Klim Verba wants to open the similar structures for a specific cluster.
Add a menu entry to the cluster plot to select the table rows for the members of the clicked on cluster. Once those rows are selected pressing the Open button will load all the structures. Also log the pdb and chain ids of all the cluster members.
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
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
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Added to ChimeraX 1.10 and daily build.
I added an entry to the similar structures cluster plot menu when you click on a node "Select rows for cluster 7zm5_B". After that pressing the Open button will open those structures. The PDB and chain ids of selected rows are also logged.