Session reset: 'Tasks' object has no attribute 'remove'

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5.dev202209112252 (2022-09-11 22:52:01 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.5.dev202209112252 (2022-09-11)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/Claudia/Desktop/SBBM/Module 1/Exercise 2/5ttu.pdb"

5ttu.pdb title:  
JAK3 with covalent inhibitor 7 [more info...]  
  
Chain information for 5ttu.pdb #1  
---  
Chain | Description | UniProt  
A | tyrosine-protein kinase JAK3 | JAK3_HUMAN  
  
Non-standard residues in 5ttu.pdb #1  
---  
7KV —
1-[(3AR,7AR)-1-(7H-pyrrolo[2,3-D]pyrimidin-4-yl)octahydro-6H-pyrrolo[2,3-C]pyridin-6-yl]propan-1-one  
SO4 — sulfate ion  
  

> select helix

1167 atoms, 1185 bonds, 144 residues, 1 model selected  

> color sel cornflower blue

> select strand

407 atoms, 402 bonds, 51 residues, 1 model selected  

> color sel yellow

> color sel byhetero

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> select clear

> select /A:830-834

13 atoms, 11 bonds, 1 pseudobond, 2 residues, 2 models selected  

> select /A:830-837

35 atoms, 33 bonds, 1 pseudobond, 5 residues, 2 models selected  

> select /A:830

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

> select /A:830-837

35 atoms, 33 bonds, 1 pseudobond, 5 residues, 2 models selected  

> select /A:830

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

> select /A:830-834

13 atoms, 11 bonds, 1 pseudobond, 2 residues, 2 models selected  

> ui tool show "Model Loops"

> modeller refine 1/A:1:16-17 numModels 5 fast false adjacentFlexible 1
> protocol DOPE-HR

Webservices job id: SLPWSVUYA2MCFKOJ  

> open 5TTU

Summary of feedback from opening 5TTU fetched from pdb  
---  
notes | Fetching compressed mmCIF 5ttu from
http://files.rcsb.org/download/5ttu.cif  
Fetching CCD 7KV from http://ligand-expo.rcsb.org/reports/7/7KV/7KV.cif  
Fetching CCD SO4 from http://ligand-expo.rcsb.org/reports/S/SO4/SO4.cif  
  
5ttu title:  
Jak3 with covalent inhibitor 7 [more info...]  
  
Chain information for 5ttu #2  
---  
Chain | Description | UniProt  
A | Tyrosine-protein kinase JAK3 | JAK3_HUMAN  
  
Non-standard residues in 5ttu #2  
---  
7KV —
1-[(3aR,7aR)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)octahydro-6H-pyrrolo[2,3-c]pyridin-6-yl]propan-1-one  
SO4 — sulfate ion  
  
Modeller job ID SLPWSVUYA2MCFKOJ finished  
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 5ttu.pdb, chain A (#1) with chain_A, chain A (#), sequence
alignment score = 1420.7  
RMSD between 271 pruned atom pairs is 0.119 angstroms; (across all 271 pairs:
0.119)  
  
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 5ttu.pdb, chain A (#1) with chain_A, chain A (#), sequence
alignment score = 1420.7  
RMSD between 271 pruned atom pairs is 0.114 angstroms; (across all 271 pairs:
0.114)  
  
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 5ttu.pdb, chain A (#1) with chain_A, chain A (#), sequence
alignment score = 1420.7  
RMSD between 271 pruned atom pairs is 0.122 angstroms; (across all 271 pairs:
0.122)  
  
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 5ttu.pdb, chain A (#1) with chain_A, chain A (#), sequence
alignment score = 1420.7  
RMSD between 271 pruned atom pairs is 0.117 angstroms; (across all 271 pairs:
0.117)  
  
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 5ttu.pdb, chain A (#1) with chain_A, chain A (#), sequence
alignment score = 1420.7  
RMSD between 271 pruned atom pairs is 0.120 angstroms; (across all 271 pairs:
0.120)  
  
Associated chain_A chain A to chain A with 0 mismatches  
[Repeated 4 time(s)] Chain information for chain_A  
---  
Chain | Description  
3.1/A 3.2/A 3.3/A 3.4/A 3.5/A | No description available  
  

> save /Users/Claudia/Desktop/ADRB_loop.cxs

> select
> #1/A:818-821,861-877,909-943,951-954,990-1002,1006-1022,1025-1038,1045-1056,1067-1078,1081-1085,1087-1099
> #3.1/A:818-821,861-877,909-943,951-954,990-1002,1006-1022,1025-1038,1045-1056,1067-1078,1081-1085,1087-1099
> #3.2/A:818-821,861-877,909-943,951-954,990-1002,1006-1022,1025-1038,1045-1056,1067-1078,1081-1085,1087-1099
> #3.3/A:818-821,861-877,909-943,951-954,990-1002,1006-1022,1025-1038,1045-1056,1067-1078,1081-1085,1087-1099
> #3.4/A:818-821,861-877,909-943,951-954,990-1002,1006-1022,1025-1038,1045-1056,1067-1078,1081-1085,1087-1099
> #3.5/A:818-821,861-877,909-943,951-954,990-1002,1006-1022,1025-1038,1045-1056,1067-1078,1081-1085,1087-1099

