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-19.5.0-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/lin.cl/Downloads/6gej.pdb

6gej.pdb title:  
Chromatin remodeller-nucleosome complex At 3.6 A resolution. [more info...]  
  
Chain information for 6gej.pdb #1  
---  
Chain | Description  
A B | histone H3  
C D | histone H4  
E F | histone H2A.1  
G H | suppressor OF TY protein 12  
I | DNA (154-mer)  
J | DNA (154-mer)  
M | SWI2/SNF2-related 1  
R | actin-like protein ARP6  
S | SWR complex protein 6  
T V X | ruvb-like protein 1  
U W Y | ruvb-like protein 2  
Z | vacuolar protein sorting-associated protein 72  
  
Non-standard residues in 6gej.pdb #1  
---  
ADP — adenosine-5'-diphosphate  
BEF — beryllium trifluoride ion  
MG — magnesium ion  
ZN — zinc ion  
  

> hide atoms

> show cartoons

> sequence chain #1/M

Alignment identifier is 1/M  

> sequence chain #1/M

Destroying pre-existing alignment with identifier 1/M  
Alignment identifier is 1/M  

> sequence chain #1/M

Destroying pre-existing alignment with identifier 1/M  
Alignment identifier is 1/M  

> select #1

43702 atoms, 44998 bonds, 40 pseudobonds, 5142 residues, 3 models selected  

> sequence chain #1/M

Destroying pre-existing alignment with identifier 1/M  
Alignment identifier is 1/M  

> select /M:682-1396

5398 atoms, 5495 bonds, 2 pseudobonds, 688 residues, 2 models selected  

> select /I:-77-76

3137 atoms, 3514 bonds, 154 residues, 1 model selected  

> select /J:-76-77

3177 atoms, 3568 bonds, 154 residues, 1 model selected  

> select /J:-76-77

3177 atoms, 3568 bonds, 154 residues, 1 model selected  

> select /I:-77-76

3137 atoms, 3514 bonds, 154 residues, 1 model selected  

> select /M:682-1396

5398 atoms, 5495 bonds, 2 pseudobonds, 688 residues, 2 models selected  

> select /J:-76-77

3177 atoms, 3568 bonds, 154 residues, 1 model selected  

> select /I:-77-76

3137 atoms, 3514 bonds, 154 residues, 1 model selected  

> select /J:-76-77

3177 atoms, 3568 bonds, 154 residues, 1 model selected  

> select /I:-77-76

3137 atoms, 3514 bonds, 154 residues, 1 model selected  

> select /J:-76-77

3177 atoms, 3568 bonds, 154 residues, 1 model selected  

> select /M:682-1396

5398 atoms, 5495 bonds, 2 pseudobonds, 688 residues, 2 models selected  

> select /J:-76-77

3177 atoms, 3568 bonds, 154 residues, 1 model selected  

> select /I:-77-76

3137 atoms, 3514 bonds, 154 residues, 1 model selected  

> select /I/J

6314 atoms, 7082 bonds, 308 residues, 1 model selected  

> select /M

5430 atoms, 5527 bonds, 4 pseudobonds, 691 residues, 3 models selected  

> open /Users/lin.cl/Downloads/5o9g.pdb

5o9g.pdb title:  
Structure of nucleosome-CHD1 complex [more info...]  
  
Chain information for 5o9g.pdb #2  
---  
Chain | Description  
A E | histone H3.2  
B F | histone H4  
C G | histone H2A  
D | H2B1.1  
H | H2B1.1  
I | DNA (162-mer)  
J | DNA (162-mer)  
W | ATP-dependent helicase CHD1  
  
Non-standard residues in 5o9g.pdb #2  
---  
ADP — adenosine-5'-diphosphate  
BEF — beryllium trifluoride ion  
  

> open /Users/lin.cl/Downloads/5z3v.pdb

5z3v.pdb title:  
Structure of SNF2-nucleosome complex At SHL-2 In adp befx state [more info...]  
  
Chain information for 5z3v.pdb #3  
---  
Chain | Description  
A E | histone H3.2  
B F | histone H4  
C G | histone H2A  
D H | H2B1.1  
I | DNA (167-mer)  
J | DNA (167-mer)  
O | transcription regulatory protein SNF2  
  
Non-standard residues in 5z3v.pdb #3  
---  
ADP — adenosine-5'-diphosphate  
BEF — beryllium trifluoride ion  
MG — magnesium ion  
  

> hide sel atoms

> hide sel atoms

> select #1

43702 atoms, 44998 bonds, 40 pseudobonds, 5142 residues, 3 models selected  

> select #2

19681 atoms, 20705 bonds, 15 pseudobonds, 1936 residues, 3 models selected  

> select #3

16758 atoms, 17640 bonds, 13 pseudobonds, 1634 residues, 3 models selected  

> hide sel atoms

> show sel cartoons

> select #2

19681 atoms, 20705 bonds, 15 pseudobonds, 1936 residues, 3 models selected  

> select #1

43702 atoms, 44998 bonds, 40 pseudobonds, 5142 residues, 3 models selected  

> select #2

19681 atoms, 20705 bonds, 15 pseudobonds, 1936 residues, 3 models selected  

> hide sel atoms

> show sel cartoons

> ui tool show "Basic Actions"

> ui tool show "Fit to Segments"

Density map not found or not selected  

> select #1

43702 atoms, 44998 bonds, 40 pseudobonds, 5142 residues, 3 models selected  

> select #3

16758 atoms, 17640 bonds, 13 pseudobonds, 1634 residues, 3 models selected  

> select #2

19681 atoms, 20705 bonds, 15 pseudobonds, 1936 residues, 3 models selected  

> select #1

43702 atoms, 44998 bonds, 40 pseudobonds, 5142 residues, 3 models selected  
Density map not found or not selected  
Density map not found or not selected  

