ChimeraX bug report submission

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-15.4.1-arm64-arm-64bit
ChimeraX Version: 1.11.dev202505062043 (2025-05-06 20:43:22 UTC)
Description
Klim Verba wants to open the similar structures for a specific cluster.

Log:
UCSF ChimeraX version: 1.11.dev202505062043 (2025-05-06)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/goddard/Downloads/ChimeraX/Foldseek/8xps_foldseek_pdb.sms format
> sms

Summary of feedback from opening
/Users/goddard/Downloads/ChimeraX/Foldseek/8xps_foldseek_pdb.sms  
---  
notes | > open /Users/goddard/Downloads/ChimeraX/PDB/8xps.cif8xps.cif title:  
Structure of Nipah virus Bangladesh string G protein ectodomain monomer bound
to single-domain antibody n425 at 3.22 Angstroms overall resolution [more
info...]  
  
  
  
  
| Chain information for 8xps.cif #1  
  
---  
  
  
Chain  
| Description  
  
  
  
  
  
  
A  
| Nipah virus Bangladesh string G protein  
  
  
  
  
B  
| single-domain antibody n425  
  
  
  
  
  
  
  
  
Non-standard residues in 8xps.cif #1  
  
---  
  
  
  
  
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)  
  
  
  
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)  
  
  
  
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)  
  
  
  
  
Found 194 similar structures to 8xps.cif #1/A in pdb database using foldseek,
name fs1  
  
Read 194 similar structures to 8xps.cif #1/A in pdb database using foldseek,
name fs1  

> similarstructures cluster /A:579,220,506,360,348 clusterDistance 1.5

Clustered 148 of 194 hits that have the specified 5 residues into 6 groups  
Selected rows for 19 hits 7txz_B, 3d12_A, 7txz_A, 2vsm_A, 6cmi_B, 7ty0_C,
2vwd_A, 7ty0_D, 6pdl_E, 2vwd_B, 6vy5_A, 7syz_A, 7syy_A, 6vy6_A, 6vy4_A,
2vsk_C, 6thb_A, 7zm6_A, 7zm5_B  
Selected rows for 14 hits 4gjt_A, 3alz_A, 3alx_A, 3alx_D, 2zb6_A, 3alx_B,
7zny_A, 3alx_C, 3inb_B, 2zb5_A, 2rkc_A, 3inb_A, 7y60_L, 7y5l_E  

> open 4gjt

Summary of feedback from opening 4gjt fetched from pdb  
---  
note | Fetching compressed mmCIF 4gjt from http://files.rcsb.org/download/4gjt.cif  
  
4gjt title:  
complex structure of nectin-4 bound to MV-H [more info...]  
  
Chain information for 4gjt #2  
---  
Chain | Description | UniProt  
A | Hemagglutinin glycoprotein | HEMA_MEASC 156-617  
B C | Poliovirus receptor-related protein 4 | PVRL4_HUMAN 1-115  
  
Non-standard residues in 4gjt #2  
---  
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)  
  
4gjt mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
Deleted 2 extra chains, 1 C-terminal residues, 11 N-terminal residues.  
Alignment of 4gjt chain A to query has RMSD 1.36 using 88 of 375 paired
residues within cutoff distance 2.0  

> open 3alz

Summary of feedback from opening 3alz fetched from pdb  
---  
note | Fetching compressed mmCIF 3alz from http://files.rcsb.org/download/3alz.cif  
  
3alz title:  
Crystal structure of the measles virus hemagglutinin bound to its cellular
receptor SLAM (Form I) [more info...]  
  
Chain information for 3alz #3  
---  
Chain | Description | UniProt  
A | Hemagglutinin | E2RZS2_9PARA 149-617  
B | CDw150 | Q9GJT3_SAGOE 1-140  
  
Non-standard residues in 3alz #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)  
  
3alz mmCIF Assemblies  
---  
1| author_defined_assembly  
2| software_defined_assembly  
  
Deleted 1 extra chains, 3 C-terminal residues, 1 N-terminal residues.  
Alignment of 3alz chain A to query has RMSD 1.37 using 90 of 370 paired
residues within cutoff distance 2.0  

> open 3alx

Summary of feedback from opening 3alx fetched from pdb  
---  
note | Fetching compressed mmCIF 3alx from http://files.rcsb.org/download/3alx.cif  
  
3alx title:  
Crystal structure of the measles virus hemagglutinin bound to its cellular
receptor SLAM (MV-H(L482R)-SLAM(N102H/R108Y) fusion) [more info...]  
  
Chain information for 3alx #4  
---  
Chain | Description | UniProt  
A B C D | Hemagglutinin,LINKER,CDw150 | E2RZS2_9MONO 184-607, Q9GJT3_SAGOE 30-140  
  
Non-standard residues in 3alx #4  
---  
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)  
  
Deleted 3 extra chains, 111 C-terminal residues, 6 N-terminal residues.  
Alignment of 3alx chain A to query has RMSD 1.32 using 93 of 361 paired
residues within cutoff distance 2.0  

> open 3alx

3alx title:  
Crystal structure of the measles virus hemagglutinin bound to its cellular
receptor SLAM (MV-H(L482R)-SLAM(N102H/R108Y) fusion) [more info...]  
  