7195 atoms, 7309 bonds, 876 residues, 6 models selected  

> select #1/A:851 #3.1/A:851 #3.2/A:851 #3.3/A:851 #3.4/A:851 #3.5/A:851

48 atoms, 42 bonds, 6 residues, 6 models selected  

> select #1/A:851-860 #3.1/A:851-860 #3.2/A:851-860 #3.3/A:851-860
> #3.4/A:851-860 #3.5/A:851-860

463 atoms, 462 bonds, 60 residues, 6 models selected  
Tyrosine-Protein Kinase JAK3 (5ttu.pdb (#1) Chain A) [ID: 1/A] region chain A
[34-43] RMSD: 0.005  
  

> ui tool show "Renumber Residues"

> renumber #1/A:815-1099 #2/A:815-1099 #3.1/A:815-1099 #3.2/A:815-1099
> #3.3/A:815-1099 #3.4/A:815-1099 #3.5/A:815-1099 seqStart 835

1897 residues renumbered  

> ui tool show "Renumber Residues"

> renumber #1/A:835-1119 #2/A:846-1130 #3.1/A:835-1119 #3.2/A:835-1119
> #3.3/A:835-1119 #3.4/A:835-1119 #3.5/A:835-1119 seqStart 835

0 residues renumbered  

> ui tool show "Renumber Residues"

> renumber #1/A:835-1119 #2/A:846-1130 #3.1/A:835-1119 #3.2/A:835-1119
> #3.3/A:835-1119 #3.4/A:835-1119 #3.5/A:835-1119 seqStart 815

1897 residues renumbered  

> select #1/A:835 #3.1/A:835 #3.2/A:835 #3.3/A:835 #3.4/A:835 #3.5/A:835

36 atoms, 30 bonds, 6 residues, 6 models selected  

> select #1/A:835-1099 #3.1/A:835-1099 #3.2/A:835-1099 #3.3/A:835-1099
> #3.4/A:835-1099 #3.5/A:835-1099

12206 atoms, 12498 bonds, 12 pseudobonds, 1524 residues, 12 models selected  
Tyrosine-Protein Kinase JAK3 (5ttu.pdb (#1) Chain A) [ID: 1/A] region chain A
[18-271] RMSD: 0.024  
  

> ui tool show "Renumber Residues"

> select #1/A:835-836 #3.1/A:835-836 #3.2/A:835-836 #3.3/A:835-836
> #3.4/A:835-836 #3.5/A:835-836

78 atoms, 72 bonds, 12 residues, 6 models selected  

> select #1/A:835-1046 #3.1/A:835-1046 #3.2/A:835-1046 #3.3/A:835-1046
> #3.4/A:835-1046 #3.5/A:835-1046

9717 atoms, 9925 bonds, 12 pseudobonds, 1206 residues, 12 models selected  
Tyrosine-Protein Kinase JAK3 (5ttu.pdb (#1) Chain A) [ID: 1/A] region chain A
[18-218] RMSD: 0.027  
  

> select #1/A:835-836 #3.1/A:835-836 #3.2/A:835-836 #3.3/A:835-836
> #3.4/A:835-836 #3.5/A:835-836

78 atoms, 72 bonds, 12 residues, 6 models selected  

> select #1/A:835-1099 #3.1/A:835-1099 #3.2/A:835-1099 #3.3/A:835-1099
> #3.4/A:835-1099 #3.5/A:835-1099

12206 atoms, 12498 bonds, 12 pseudobonds, 1524 residues, 12 models selected  
Tyrosine-Protein Kinase JAK3 (5ttu.pdb (#1) Chain A) [ID: 1/A] region chain A
[18-271] RMSD: 0.024  
  

> renumber #1/A:835-1099 #3.1/A:835-1099 #3.2/A:835-1099 #3.3/A:835-1099
> #3.4/A:835-1099 #3.5/A:835-1099 start 835

0 residues renumbered  

> ui tool show "Renumber Residues"

> renumber #1/A:815-1099 #2/A:826-1110 #3.1/A:815-1099 #3.2/A:815-1099
> #3.3/A:815-1099 #3.4/A:815-1099 #3.5/A:815-1099 seqStart 815

0 residues renumbered  

> select clear

> select #1/A:835-1099 #3.1/A:835-1099 #3.2/A:835-1099 #3.3/A:835-1099
> #3.4/A:835-1099 #3.5/A:835-1099

12206 atoms, 12498 bonds, 12 pseudobonds, 1524 residues, 12 models selected  

> select add #3

14226 atoms, 13388 bonds, 12 pseudobonds, 2774 residues, 13 models selected  

> select subtract #3.1

11781 atoms, 11120 bonds, 10 pseudobonds, 2270 residues, 11 models selected  

> select add #3

14226 atoms, 13388 bonds, 12 pseudobonds, 2774 residues, 13 models selected  

> select clear

> hide #!3 models

> show #!3 models

> hide #!2 models

> hide #!1 models

> show #!1 models

> show #!2 models

> hide #!2 models

> hide #!1 models

> select #1/A:835-1099 #3.1/A:835-1099 #3.2/A:835-1099 #3.3/A:835-1099
> #3.4/A:835-1099 #3.5/A:835-1099

