Sequence identity selection broken

[Tristan Croll]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
The "select by sequence identity" options no longer seem to be working as they used to - with two related sequences loaded and aligned, "Select by column identity":100% selects everything regardless of identity, and <100% selects nothing. Labelling the residues with the `seq_identity` attribute, looks like all the matching residues have been given the value 200.0, and all non-matching ones 100.0.

Log:
> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  
UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7hqr

Summary of feedback from opening 7hqr fetched from pdb  
---  
notes | Fetching compressed mmCIF 7hqr from http://files.rcsb.org/download/7hqr.cif  
Fetching CCD 5RG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/5RG/5RG.cif  
  
7hqr title:  
PanDDA analysis group deposition -- Crystal Structure of FatA in complex with
Z56946871 [more info...]  
  
Chain information for 7hqr #1  
---  
Chain | Description | UniProt  
A B | Oleoyl-acyl carrier protein thioesterase 1, chloroplastic | FATA1_ARATH 75-362  
  
Non-standard residues in 7hqr #1  
---  
5RG — 2-amino-5-fluorobenzoic acid  
SO4 — sulfate ion  
  
57 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> alphafold fetch O04792

Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json  
Fetching compressed AlphaFold O04792 from
https://alphafold.ebi.ac.uk/files/AF-O04792-F1-model_v3.cif  
Chain information for AlphaFold O04792 #2  
---  
Chain | Description | UniProt  
A | Acyl-[acyl-carrier-protein] hydrolase | O04792_GARMA 1-352  
  
Color AlphaFold O04792 by residue attribute pLDDT_score  

> matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
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 7hqr, chain A (#1) with AlphaFold O04792, chain A (#2), sequence
alignment score = 1211.3  
RMSD between 257 pruned atom pairs is 0.661 angstroms; (across all 265 pairs:
0.878)  
  

> sequence align #1/A|#2

Alignment identifier is 1  
Associated 7hqr chain A to #1/A with 0 mismatches  
Associated 7hqr chain B to #1/A with 0 mismatches  
Associated AlphaFold O04792 chain A to #2/A with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: AFGSTLTD12QC15LF  
Webservices job finished: AFGSTLTD12QC15LF  

> select ::seq_identity>=100 & #1/A-B:75-359 #2/A

7063 atoms, 7193 bonds, 4 pseudobonds, 880 residues, 3 models selected  

> select ::seq_identity<100 & #1/A-B:75-359 #2/A

Nothing selected  

> select clear

> label /A ::seq_identity

> undo

> ~label

> label /A text {0.seq_identity}

> hide #!2 models

> select #1/A:153@CB

1 atom, 1 residue, 1 model selected  

> select #1/A:315

6 atoms, 5 bonds, 1 residue, 1 model selected  

> show #!2 models

> hide #!2 models




OpenGL version: 3.3.0 NVIDIA 576.57
OpenGL renderer: NVIDIA GeForce RTX 3070 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_GB.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

Manufacturer: HP
Model: HP ZBook Studio 15.6 inch G8 Mobile Workstation PC
OS: Microsoft Windows 11 Pro (Build 26100)
Memory: 34,007,068,672
MaxProcessMemory: 137,438,953,344
CPU: 16 11th Gen Intel(R) Core(TM) i7-11800H @ 2.30GHz
OSLanguage: en-GB

Installed Packages:
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    ChimeraX-Smiles: 2.1.2
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    ChimeraX-TapeMeasure: 1.0
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[Eric Pettersen]

Fix: ​https://github.com/RBVI/ChimeraX/commit/e2c8148d2e0296646c86c67f58d7098a2a7c116e