Chain information for 3alx #5  
---  
Chain | Description | UniProt  
A B C D | Hemagglutinin,LINKER,CDw150 | E2RZS2_9MONO 184-607, Q9GJT3_SAGOE 30-140  
  
Non-standard residues in 3alx #5  
---  
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)  
  
Deleted 3 extra chains, 107 C-terminal residues, 3 N-terminal residues.  
Alignment of 3alx chain D to query has RMSD 1.32 using 103 of 362 paired
residues within cutoff distance 2.0  

> open 2zb6

Summary of feedback from opening 2zb6 fetched from pdb  
---  
note | Fetching compressed mmCIF 2zb6 from http://files.rcsb.org/download/2zb6.cif  
  
2zb6 title:  
Crystal structure of the measles virus hemagglutinin (oligo-sugar type) [more
info...]  
  
Chain information for 2zb6 #6  
---  
Chain | Description | UniProt  
A | Hemagglutinin protein | Q83625_9PARA 149-617  
  
Non-standard residues in 2zb6 #6  
---  
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)  
  
2zb6 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
Deleted 0 extra chains, 8 N-terminal residues.  
Alignment of 2zb6 chain A to query has RMSD 1.38 using 91 of 383 paired
residues within cutoff distance 2.0  

> open 3alx

3alx title:  
Crystal structure of the measles virus hemagglutinin bound to its cellular
receptor SLAM (MV-H(L482R)-SLAM(N102H/R108Y) fusion) [more info...]  
  
Chain information for 3alx #7  
---  
Chain | Description | UniProt  
A B C D | Hemagglutinin,LINKER,CDw150 | E2RZS2_9MONO 184-607, Q9GJT3_SAGOE 30-140  
  
Non-standard residues in 3alx #7  
---  
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)  
  
Deleted 3 extra chains, 112 C-terminal residues.  
Alignment of 3alx chain B to query has RMSD 1.31 using 85 of 372 paired
residues within cutoff distance 2.0  

> open 7zny

Summary of feedback from opening 7zny fetched from pdb  
---  
note | Fetching compressed mmCIF 7zny from http://files.rcsb.org/download/7zny.cif  
  
7zny title:  
Cryo-EM structure of the canine distemper virus tetrameric attachment
glycoprotein [more info...]  
  
Chain information for 7zny #8  
---  
Chain | Description | UniProt  
A B C D | Hemagglutinin glycoprotein | Q9QPQ8_9MONO 1-607  
  
Deleted 3 extra chains, 3 C-terminal residues, 52 N-terminal residues.  
Alignment of 7zny chain A to query has RMSD 1.22 using 94 of 377 paired
residues within cutoff distance 2.0  

> open 3alx

3alx title:  
Crystal structure of the measles virus hemagglutinin bound to its cellular
receptor SLAM (MV-H(L482R)-SLAM(N102H/R108Y) fusion) [more info...]  
  
Chain information for 3alx #9  
---  
Chain | Description | UniProt  
A B C D | Hemagglutinin,LINKER,CDw150 | E2RZS2_9MONO 184-607, Q9GJT3_SAGOE 30-140  
  
Non-standard residues in 3alx #9  
---  
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)  
  
Deleted 3 extra chains, 108 C-terminal residues, 6 N-terminal residues.  
Alignment of 3alx chain C to query has RMSD 1.32 using 98 of 360 paired
residues within cutoff distance 2.0  

> open 3inb

Summary of feedback from opening 3inb fetched from pdb  
---  
note | Fetching compressed mmCIF 3inb from http://files.rcsb.org/download/3inb.cif  
  
3inb title:  
Structure of the measles virus hemagglutinin bound to the CD46 receptor [more
info...]  
  
Chain information for 3inb #10  
---  
Chain | Description | UniProt  
A B | Hemagglutinin glycoprotein | HEMA_MEASE 179-617  
C D | Membrane cofactor protein | MCP_HUMAN 1-126  
  
Non-standard residues in 3inb #10  
---  
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)  
SO4 — sulfate ion  
  
8 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Deleted 3 extra chains, 1 C-terminal residues, 1 N-terminal residues.  
Alignment of 3inb chain B to query has RMSD 1.29 using 90 of 354 paired
residues within cutoff distance 2.0  

> open 2zb5

Summary of feedback from opening 2zb5 fetched from pdb  
---  
note | Fetching compressed mmCIF 2zb5 from http://files.rcsb.org/download/2zb5.cif  
  
2zb5 title:  
Crystal structure of the measles virus hemagglutinin (complex-sugar-type)
[more info...]  
  
