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

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Darwin-19.6.0-x86_64-i386-64bit
ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/Ryan/Desktop/M-T7/MT7-IFNgamma/rank_1_model_5_ptm_seed_2_relaxed.pdb

Chain information for rank_1_model_5_ptm_seed_2_relaxed.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> open /Users/Ryan/Desktop/M-T7/MT7-IFNgamma/1fg9.pdb

1fg9.pdb title:  
3:1 complex of interferon-γ receptor with interferon- γ dimer [more info...]  
  
Chain information for 1fg9.pdb #2  
---  
Chain | Description  
A B | interferon γ  
C D E | interferon-γ receptor α chain  
  

> show cartoons

> show atoms

> style sphere

Changed 13118 atom styles  

> style sphere

Changed 13118 atom styles  

> style stick

Changed 13118 atom styles  
Alignment identifier is 1/A  
Alignment identifier is 1/B  
Alignment identifier is 1/C  
Alignment identifier is 1  
Alignment identifier is 2  
Destroying pre-existing alignment with identifier 1/A  
Alignment identifier is 1/A  
Destroying pre-existing alignment with identifier 1/B  
Alignment identifier is 1/B  
Destroying pre-existing alignment with identifier 1/C  
Alignment identifier is 1/C  
Alignment identifier is 3  
Alignment identifier is 4  

> hide target m

> hide target m

> show #1 models

> preset cartoons/nucleotides ribbons/slabs

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
    nucleotides tube/slab shape box

  

> 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" "original look"

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

> preset "molecular surfaces" "ghostly white"

Changed 6905 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color white targ s trans 80

  

> preset cartoons/nucleotides ribbons/slabs

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
    nucleotides tube/slab shape box

  

> preset "molecular surfaces" "atomic coloring (transparent)"

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color fromatoms targ s trans 70

  

> preset "molecular surfaces" "chain id coloring (opaque)"

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color bychain targ s trans 0

  

> hide #!1 surfaces

> color bfactor #!1

6213 atoms, 387 residues, 3 surfaces, atom bfactor range 31 to 96.7  

> rainbow #!1

> select #1/A

4115 atoms, 4161 bonds, 260 residues, 1 model selected  

> color (#!1 & sel) cyan

> select #1/C

720 atoms, 723 bonds, 44 residues, 1 model selected  

> color (#!1 & sel) orange red

> select #1/B

1378 atoms, 1392 bonds, 83 residues, 1 model selected  

> color (#!1 & sel) yellow

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> show sel atoms

> select #1.3

720 atoms, 44 residues, 1 model selected  

> style sel stick

Changed 720 atom styles  

> show sel atoms

> style sel stick

Changed 720 atom styles  

> color sel byhetero

> ~select #1.3

1 model selected  

> select #1.2

1378 atoms, 83 residues, 1 model selected  

> select #1.3

720 atoms, 44 residues, 1 model selected  

> select #1.2

1378 atoms, 83 residues, 1 model selected  

> select #1.3

720 atoms, 44 residues, 1 model selected  

> select #1

6213 atoms, 6276 bonds, 387 residues, 1 model selected  

> ~select #1.1

2098 atoms, 6276 bonds, 127 residues, 4 models selected  

> hide sel atoms

> select #1

6213 atoms, 6276 bonds, 387 residues, 1 model selected  

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> preset "overall look" interactive

Preset expands to these ChimeraX commands:

    
    
    ~set bg
    graphics silhouettes f

  

> preset "molecular surfaces" "chain id coloring (opaque)"

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color bychain targ s trans 0

  

> preset "initial styles" "space-filling (single color)"

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

> preset "initial styles" "space-filling (chain colors)"

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

> preset "initial styles" cartoon

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

> preset "initial styles" sticks

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

> preset "initial styles" "original look"

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

> preset cartoons/nucleotides ribbons/slabs

Changed 6905 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
    nucleotides tube/slab shape box

  

> ui tool show "Color Actions"

> color sel bypolymer

> color sel bychain

> ~select #1

3 models selected  

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> 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 rank_1_model_5_ptm_seed_2_relaxed.pdb, chain B (#1) with 1fg9.pdb,
chain B (#2), sequence alignment score = 420  
RMSD between 81 pruned atom pairs is 0.735 angstroms; (across all 83 pairs:
0.866)  
  

> show #!1 models

> ui tool show Matchmaker

> matchmaker #!1 to #2/D pairing bs

Parameters  
---  
Chain pairing | bs  
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 1fg9.pdb, chain D (#2) with rank_1_model_5_ptm_seed_2_relaxed.pdb,
chain A (#1), sequence alignment score = 188.7  
RMSD between 60 pruned atom pairs is 0.900 angstroms; (across all 183 pairs:
4.625)  
  

> undo

> close #1

> open
> /Users/Ryan/Desktop/M-T7/MT7-IFNgamma/rank_1_model_5_ptm_seed_2_relaxed.pdb

Chain information for rank_1_model_5_ptm_seed_2_relaxed.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> 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 rank_1_model_5_ptm_seed_2_relaxed.pdb, chain B (#1) with 1fg9.pdb,
chain B (#2), sequence alignment score = 420  
RMSD between 81 pruned atom pairs is 0.735 angstroms; (across all 83 pairs:
0.866)  
  

