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:        Linux-5.8.0-45-generic-x86_64-with-debian-bullseye-sid
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Successfully installed ChimeraX-AddH-2.1.3 ChimeraX-HKCage-1.3  
Installed ChimeraX-AddH (2.1.3)  
Installed ChimeraX-HKCage (1.3)  

> open 7kkj

Summary of feedback from opening 7kkj fetched from pdb  
---  
notes | Fetching compressed mmCIF 7kkj from
http://files.rcsb.org/download/7kkj.cif  
Fetching CCD SO4 from http://ligand-expo.rcsb.org/reports/S/SO4/SO4.cif  
Fetching CCD CL from http://ligand-expo.rcsb.org/reports/C/CL/CL.cif  
  
7kkj title:  
Structure of anti-SARS-CoV-2 Spike nanobody mNb6 [more info...]  
  
Chain information for 7kkj #1  
---  
Chain | Description  
A C | Synthetic nanobody mNb6  
  
Non-standard residues in 7kkj #1  
---  
CL — chloride ion  
SO4 — sulfate ion  
  
7kkj mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> select /A:1-118

1762 atoms, 1781 bonds, 118 residues, 1 model selected  

> select /C:1-119

1769 atoms, 1788 bonds, 119 residues, 1 model selected  

> select :CL

1 atom, 1 residue, 1 model selected  

> select :CL

1 atom, 1 residue, 1 model selected  

> select :CL

1 atom, 1 residue, 1 model selected  

> show sel atoms

> select :SO4

20 atoms, 16 bonds, 4 residues, 1 model selected  

> sym #1 assembly 1

> view

> sym #1 assembly 2

> view

> close #2

> close #3

> show #1 models

> hide #1 models

> show #1 models

> show sel atoms

> select clear

> show atoms

> hide atoms

> style sphere

Changed 3683 atom styles  

> show atoms

> lighting soft

> hide atoms

> lighting simple

> color yellow

> undo

> color bychain

> select clear

> color bychain

> rainbow

> hide atoms

> show cartoons

> preset "initial styles" "original look"

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" "original look"

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

> show surfaces

> lighting soft

> coulombic

Atoms with non-standard names found in standard residues: /A CYS 96 HG and /A
CYS 22 HG. Try deleting all hydrogens first.  

> coulombic

Atoms with non-standard names found in standard residues: /A CYS 96 HG and /A
CYS 22 HG. Try deleting all hydrogens first.  

> delete H

> coulombic

The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics: /C SER 119 OG  

> mlp

Map values for surface "7kkj_A SES surface": minimum -26.2, mean -6.039,
maximum 19.75  
Map values for surface "7kkj_C SES surface": minimum -25.35, mean -5.999,
maximum 20.09  

> color bfactor

1945 atoms, 373 residues, 2 surfaces, atom bfactor range 18.9 to 86.1  

> hide surfaces

> show cartoons

> select /C:63

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select /C:63

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select /C:64

7 atoms, 6 bonds, 1 residue, 1 model selected  
Drag select of 13 residues  

> select /C:64

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /C:62

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /C:63

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select up

30 atoms, 29 bonds, 4 residues, 2 models selected  

> mlp sel

Map values for surface "7kkj_C SES surface": minimum -25.35, mean -5.999,
maximum 20.09  

> mlp sel

Map values for surface "7kkj_C SES surface": minimum -25.35, mean -5.999,
maximum 20.09  

> color sel bychain

> hide sel surfaces

> show sel surfaces

> mlp sel

Map values for surface "7kkj_C SES surface": minimum -25.35, mean -5.999,
maximum 20.09  

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> show sel surfaces

> hide sel cartoons

> hide sel atoms

> hide sel surfaces

> style sel sphere

Changed 62 atom styles  

> preset "initial styles" "original look"

