Sequence alignment identifiers containing spaces need to be quoted in commands
The following bug report has been submitted:
Platform: macOS-26.5.1-arm64-arm-64bit
ChimeraX Version: 1.13.dev202606221815 (2026-06-22 18:15:02 UTC)
Description
Changing headers shown on a sequence alignment which has an identifier name with spaces using the context menu gives errors because it issues the command "sequence header id with spaces conservation show" where the identifier (in this case "id with spaces") is not quoted.
Log:
UCSF ChimeraX version: 1.13.dev202606221815 (2026-06-22)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/goddard/ucsf/data/oprm_uniref100/P35372_msa_10_len350.fasta
> ident "id with spaces"
Summary of feedback from opening
/Users/goddard/ucsf/data/oprm_uniref100/P35372_msa_10_len350.fasta
---
notes | Alignment identifier is id with spaces
Showing conservation header ("seq_conservation" residue attribute) for
alignment id with spaces
Opened 54 sequences from P35372_msa_10_len350.fasta
> sequence header conservation hide
Hiding conservation header for alignment id with spaces
> open /Users/goddard/ucsf/data/oprm_uniref100/P35372_msa_10_len300.fasta
Summary of feedback from opening
/Users/goddard/ucsf/data/oprm_uniref100/P35372_msa_10_len300.fasta
---
notes | Alignment identifier is P35372_msa_10_len300.fasta
Showing conservation header ("seq_conservation" residue attribute) for
alignment P35372_msa_10_len300.fasta
Opened 85 sequences from P35372_msa_10_len300.fasta
> sequence header id with spaces conservation show
Should be one of 'consensus', 'conservation', or 'rmsd'
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M2 Ultra
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.2
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: 18000.120.36
OS Loader Version: 18000.120.36
Software:
System Software Overview:
System Version: macOS 26.5.1 (25F80)
Kernel Version: Darwin 25.5.0
Time since boot: 19 days, 21 hours, 6 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 4
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:
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aiohappyeyeballs: 2.6.2
aiohttp: 3.13.4
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.13.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 26.1.0
babel: 2.18.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 4.4.2
build: 1.3.0
certifi: 2025.8.3
cftime: 1.6.5
charset-normalizer: 3.4.7
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.2
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.2.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.69.1
ChimeraX-AtomicLibrary: 14.4
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: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4.1
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.4
ChimeraX-Cluster: 1.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.1
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.13.dev202606221815
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DAQplugin: 1.0.0
ChimeraX-DataFormats: 1.2.4
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.2.2
ChimeraX-Dssp: 2.0
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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: 2.5.3
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ChimeraX-HKCage: 1.3
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ChimeraX-IO: 1.0.4
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ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.23
ChimeraX-ModelPanel: 1.6.1
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: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-Nucleotides: 2.0.3
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ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.13
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ChimeraX-ProfileGrids: 1.10.1
ChimeraX-ProNA3D: 0.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
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ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
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ChimeraX-SDF: 2.0.3
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ChimeraX-SeqView: 2.19
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ChimeraX-ShowSequences: 1.0.3
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ChimeraX-SmoothLines: 1.0
ChimeraX-SNFG: 1.0
ChimeraX-SpaceNavigator: 1.0
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ChimeraX-Struts: 1.0.1
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ChimeraX-Tug: 1.0.1
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ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.6.3
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ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
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ChimeraX-WavefrontOBJ: 1.0
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comm: 0.2.3
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![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Other commands from the sequence viewer tool such as associating a structure to a sequence also fails due to unquoted alignment identifiers containing spaces.