select of 379 residues, 10 pseudobonds  

> color bfactor sel

5201 atoms, 345 residues, atom bfactor range 71.3 to 224  

> select clear

> color byhetero

Drag select of 379 residues, 10 pseudobonds  

> color sel byhetero

[Repeated 1 time(s)]

> color sel bychain

> coulombic sel

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
/C TYR 3  
/C LYS 65  
/C GLU 67  
/C GLU 161  
/C LYS 162  
/C GLU 163  
/C GLU 182  
/C GLU 184  
/C ARG 185  

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for MdTMPK_refine_209.pdb_A SES surface #1.2: minimum,
-13.17, mean -1.99, maximum 10.33  
Coulombic values for MdTMPK_refine_209.pdb_C SES surface #1.3: minimum,
-14.56, mean -0.82, maximum 8.53  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide sel surfaces

> select clear

> preset "overall look" interactive

Preset expands to these ChimeraX commands:

    
    
    ~set bg
    graphics silhouettes f

  

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> preset cartoons/nucleotides licorice/ovals

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh default arrows f x round width 1 thick 1
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides tube/slab shape ellipsoid

  

> preset "initial styles" cartoon

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset cartoons/nucleotides cylinders/stubs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> preset "initial styles" cartoon

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> select

10044 atoms, 10120 bonds, 20 pseudobonds, 666 residues, 2 models selected  

> hide sel atoms

> select clear

> select add /B

3011 atoms, 3035 bonds, 2 pseudobonds, 199 residues, 2 models selected  

> select add /D

4801 atoms, 4835 bonds, 10 pseudobonds, 319 residues, 2 models selected  

> hide sel cartoons

Drag select of 379 residues, 10 pseudobonds  

> cartoon style (#!1 & sel) xsection oval modeHelix default

> cartoon style (#!1 & sel & coil) xsection oval

> cartoon style (#!1 & sel) xsection barbell modeHelix default

> cartoon style (#!1 & sel) xsection oval modeHelix default

> cartoon style (#!1 & sel) modeHelix tube sides 20

> select clear

> select add ::name="TMP"

42 atoms, 44 bonds, 2 residues, 1 model selected  

> show sel atoms

> select clear

Drag select of 21 atoms, 22 bonds  

> hide sel atoms

Drag select of 21 atoms, 220 residues, 2 pseudobonds, 22 bonds  

> ui tool show "Color Actions"