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

> select up

98 atoms, 97 bonds, 15 residues, 2 models selected  

> select up

974 atoms, 925 bonds, 186 residues, 2 models selected  

> select down

98 atoms, 97 bonds, 15 residues, 2 models selected  

> select up

974 atoms, 925 bonds, 186 residues, 2 models selected  

> select down

98 atoms, 97 bonds, 15 residues, 2 models selected  

> select up

974 atoms, 925 bonds, 186 residues, 2 models selected  

> select down

98 atoms, 97 bonds, 15 residues, 2 models selected  

> select up

974 atoms, 925 bonds, 186 residues, 2 models selected  

> select up

1945 atoms, 1847 bonds, 373 residues, 2 models selected  

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> log metadata #1

Metadata for 7kkj #1  
---  
Title | Structure of anti-SARS-CoV-2 Spike nanobody mNb6  
Citation | Schoof, M., Faust, B., Saunders, R.A., Sangwan, S., Rezelj, V.,
Hoppe, N., Boone, M., Billesbolle, C.B., Puchades, C., Azumaya, C.M.,
Kratochvil, H.T., Zimanyi, M., Deshpande, I., Liang, J., Dickinson, S.,
Nguyen, H.C., Chio, C.M., Merz, G.E., Thompson, M.C., Diwanji, D., Schaefer,
K., Anand, A.A., Dobzinski, N., Zha, B.S., Simoneau, C.R., Leon, K., White,
K.M., Chio, U.S., Gupta, M., Jin, M., Li, F., Liu, Y., Zhang, K., Bulkley, D.,
Sun, M., Smith, A.M., Rizo, A.N., Moss, F., Brilot, A.F., Pourmal, S.,
Trenker, R., Pospiech, T., Gupta, S., Barsi-Rhyne, B., Belyy, V., Barile-Hill,
A.W., Nock, S., Liu, Y., Krogan, N.J., Ralston, C.Y., Swaney, D.L., Garcia-
Sastre, A., Ott, M., Vignuzzi, M., Walter, P., Manglik, A. (2020). An
ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive
Spike. Science, 370, 1473-1479. PMID: 33154106. DOI: 10.1126/science.abe3255  
Non-standard residues | CL — chloride ion  
SO4 — sulfate ion  
Gene source | synthetic construct  
Experimental method | X-ray diffraction  
Resolution | 2.05Å  
  
> open 7kkj fromDatabase eds

Summary of feedback from opening 7kkj fetched from eds  
---  
note | Fetching map 7kkj from
http://www.ebi.ac.uk/pdbe/coordinates/files/7kkj.ccp4  
  
Opened 7kkj.ccp4, grid size 118,103,128, pixel 0.619,0.594,0.611, shown at
level 1.16, step 1, values float32  

> color sel byhetero

> volume showOutlineBox true

> volume zone #2 nearAtoms #1

> volume showOutlineBox false

> volume #2 level 0.7315

> lighting simple

> lighting soft

> lighting full

> lighting soft

> lighting simple

> ui mousemode right clip

> ui mousemode right clip

Drag select of 79 atoms, 177 residues, 67 bonds, 2 eds 7kkj  

> help volume zone

> show sel atoms

> hide sel cartoons

> hide sel surfaces

> close

> open 7kkl

Summary of feedback from opening 7kkl fetched from pdb  
---  
notes | Fetching compressed mmCIF 7kkl from
http://files.rcsb.org/download/7kkl.cif  
Fetching CCD NAG from http://ligand-expo.rcsb.org/reports/N/NAG/NAG.cif  
  
7kkl title:  
SARS-CoV-2 Spike in complex with neutralizing nanobody mNb6 [more info...]  
  
Chain information for 7kkl #1  
---  
Chain | Description  
A C D | Spike glycoprotein  
B E F | Synthetic nanobody mNb6  
  
Non-standard residues in 7kkl #1  
---  
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)  
  

> color yellow

> undo

> color /B,E,F gold

> set bgColor white

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting soft

> save /home/simeons/Desktop/image1.png supersample 3

> save spike.pdf width 1500

No known data format for file suffix '.pdf'  

> open /home/simeons/Downloads/emd_22910_trimmed.mrc

Opened emd_22910_trimmed.mrc, grid size 109,109,151, pixel 1.67,1.67,1.67,
shown at level 3.56, step 1, values float32  

> hide #!1 models

> open 6vxx

Summary of feedback from opening 6vxx fetched from pdb  
---  
note | Fetching compressed mmCIF 6vxx from
http://files.rcsb.org/download/6vxx.cif  
  
6vxx title:  
Structure of the SARS-CoV-2 spike glycoprotein (closed state) [more info...]  
  
