Crash in event loop after swapaa

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22000
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted

Thread 0x00002dc0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x000038bc (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 576 in _handle_results
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x000044f8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 528 in _handle_tasks
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x000052a0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 816 in _exhaustive_wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 884 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 499 in _wait_for_updates
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 519 in _handle_workers
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00002288 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x000008e8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x0000298c (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x000031ac (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00001608 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00002e0c (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00004f3c (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00004a90 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Current thread 0x00001654 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/camrh/Downloads/1dzo_coord.pdb

Chain information for 1dzo_coord.pdb #1  
---  
Chain | Description  
A | No description available  
  

> select :128-144

127 atoms, 128 bonds, 17 residues, 1 model selected  

> color sel magenta

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> select /A:100

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

> show sel target ab

> select sel @ show sel target ab

> select /A:100

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

> color cyan

> color sel cyan

> ui tool show Rotamers

> swapaa interactive sel LEU rotLib Dynameomics

/A LEU 100: phi -116.1, psi 123.9 trans  
Changed 45 bond radii  

> hbonds #!1 & ~#1/A:100 & ~solvent reveal true restrict #1.1 & ~@c,ca,n

0 hydrogen bonds found  

> clashes #!1 & ~#1/A:100 & ~solvent radius 0.075 reveal true restrict #1.1 &
> ~@c,ca,n

26 clashes  

> select

900 atoms, 903 bonds, 26 pseudobonds, 129 residues, 12 models selected  

> show (#1.1.1-9#!1 & sel) target ab

> undo

> swapaa #1/A:100 LEU criteria 1 rotLib Dynameomics retain false

Using Dynameomics library  
1dzo_coord.pdb #1/A LEU 100: phi -116.1, psi 123.9 trans  
Applying LEU rotamer (chi angles: -69.0 168.5) to 1dzo_coord.pdb #1/A LEU 100  

> ~select

Nothing selected  

> select /A:100

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

> select zone

Missing or invalid "near" argument: empty atom specifier  

> select zone near :100

Missing or invalid "near" argument: invalid objects specifier  

> select zone near

Missing or invalid "near" argument: invalid objects specifier  

> select /A:99

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

> select add /A:100

15 atoms, 13 bonds, 2 residues, 1 model selected  

> select add /A:101

22 atoms, 19 bonds, 3 residues, 1 model selected  
Drag select of 1 atoms, 3 residues, 1 bonds  

> select clear

> hide atoms

> select /A:84

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

> show sel

> select sel @ show sel

> show sel target ab

> select clear

> hide atoms

> select /A:111

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

> select sel @ show sel target ab

> select /A:111

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

> color sel cyan

> ui tool show Rotamers

> swapaa interactive sel ASN rotLib Dynameomics

/A ASN 111: phi -108.5, psi -6.5 trans  
Changed 90 bond radii  

> hbonds #!1 & ~#1/A:111 & ~solvent reveal true restrict #1.1 & ~@c,ca,n

10 hydrogen bonds found  

> clashes #!1 & ~#1/A:111 & ~solvent radius 0.075 reveal true restrict #1.1 &
> ~@c,ca,n

57 clashes  

> swapaa #1/A:111 ASN criteria 4 rotLib Dynameomics retain false

Using Dynameomics library  
1dzo_coord.pdb #1/A ASN 111: phi -108.5, psi -6.5 trans  
Applying ASN rotamer (chi angles: -173.2 7.5) to 1dzo_coord.pdb #1/A ASN 111  

> addh

Summary of feedback from adding hydrogens to 1dzo_coord.pdb #1  
---  
warnings | Not adding hydrogens to /A ARG 30 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /A LYS 68 CD because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A LYS 88 CG (alt loc A) because it is missing heavy-
atom bond partners  
Not adding hydrogens to /A LYS 110 CG because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A LYS 128 CG because it is missing heavy-atom bond
partners  
1 messages similar to the above omitted  
notes | No usable SEQRES records for 1dzo_coord.pdb (#1) chain A; guessing
termini instead  
Chain-initial residues that are actual N termini: /A GLY 25  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ARG 144  
Chain-final residues that are not actual C termini:  
103 hydrogen bonds  
825 hydrogens added  
  

> select clear

> addh

Summary of feedback from adding hydrogens to 1dzo_coord.pdb #1  
---  
warnings | Not adding hydrogens to /A ARG 30 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /A LYS 68 CD because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A LYS 88 CG (alt loc A) because it is missing heavy-
atom bond partners  
Not adding hydrogens to /A LYS 110 CG because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A LYS 128 CG because it is missing heavy-atom bond
partners  
1 messages similar to the above omitted  
notes | No usable SEQRES records for 1dzo_coord.pdb (#1) chain A; guessing
termini instead  
Chain-initial residues that are actual N termini: /A GLY 25  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ARG 144  
Chain-final residues that are not actual C termini:  
100 hydrogen bonds  
0 hydrogens added  
  