> color sel cornflower blue

> color sel byhetero

> color sel byelement

> select clear

Drag select of 159 residues, 8 pseudobonds  

> color sel salmon

> select clear

> select /A:164

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select add /A:163

29 atoms, 27 bonds, 2 residues, 2 models selected  

> select add /A:162

51 atoms, 48 bonds, 3 residues, 2 models selected  

> select add /A:161

66 atoms, 62 bonds, 4 residues, 2 models selected  

> select add /A:187

85 atoms, 80 bonds, 5 residues, 2 models selected  

> select add /A:159

109 atoms, 103 bonds, 6 residues, 2 models selected  

> select add /A:158

120 atoms, 113 bonds, 7 residues, 2 models selected  

> select subtract /A:187

101 atoms, 95 bonds, 6 residues, 2 models selected  

> select add /A:160

121 atoms, 115 bonds, 7 residues, 2 models selected  

> select add /A:148

135 atoms, 128 bonds, 1 pseudobond, 8 residues, 3 models selected  

> select add /A:97

159 atoms, 151 bonds, 1 pseudobond, 9 residues, 3 models selected  

> select add /A:98

179 atoms, 171 bonds, 1 pseudobond, 10 residues, 3 models selected  

> select add /A:99

196 atoms, 187 bonds, 1 pseudobond, 11 residues, 3 models selected  

> select add /A:12

203 atoms, 193 bonds, 1 pseudobond, 12 residues, 3 models selected  

> select add /A:13

218 atoms, 207 bonds, 1 pseudobond, 13 residues, 3 models selected  

> select add /A:14

225 atoms, 213 bonds, 1 pseudobond, 14 residues, 3 models selected  

> select add /A:15

235 atoms, 222 bonds, 1 pseudobond, 15 residues, 3 models selected  

> select add /A:16

242 atoms, 228 bonds, 1 pseudobond, 16 residues, 3 models selected  

> color sel burly wood

> color sel rosy brown

> color sel burly wood

> select add /C:16

248 atoms, 233 bonds, 2 pseudobonds, 17 residues, 3 models selected  

> select add /C:17

270 atoms, 254 bonds, 2 pseudobonds, 18 residues, 4 models selected  

> select add /C:97

294 atoms, 277 bonds, 2 pseudobonds, 19 residues, 4 models selected  

> select add /C:96

306 atoms, 288 bonds, 2 pseudobonds, 20 residues, 4 models selected  

> select subtract /C:96

294 atoms, 277 bonds, 2 pseudobonds, 19 residues, 4 models selected  

> select add /C:161

300 atoms, 282 bonds, 2 pseudobonds, 20 residues, 4 models selected  

> color sel burly wood

> select clear

> save "/Users/stefan/Dropbox/MdTMPK
> manuscript/Figures/MdTMPK_dimer_ribbon_tubes_side_view_2.png" width 4800
> height 2819 supersample 4 transparentBackground true

> select add /A

3032 atoms, 3057 bonds, 2 pseudobonds, 200 residues, 2 models selected  

> select clear

> open "/Users/stefan/Dropbox/MdTMPK manuscript/3ld9_dimer.pdb"

3ld9_dimer.pdb title:  
Crystal structure of thymidylate kinase from ehrlichia chaffeensis At 2.15A
resolution [more info...]  
  
Chain information for 3ld9_dimer.pdb #2  
---  
Chain | Description  
A B C D | DTMP kinase  
  
Non-standard residues in 3ld9_dimer.pdb #2  
---  
EDO — 1,2-ethanediol (ethylene glycol)  
SO4 — sulfate ion  
  

> open /Users/stefan/Dropbox/MdTMPK/Refine_209/MdTMPK_refine_209.pdb

Summary of feedback from opening
/Users/stefan/Dropbox/MdTMPK/Refine_209/MdTMPK_refine_209.pdb  
---  
warning | Ignored bad PDB record found on line 61  
  
Chain information for MdTMPK_refine_209.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  

> select

26117 atoms, 26066 bonds, 54 pseudobonds, 2363 residues, 6 models selected  

> select subtract #1/A

23085 atoms, 23009 bonds, 52 pseudobonds, 2163 residues, 8 models selected  

> select subtract #1/C

20916 atoms, 20825 bonds, 44 pseudobonds, 2018 residues, 7 models selected  

> hide sel atoms

> hide sel cartoons

> ui tool show Matchmaker

> matchmaker #3/A to #1/C 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 MdTMPK_refine_209.pdb, chain C (#1) with MdTMPK_refine_209.pdb,
chain A (#3), sequence alignment score = 621.5  
RMSD between 102 pruned atom pairs is 0.776 angstroms; (across all 145 pairs:
3.726)  
[Repeated 1 time(s)]Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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: 4.1 INTEL-16.1.12
OpenGL renderer: Intel(R) Iris(TM) Pro Graphics 6200
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac16,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 3,1 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Memory: 16 GB
      System Firmware Version: 426.0.0.0.0
      SMC Version (system): 2.32f21

Software:

    System Software Overview:

      System Version: macOS 11.2.3 (20D91)
      Kernel Version: Darwin 20.3.0
      Time since boot: 3 days 11:01

Graphics/Displays:

    Intel Iris Pro Graphics 6200:

      Chipset Model: Intel Iris Pro Graphics 6200
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x1622
      Revision ID: 0x000a
      Metal Family: Supported, Metal GPUFamily macOS 1
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: 4096 x 2304 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Display Serial Number: 58C231756C929
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.4.1
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.1.1
    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: 1.18
    ChimeraX-AtomicLibrary: 3.2
    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: 1.3
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202104230049
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.2.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.1
    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: 1.1
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.3
    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: 1.2
    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
    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: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0
    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-SelInspector: 1.0
    ChimeraX-SeqView: 2.4
    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: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.5
    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: 1.8
    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: 5.0.7
    distlib: 0.3.1
    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: 1.1.1
    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: 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: 2020.9.3
    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

[pett]

Fix available in next daily build and 1.2.2 release candidate