Chain information for 2zb5 #11  
---  
Chain | Description | UniProt  
A | Hemagglutinin protein | Q83625_9PARA 149-617  
  
Non-standard residues in 2zb5 #11  
---  
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)  
  
2zb5 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
Deleted 17 N-terminal residues.  
Alignment of 2zb5 chain A to query has RMSD 1.35 using 88 of 375 paired
residues within cutoff distance 2.0  

> open 2rkc

Summary of feedback from opening 2rkc fetched from pdb  
---  
note | Fetching compressed mmCIF 2rkc from http://files.rcsb.org/download/2rkc.cif  
  
2rkc title:  
Crystal structure of the measles virus hemagglutinin [more info...]  
  
Chain information for 2rkc #12  
---  
Chain | Description | UniProt  
A | Hemagglutinin | Q83531_9PARA 156-617  
  
Non-standard residues in 2rkc #12  
---  
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)  
  
Deleted 3 C-terminal residues.  
Alignment of 2rkc chain A to query has RMSD 1.28 using 85 of 364 paired
residues within cutoff distance 2.0  

> open 3inb

3inb title:  
Structure of the measles virus hemagglutinin bound to the CD46 receptor [more
info...]  
  
Chain information for 3inb #13  
---  
Chain | Description | UniProt  
A B | Hemagglutinin glycoprotein | HEMA_MEASE 179-617  
C D | Membrane cofactor protein | MCP_HUMAN 1-126  
  
Non-standard residues in 3inb #13  
---  
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)  
SO4 — sulfate ion  
  
8 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Deleted 3 extra chains, 1 C-terminal residues, 2 N-terminal residues.  
Alignment of 3inb chain A to query has RMSD 1.29 using 86 of 351 paired
residues within cutoff distance 2.0  

> open 7y60

7y60 title:  
Cryo-EM structure of human CAF1LC bound right-handed Di-tetrasome [more
info...]  
  
Chain information for 7y60 #14  
---  
Chain | Description | UniProt  
A C E G | Histone H3.1 | H31_HUMAN 0-135  
B D F H | Histone H4 | H4_HUMAN 0-102  
I | Widom 601 DNA (147-MER) |   
J | Widom 601 DNA (147-MER) |   
K | Chromatin assembly factor 1 subunit A | CAF1A_HUMAN 442-853  
L | Chromatin assembly factor 1 subunit B | CAF1B_HUMAN 1-419  
  
Deleted 11 extra chains, 59 C-terminal residues, 1 N-terminal residues.  
Alignment of 7y60 chain L to query has RMSD 1.26 using 20 of 268 paired
residues within cutoff distance 2.0  

> open 7y5l

7y5l title:  
Crystal structure of human CAF-1 core complex in spacegroup C2 [more info...]  
  
Chain information for 7y5l #15  
---  
Chain | Description | UniProt  
A D | Chromatin assembly factor 1 subunit A | CAF1A_HUMAN 442-714  
B E | Chromatin assembly factor 1 subunit B | CAF1B_HUMAN 1-419  
C F | Histone-binding protein RBBP4 | RBBP4_HUMAN 1-425  
  
Non-standard residues in 7y5l #15  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
  
7y5l mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  
Deleted 5 extra chains, 69 C-terminal residues, 1 N-terminal residues.  
Alignment of 7y5l chain E to query has RMSD 1.45 using 23 of 276 paired
residues within cutoff distance 2.0  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2 Ultra
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac Studio
      Model Identifier: Mac14,14
      Model Number: Z1800003VLL/A
      Chip: Apple M2 Ultra
      Total Number of Cores: 24 (16 performance and 8 efficiency)
      Memory: 64 GB
      System Firmware Version: 11881.101.1
      OS Loader Version: 11881.101.1

Software:

    System Software Overview:

      System Version: macOS 15.4.1 (24E263)
      Kernel Version: Darwin 24.4.0
      Time since boot: 10 days, 11 hours, 44 minutes

Graphics/Displays:

    Apple M2 Ultra:

      Chipset Model: Apple M2 Ultra
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 60
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        PHL 278B1:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.3.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.3.2
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.3
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.5
    ChimeraX-AtomicLibrary: 14.1.17
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.2.6
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.11.dev202505062043
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.6.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.2.1
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PhenixUI: 1.3.7
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.3
    ChimeraX-ProfileGrids: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.45.1
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.2
    coverage: 7.8.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.14
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.57.0
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.13.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    joblib: 1.5.0
    jupyter_client: 8.6.3
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    llvmlite: 0.44.0
    lxml: 5.3.1
    lz4: 4.4.4
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numba: 0.61.2
    numexpr: 2.10.2
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.7
    pluggy: 1.5.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.32
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynndescent: 0.5.13
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.3.5
    pytest-cov: 6.1.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 26.4.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scikit-learn: 1.6.1
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    threadpoolctl: 3.6.0
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.4.2
    tqdm: 4.67.1
    traitlets: 5.14.3
    typing_extensions: 4.13.2
    tzdata: 2025.2
    umap-learn: 0.5.7
    urllib3: 2.4.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14