> save C:/Chimera/pilin_ID.pdb relModel #1

> show atoms

> ~display h

> hide h

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> ~display hydrogen

> hide hydrogen

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> select h

Expected an objects specifier or a keyword  

> toolshed show

> delete :1-53

> delete :54-64

> delete :64-69

> save C:/Chimera/pilin_FWT.pdb relModel #1

> delete :69-72

> save C:/Chimera/pilin_FWT.pdb relModel #1

> open C:/Chimera/pilin_ID.pdb

Chain information for pilin_ID.pdb #4  
---  
Chain | Description  
A | No description available  
  

> hide #1 models

> hide #2 models

> hide #3 models

> show #4 atoms

> hide (#4 & (protein|nucleic)) target a

> cartoon hide #4

> show (#4 & ((protein&@ca)|(nucleic&@p))) target ab

> undo

> redo

> hide (#4 & (protein|nucleic)) target a

> cartoon hide #4

> show (#4 & backbone) target ab

> show #4 cartoons

> show #4 atoms

> select H

1323 atoms, 192 residues, 2 models selected  

> hide (#4 & sel) target a

> select clear

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> color gold

> color red

> ui tool show "Color Actions"

> color goldenrod

> color tan

> color burly wood

> color tan

> color burly wood

> color #4 byhetero

> select backbone

1169 atoms, 1167 bonds, 192 residues, 2 models selected  

> color sel gray

> color sel black

> select clear

> select #4/A:81@CB

1 atom, 1 residue, 1 model selected  

> select clear

> select #4/A:81

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select sel @ ui tool show Rotamers

> select #4/A:81

22 atoms, 21 bonds, 1 residue, 1 model selected  

> ui tool show Rotamers

> swapaa interactive sel LYS rotLib Dynameomics

pilin_ID.pdb #4/A LYS 81: phi -65.7, psi -1.2 trans  
Changed 486 bond radii  

> hbonds #!4 & ~#4/A:81 & ~solvent reveal true restrict #4.1 & ~@c,ca,n

9 hydrogen bonds found  

> clashes #!4 & ~#4/A:81 & ~solvent radius 0.075 reveal true restrict #4.1 &
> ~@c,ca,n

12 clashes  

> swapaa #4/A:81 LYS criteria 1 rotLib Dynameomics retain false

Using Dynameomics library  
pilin_ID.pdb #4/A LYS 81: phi -65.7, psi -1.2 trans  
Applying LYS rotamer (chi angles: -68.4 -176.1 -171.6 -61.7) to pilin_ID.pdb
#4/A LYS 81  

> color sel purple

> select #4/A:81

11 atoms, 10 bonds, 1 residue, 1 model selected  

> color sel purple

> color sel lightblue purple

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color sel cyan

> select #4/A:115

19 atoms, 18 bonds, 1 residue, 1 model selected  

> ui tool show Rotamers

> swapaa interactive sel ASN rotLib Dynameomics

pilin_ID.pdb #4/A ILE 115: phi -131.3, psi 130.5 trans  
Changed 90 bond radii  

> hbonds #!4 & ~#4/A:115 & ~solvent reveal true restrict #4.1 & ~@c,ca,n

5 hydrogen bonds found  

> clashes #!4 & ~#4/A:115 & ~solvent radius 0.075 reveal true restrict #4.1 &
> ~@c,ca,n

8 clashes  

> swapaa #4/A:115 ASN criteria 3 rotLib Dynameomics

Using Dynameomics library  
pilin_ID.pdb #4/A ILE 115: phi -131.3, psi 130.5 trans  
Applying ASN rotamer (chi angles: -171.7 -71.4) to pilin_ID.pdb #4/A ASN 115  


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Updating list of available bundles failed: [WinError 10061] No connection
could be made because the target machine actively refused it  




OpenGL version: 3.3.13521 Core Profile Forward-Compatible Context 24.20.11001.8003
OpenGL renderer: Radeon RX Vega M GL Graphics
OpenGL vendor: ATI Technologies Inc.
Manufacturer: Dell Inc.
Model: XPS 15 9575
OS: Microsoft Windows 11 Home (Build 22000)
Memory: 16,982,163,456
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-8705G CPU @ 3.10GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
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    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    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: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    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: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    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: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    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: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    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: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 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: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1