Foldseek: AttributeError: 'Sequence' object has no attribute 'match_maps'

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-15.3.1-arm64-arm-64bit
ChimeraX Version: 1.10.dev202503040129 (2025-03-04 01:29:19 UTC)
Description
Tried sim seqalign command.

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.10.dev202503040129 (2025-03-04)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> usage simia

"simia" is not a command name  

> usage simia

"simia" is not a command name  

> usage simil

Subcommands are:

  * similarstructures blast
  * similarstructures close
  * similarstructures cluster
  * similarstructures fetchcoords
  * similarstructures fromblast
  * similarstructures ligands
  * similarstructures list
  * similarstructures open
  * similarstructures pairing
  * similarstructures scrollto
  * similarstructures seqalign
  * similarstructures sequences
  * similarstructures traces

  

> open /Users/goddard/Downloads/ChimeraX/Foldseek/9g3n_IF_foldseek_pdb.sms
> format sms

Summary of feedback from opening
/Users/goddard/Downloads/ChimeraX/Foldseek/9g3n_IF_foldseek_pdb.sms  
---  
notes | > open /Users/goddard/Downloads/ChimeraX/PDB/9g3n.cif9g3n.cif title:  
Circularly permuted lumazine synthase 36-pentamer spherical cage [more
info...]  
  
  
  
  
| Chain information for 9g3n.cif #1  
  
---  
  
  
Chain  
| Description  
| UniProt  
  
  
  
  
  
A AA AB AC AD AE AF B BA BB BC BD BE BF C CA CB CC CD CE CF D DA DB DC DD DE
DF E EA EB EC ED EE EF F FA FB FC FD FE FF G GA GB GC GD GE GF H HA HB HC HD
HE HF I IA IB IC ID IE IF J JA JB JC JD JE JF K KA KB KC KD KE KF L LA LB LC
LD LE LF M MA MB MC MD ME MF N NA NB NC ND NE NF O OA OB OC OD OE OF P PA PB
PC PD PE PF Q QA QB QC QD QE QF R RA RB RC RD RE RF S SA SB SC SD SE SF T TA
TB TC TD TE TF U UA UB UC UD UE UF V VA VB VC VD VE VF W WA WB WC WD WE WF X
XA XB XC XD XE XF Y YA YB YC YD YE Z ZA ZB ZC ZD ZE  
| 6,7-dimethyl-8-ribityllumazine synthase  
| RISB_AQUAE 2-36 47-163  
  
  
  
  
Found 305 similar structures to 9g3n.cif #1/IF in pdb database using foldseek,
name fs1  
  
Read 305 similar structures to 9g3n.cif #1/IF in pdb database using foldseek,
name fs1  

> open 2c9b

Summary of feedback from opening 2c9b fetched from pdb  
---  
notes | Fetching compressed mmCIF 2c9b from http://files.rcsb.org/download/2c9b.cif  
Fetching CCD PUG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/PUG/PUG.cif  
  
2c9b title:  
Lumazine Synthase from Mycobacterium tuberculosus Bound to 3-(1,3,7-
TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL) [more info...]  
  
Chain information for 2c9b #2  
---  
Chain | Description | UniProt  
A B C D E F G H I J | 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE | RISB_MYCTU 1-160  
  
Non-standard residues in 2c9b #2  
---  
K — potassium ion  
MPD — (4S)-2-methyl-2,4-pentanediol  
PO4 — phosphate ion  
PUG — 3-(1,3,7-trihydro-9-D-ribityl-2,6,8-purinetrione-7-yl)  
  
2c9b mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
Deleted 9 extra chains, 41 C-terminal residues, 1 N-terminal residues, 657
non-polymer residues more than 3.0 Angstroms away.  
Alignment of 2c9b chain G to query has RMSD 0.94 using 91 of 105 paired
residues within cutoff distance 2.0  

> usage sim seqa

similarstructures seqalign hitStructure [fromSet a text string]  
— Show sequence alignment from a similar structures search for one hit  

> similarstructures seqalign #2

Alignment identifier is 2c9b_G  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2c9b_G  
Traceback (most recent call last):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3215, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/similarstructures/simstruct.py", line 1228, in
similar_structures_sequence_alignment  
a.prematched_assoc_structure(query_match_map, errors, reassoc) # Associate
query  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 759, in
prematched_assoc_structure  
aseq.match_maps[chain] = match_map  
^^^^^^^^^^^^^^^  
AttributeError: 'Sequence' object has no attribute 'match_maps'  
  
AttributeError: 'Sequence' object has no attribute 'match_maps'  
  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 759, in
prematched_assoc_structure  
aseq.match_maps[chain] = match_map  
^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M2 Ultra
OpenGL vendor: Apple

Python: 3.11.4
Locale: 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: 11881.81.4
      OS Loader Version: 11881.81.4

Software:

    System Software Overview:

      System Version: macOS 15.3.1 (24D70)
      Kernel Version: Darwin 24.3.0
      Time since boot: 16 hours, 57 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


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