Chain information for 6vxx #3  
---  
Chain | Description  
A B C | Spike glycoprotein  
  
Non-standard residues in 6vxx #3  
---  
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)  
  

> hide #!3 cartoons

> show #!3 atoms

> style #!3 sphere

Changed 23694 atom styles  

> select #3/B:557@O

1 atom, 1 residue, 1 model selected  

> ui mousemode right "translate selected models"

> select #3/C:125@CG

1 atom, 1 residue, 1 model selected  

> ui mousemode right "translate selected models"

> lighting simple

> set bgColor black

> select clear

> select #3/C:213@CB

1 atom, 1 residue, 1 model selected  

> ui mousemode right "translate selected models"

> ui mousemode right "translate selected models"

> select clear

> ui mousemode right "translate selected models"

> ui tool show "Fit in Map"

Fit molecule 6vxx (#3) to map emd_22910_trimmed.mrc (#2) using 23694 atoms  
average map value = 0.7506, steps = 216  
shifted from previous position = 53.8  
rotated from previous position = 3.54 degrees  
atoms outside contour = 22045, contour level = 3.555  
  
Position of 6vxx (#3) relative to emd_22910_trimmed.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99894283 0.04136371 0.02005664 -53.66760554  
-0.04050105 0.99831054 -0.04166214 -16.05251636  
-0.02174605 0.04080578 0.99893043 -12.83615854  
Axis 0.66779997 0.33850536 -0.66291577  
Axis point 0.00000000 842.81828800 -153.27356834  
Rotation angle (degrees) 3.54003564  
Shift along axis -32.76379637  
  
Fit molecule 6vxx (#3) to map emd_22910_trimmed.mrc (#2) using 23694 atoms  
average map value = 0.7506, steps = 40  
shifted from previous position = 0.00393  
rotated from previous position = 0.00989 degrees  
atoms outside contour = 22045, contour level = 3.555  
  
Position of 6vxx (#3) relative to emd_22910_trimmed.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99893541 0.04149569 0.02015347 -53.71162630  
-0.04063012 0.99830745 -0.04161039 -16.03256607  
-0.02184601 0.04074725 0.99893063 -12.80132871  
Axis 0.66600958 0.33964131 -0.66413480  
Axis point 0.00000000 843.39417278 -152.56660834  
Rotation angle (degrees) 3.54481148  
Shift along axis -32.71597132  
  

> color #!3 bychain

> volume #2 level 1.174

> volume #2 level 3.325

> color zone #2 near #3

> hide #!3 models

> lighting soft

> color zone #2 near #3 distance 6

> open 7kkj

7kkj title:  
Structure of anti-SARS-CoV-2 Spike nanobody mNb6 [more info...]  
  
Chain information for 7kkj #4  
---  
Chain | Description  
A C | Synthetic nanobody mNb6  
  
Non-standard residues in 7kkj #4  
---  
CL — chloride ion  
SO4 — sulfate ion  
  
7kkj mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> volume #2 level 5.477

> volume #2 level 0.3128

> select #4/C

1841 atoms, 1792 bonds, 187 residues, 1 model selected  

> volume #2 level 1.633

> hide sel atoms

> show sel cartoons

> hide sel atoms

> show sel cartoons

> delete atoms sel

> delete bonds sel

> show #!1 models

> hide #!2 models

> ui tool show Matchmaker

> matchmaker #4/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 7kkl, chain B (#1) with 7kkj, chain A (#4), sequence alignment
score = 589.7  
RMSD between 90 pruned atom pairs is 0.751 angstroms; (across all 117 pairs:
3.062)  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/usr/lib/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 "/usr/lib/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: 4.5 (Core Profile) Mesa 20.2.6
OpenGL renderer: AMD OLAND (DRM 2.50.0, 5.8.0-45-generic, LLVM 11.0.0)
OpenGL vendor: X.Org
Manufacturer: Dell Inc.
Model: Precision Tower 7910
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
CPU: 40 Intel(R) Xeon(R) CPU E5-2650 v3 @ 2.30GHz
Cache Size: 25600 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           62Gi       8.6Gi        30Gi       860Mi        23Gi        52Gi
	Swap:          63Gi          0B        63Gi

Graphics:
	03:00.0 VGA compatible controller [0300]: Advanced Micro Devices, Inc. [AMD/ATI] Oland GL [FirePro W2100] [1002:6608]	
	Subsystem: Dell Oland GL [FirePro W2100] [1028:2120]	
	Kernel driver in use: radeon
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-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-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
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    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
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    tifffile: 2020.6.3
    tinyarray: 1.2.2
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    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2