> matchmaker

Missing or invalid "matchAtoms" argument: empty atom specifier  
Alignment identifier is 1/Z  
Alignment identifier is 1  
Alignment identifier is 2  
Alignment identifier is 3  
Alignment identifier is 4  
Alignment identifier is 1/I  
Alignment identifier is 1/J  
Destroying pre-existing alignment with identifier 1/M  
Alignment identifier is 1/M  
Alignment identifier is 1/R  
Alignment identifier is 1/S  
Alignment identifier is 5  
Alignment identifier is 6  

> select #2

19681 atoms, 20705 bonds, 15 pseudobonds, 1936 residues, 3 models selected  

> select #3

16758 atoms, 17640 bonds, 13 pseudobonds, 1634 residues, 3 models selected  

> select #2

19681 atoms, 20705 bonds, 15 pseudobonds, 1936 residues, 3 models selected  

> toolshed show

> ui tool show "Modeller Comparative"

> ui tool show "Blast Protein"

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A #1/B

Alignment identifier is 1  

> ~select #2

Nothing selected  

> mmaker #3 to #2 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 5o9g.pdb, chain W (#2) with 5z3v.pdb, chain O (#3), sequence
alignment score = 1098.5  
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: 5o9g.pdb #2/W, 5z3v.pdb #3/O  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 294 pruned atom pairs is 1.221 angstroms; (across all 459 pairs:
14.231)  
  

> hide #!1 models

> mmaker #1 to #2 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 5o9g.pdb, chain W (#2) with 6gej.pdb, chain M (#1), sequence
alignment score = 780.8  
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: 6gej.pdb #1/M, 5o9g.pdb #2/W  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2  
RMSD between 307 pruned atom pairs is 1.168 angstroms; (across all 436 pairs:
10.641)  
  

> show #!1 models

> hide #!3 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> ui mousemode right select

> select #2/J:32

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #2/J:32

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #2/J:32

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select clear

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected atoms"

> ui mousemode right pivot

> ui mousemode right translate

> ui mousemode right select

> select clear

> select clear

> select clear

> ui tool show "Modeller Comparative"

> show #!3 models

> ui tool show "Show Sequence Viewer"

> sequence chain #1/I

Alignment identifier is 1/I  

> sequence chain #1/J

Alignment identifier is 1/J  

> sequence chain #2/I

Alignment identifier is 2/I  

> sequence chain #2/J

Alignment identifier is 2/J  

> sequence chain #3/I

Alignment identifier is 3/I  

> sequence chain #3/J

Alignment identifier is 3/J  

> ui tool show "Modeller Comparative"

> modeller comparative 1/I:1 1/J:1 2/I:1 2/J:1 3/I:1 3/J:1 multichain true
> numModels 5 fast false hetPreserve false hydrogens false waterPreserve false

No Modeller license key provided. Get a license key by registering at the
Modeller web site.  

> modeller comparative 1/I:1 1/J:1 multichain true numModels 5 fast false
> hetPreserve false hydrogens false waterPreserve false

No Modeller license key provided. Get a license key by registering at the
Modeller web site.  

> mmaker #1 to #2 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 5o9g.pdb, chain W (#2) with 6gej.pdb, chain M (#1), sequence
alignment score = 780.8  
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: 6gej.pdb #1/M, 5o9g.pdb #2/W  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 307 pruned atom pairs is 1.168 angstroms; (across all 436 pairs:
10.641)  
  

> select #1

43702 atoms, 44998 bonds, 40 pseudobonds, 5142 residues, 3 models selected  

> ~select #1

Nothing selected  

> show target m

> select #1

43702 atoms, 44998 bonds, 40 pseudobonds, 5142 residues, 3 models selected  

> select #2

19681 atoms, 20705 bonds, 15 pseudobonds, 1936 residues, 3 models selected  

> select #3

16758 atoms, 17640 bonds, 13 pseudobonds, 1634 residues, 3 models selected  

> select #2

19681 atoms, 20705 bonds, 15 pseudobonds, 1936 residues, 3 models selected  

> select #1

43702 atoms, 44998 bonds, 40 pseudobonds, 5142 residues, 3 models selected  

> select clear

> select clear

> select clear

> select clear

> undo

> select #2/W

7048 atoms, 7184 bonds, 15 pseudobonds, 857 residues, 3 models selected  

> select #3/I#3/J

5986 atoms, 6714 bonds, 292 residues, 1 model selected  

> ui tool show Matchmaker

> matchmaker #!2 & sel to #1/I & sel pairing bs

No 'to' chains specified  

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

Reference chain (6gej.pdb (#1) chain I) not compatible with BLOSUM-62
similarity matrix  

> matchmaker #!2 to #1/I pairing bs matrix Nucleic

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
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 6gej.pdb, chain I (#1) with 5o9g.pdb, chain I (#2), sequence
alignment score = 559.4  
RMSD between 73 pruned atom pairs is 1.197 angstroms; (across all 149 pairs:
9.479)  
  
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.  
  
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.  
  
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.  
  
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.  
  
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.  
  
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.  
  
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.  
  
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-14.6.18
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 512 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 1037.120.87.0.0 (iBridge: 17.16.15300.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.5 (19F101)
      Kernel Version: Darwin 19.5.0
      Time since boot: 10 days 5 minutes

Graphics/Displays:

    Intel Iris Plus Graphics:

      Chipset Model: Intel Iris Plus Graphics
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x8a53
      Revision ID: 0x0007
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        VG2755-2K:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 59 Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: VKL201800406
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: Thunderbolt/DisplayPort

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: 2.1.1
    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-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-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