> select #1

6213 atoms, 6276 bonds, 387 residues, 1 model selected  

> ~select #1

Nothing selected  

> show #2.5 models

> hide #2.5 models

> select #2.5

1617 atoms, 205 residues, 1 model selected  

> color (#!2 & sel) magenta

> select #1/A

4115 atoms, 4161 bonds, 260 residues, 1 model selected  

> color sel cyan

> select #1/B

1378 atoms, 1392 bonds, 83 residues, 1 model selected  

> show #2.5 models

> hide #2.5 models

> select #2.6

1537 atoms, 193 residues, 1 model selected  

> hide #1 target m

> hide #1 target m

> show #1 target m

> hide #1 models

> hide #!2 models

> show #!2 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> select #2

6905 atoms, 7061 bonds, 8 pseudobonds, 862 residues, 2 models selected  

> ~select #2

5 models selected  

> select #2.6

1537 atoms, 193 residues, 1 model selected  

> hide #1 target m

> select #2.4

1661 atoms, 210 residues, 1 model selected  

> hide #1 target m

> hide #!2 models

> show #2.1 models

> hide #!2 models

> show #2.2 models

> hide #2.1 models

> show #2.3 models

> hide #!2 models

> hide #2.3 models

> show #2.3 models

> ~select #2.4

1 model selected  

> show #1 models

> close #2.6

> close #2.3

> select #2/D

1617 atoms, 1657 bonds, 2 pseudobonds, 205 residues, 2 models selected  

> select #2/C

1661 atoms, 1703 bonds, 2 pseudobonds, 210 residues, 2 models selected  

> close #1

> hide #!2 models

> show #!2 models

> show #2.1 models

> hide #2.1 models

> show #2.1 models

> hide #2.1 models

> close #2

> open /Users/Ryan/Desktop/M-T7/MT7-IFNgamma/1fg9.pdb format pdb

1fg9.pdb title:  
3:1 complex of interferon-γ receptor with interferon- γ dimer [more info...]  
  
Chain information for 1fg9.pdb #1  
---  
Chain | Description  
A B | interferon γ  
C D E | interferon-γ receptor α chain  
  

> hide surfaces

> hide surfaces

> show cartoons

> hide surfaces

> style stick

Changed 6905 atom styles  

> hide atoms

> select #1.1

8 pseudobonds, 1 model selected  

> ~select #1.1

Nothing selected  

> select #1.1

8 pseudobonds, 1 model selected  

> ~select #1.1

Nothing selected  

> select #1.1

8 pseudobonds, 1 model selected  

> select /D

1617 atoms, 1657 bonds, 2 pseudobonds, 205 residues, 2 models selected  

> hide target m

> hide target m

> show target m

> color (#!1 & sel) black

> hide #!1 models

> show #!1 models

> select #1.1

8 pseudobonds, 1 model selected  

> select #1

6905 atoms, 7061 bonds, 8 pseudobonds, 862 residues, 2 models selected  

> ~select #1.1

6905 atoms, 7061 bonds, 862 residues, 1 model selected  

> select #1.1

8 pseudobonds, 1 model selected  

> select /D

1617 atoms, 1657 bonds, 2 pseudobonds, 205 residues, 2 models selected  

> select /D

1617 atoms, 1657 bonds, 2 pseudobonds, 205 residues, 2 models selected  

> select /C

1661 atoms, 1703 bonds, 2 pseudobonds, 210 residues, 2 models selected  

> select /D

1617 atoms, 1657 bonds, 2 pseudobonds, 205 residues, 2 models selected  

> delete /D

> open
> /Users/Ryan/Desktop/M-T7/MT7-IFNgamma/rank_1_model_5_ptm_seed_2_relaxed.pdb

Chain information for rank_1_model_5_ptm_seed_2_relaxed.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> 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 1fg9.pdb, chain B (#1) with rank_1_model_5_ptm_seed_2_relaxed.pdb,
chain B (#2), sequence alignment score = 420  
RMSD between 81 pruned atom pairs is 0.735 angstroms; (across all 83 pairs:
0.866)  
  

> ui tool show Matchmaker

> ui tool show Matchmaker

> select /C

2381 atoms, 2426 bonds, 2 pseudobonds, 254 residues, 3 models selected  

> select 1/C

Expected an objects specifier or a keyword  

> select #1/C

1661 atoms, 1703 bonds, 2 pseudobonds, 210 residues, 2 models selected  

> ui tool show Matchmaker

> select /A

5161 atoms, 5225 bonds, 387 residues, 2 models selected  

> select down

5161 atoms, 5225 bonds, 387 residues, 2 models selected  

> ui tool show Matchmaker

> matchmaker #2/A to #1/B 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 1fg9.pdb, chain B (#1) with rank_1_model_5_ptm_seed_2_relaxed.pdb,
chain A (#2), sequence alignment score = 38.1  
RMSD between 23 pruned atom pairs is 0.948 angstroms; (across all 45 pairs:
17.168)  
  

> ui tool show Matchmaker

> matchmaker #2/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 1fg9.pdb, chain C (#1) with rank_1_model_5_ptm_seed_2_relaxed.pdb,
chain A (#2), sequence alignment score = 194  
RMSD between 62 pruned atom pairs is 0.860 angstroms; (across all 188 pairs:
4.567)  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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.  
  

> select #2

6213 atoms, 6276 bonds, 387 residues, 1 model selected  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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.  
  

> ~select #2

Nothing selected  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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: 4.1 INTEL-14.7.8
OpenGL renderer: Intel(R) Iris(TM) Graphics 6100
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro12,1
      Processor Name: Dual-Core Intel Core i5
      Processor Speed: 2.7 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 3 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      Boot ROM Version: 192.0.0.0.0
      SMC Version (system): 2.28f7

Software:

    System Software Overview:

      System Version: macOS 10.15.6 (19G2021)
      Kernel Version: Darwin 19.6.0
      Time since boot: 2 days 22:05

Graphics/Displays:

    Intel Iris Graphics 6100:

      Chipset Model: Intel Iris Graphics 6100
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x162b
      Revision ID: 0x0009
      Metal: Supported, feature set macOS GPUFamily1 v4
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

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
    appnope: 0.1.0
    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: 1.1.1
    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-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
    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