12206 atoms, 12498 bonds, 12 pseudobonds, 1524 residues, 12 models selected  

> select #1/A:854-855 #3.1/A:854-855 #3.2/A:854-855 #3.3/A:854-855
> #3.4/A:854-855 #3.5/A:854-855

96 atoms, 90 bonds, 12 residues, 6 models selected  

> select #1/A:854-855 #3.1/A:854-855 #3.2/A:854-855 #3.3/A:854-855
> #3.4/A:854-855 #3.5/A:854-855

96 atoms, 90 bonds, 12 residues, 6 models selected  
Tyrosine-Protein Kinase JAK3 (5ttu.pdb (#1) Chain A) [ID: 1/A] region chain A
[37-38] RMSD: 0.005  
  

> color (#!3.3 & sel) orange

> select clear

> ui mousemode right select

> select #3.3/A:855

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

> color sel orange red

> select

17035 atoms, 15792 bonds, 16 pseudobonds, 3528 residues, 15 models selected  

> surface hidePatches (#!3.3 & sel)

> ui tool show Distances

Drag select of 1 atoms  

> select clear

> select add #3.3/A:855@NZ

1 atom, 1 bond, 1 residue, 1 model selected  

> select add #3.3/A:274@O2

2 atoms, 1 bond, 2 residues, 1 model selected  

> select subtract #3.3/A:274@O2

1 atom, 1 bond, 1 residue, 1 model selected  

> select add #3.3/A:274@O2

2 atoms, 1 bond, 2 residues, 1 model selected  

> select #3.3/A:274@O2

1 atom, 1 residue, 1 model selected  

> select add #3.3/A:855@NZ

2 atoms, 2 residues, 1 model selected  

> distance #3.3/A:274@O2 #3.3/A:855@NZ

Distance between chain_A #3.3/A SO4 274 O2 and LYS 855 NZ: 2.760Å  

> open /Users/Claudia/Desktop/ADRB_loop.cxs

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Users/Claudia/Desktop/SBBM/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 697, in restore  
self.reset()  
File
"/Users/Claudia/Desktop/SBBM/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 541, in reset  
sm.reset_state(container, self)  
File
"/Users/Claudia/Desktop/SBBM/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tasks.py", line 547, in reset_state  
task.terminate()  
File
"/Users/Claudia/Desktop/SBBM/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tasks.py", line 155, in terminate  
self.session.tasks.remove(self)  
AttributeError: 'Tasks' object has no attribute 'remove'  
  

Failed opening file /Users/Claudia/Desktop/ADRB_loop.cxs:  
'Tasks' object has no attribute 'remove'  

> open /Users/Claudia/Desktop/ADRB_loop.cxs

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Users/Claudia/Desktop/SBBM/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 697, in restore  
self.reset()  
File
"/Users/Claudia/Desktop/SBBM/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 541, in reset  
sm.reset_state(container, self)  
File
"/Users/Claudia/Desktop/SBBM/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tasks.py", line 547, in reset_state  
task.terminate()  
File
"/Users/Claudia/Desktop/SBBM/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tasks.py", line 155, in terminate  
self.session.tasks.remove(self)  
AttributeError: 'Tasks' object has no attribute 'remove'  
  

Failed opening file /Users/Claudia/Desktop/ADRB_loop.cxs:  
'Tasks' object has no attribute 'remove'  




OpenGL version: 4.1 INTEL-18.8.5
OpenGL renderer: Intel(R) Iris(TM) Graphics 6100
OpenGL vendor: Intel Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.1
Qt platform: cocoa
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
      System Firmware Version: 430.140.3.0.0
      OS Loader Version: 540.120.3~22
      SMC Version (system): 2.28f7

Software:

    System Software Overview:

      System Version: macOS 12.6 (21G115)
      Kernel Version: Darwin 21.6.0
      Time since boot: 7:51

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 Family: Supported, Metal GPUFamily macOS 1
      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: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.0.8
    Babel: 2.10.3
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.1
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.2
    ChimeraX-AtomicLibrary: 7.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0
    ChimeraX-CheckWaters: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.2
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5.dev202209112252
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.7
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    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: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.9
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.3
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.0.0
    filelock: 3.7.1
    fonttools: 4.37.1
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 4.12.0
    ipykernel: 6.15.1
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 4.11.1
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.5
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.3
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    prompt-toolkit: 3.0.31
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.1
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.1
    python-dateutil: 2.8.2
    pytz: 2022.2.1
    pyzmq: 23.2.1
    qtconsole: 5.3.1
    QtPy: 2.2.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    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
    stack-data: 0.5.0
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    urllib3: 1.26.12
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.8.1