Opened 4 months ago

Closed 4 months ago

#18038 closed defect (fixed)

Modeller: 'Sequence' object has no attribute 'match_maps'

Reported by: chimerax-bug-report@… Owned by: pett
Priority: normal Milestone:
Component: Sequence Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.11.dev202506120207 (2025-06-12 02:07:37 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.11.dev202506120207 (2025-06-12)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Users/ASM/Desktop/MD/BET vs TNFa Docking/BET vs TNFa Docking/TNFa
> (Receptor)/2az5.pdb"

2az5.pdb title:  
Crystal structure of TNF-α with A small molecule inhibitor [more info...]  
  
Chain information for 2az5.pdb #1  
---  
Chain | Description | UniProt  
A B C D | tumor necrosis factor (TNF-α) (tumor necrosis factor ligand superfamily member 2) (TNF-A) (cachectin) [contains: tumor necrosis factor, membrane form; tumor necrosis factor, soluble form] | TNFA_HUMAN 10-157  
  
Non-standard residues in 2az5.pdb #1  
---  
307 —
6,7-dimethyl-3-[(methyl{2-[methyl({1-[3-(trifluoromethyl)phenyl]-1H-indol-3-yl}methyl)amino]ethyl}amino)methyl]-4H-chromen-4-one  
  

> log metadata #1

Metadata for 2az5.pdb #1  
---  
Title | Crystal structure of TNF-α with A small molecule inhibitor  
Citation | Small-molecule inhibition of TNF-α. PMID: 16284179  
Non-standard residue | 307 — 6,7-dimethyl-3-[(methyl{2-[methyl({1-[3-(trifluoromethyl)phenyl]-1H-indol-3-yl}methyl)amino]ethyl}amino)methyl]-4H-chromen-4-one  
Gene source | Homo sapiens (human)  
Experimental method | X-ray diffraction  
Resolution | 2.10Å  
  
> help help:credits.html

[Repeated 1 time(s)]

> open "C:/Users/ASM/Downloads/rcsb_pdb_2AZ5 (1).fasta"

Summary of feedback from opening C:/Users/ASM/Downloads/rcsb_pdb_2AZ5
(1).fasta  
---  
notes | Alignment identifier is rcsb_pdb_2AZ5 (1).fasta  
Associated 2az5.pdb chain A to 2AZ5_1|Chains A, B, C, D|Tumor necrosis factor
(TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF-a)
(Cachectin) [Contains: Tumor necrosis factor, membrane form; Tumor necrosis
factor, soluble form]|Homo sapiens (9606) with 0 mismatches  
Associated 2az5.pdb chain B to 2AZ5_1|Chains A, B, C, D|Tumor necrosis factor
(TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF-a)
(Cachectin) [Contains: Tumor necrosis factor, membrane form; Tumor necrosis
factor, soluble form]|Homo sapiens (9606) with 0 mismatches  
Associated 2az5.pdb chain C to 2AZ5_1|Chains A, B, C, D|Tumor necrosis factor
(TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF-a)
(Cachectin) [Contains: Tumor necrosis factor, membrane form; Tumor necrosis
factor, soluble form]|Homo sapiens (9606) with 0 mismatches  
Associated 2az5.pdb chain D to 2AZ5_1|Chains A, B, C, D|Tumor necrosis factor
(TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF-a)
(Cachectin) [Contains: Tumor necrosis factor, membrane form; Tumor necrosis
factor, soluble form]|Homo sapiens (9606) with 0 mismatches  
  
Opened 1 sequence from rcsb_pdb_2AZ5 (1).fasta  

> select /A:86-88/B,D:31-35,86-88,102-112

194 atoms, 186 bonds, 2 pseudobonds, 26 residues, 2 models selected  

> select add #1

4500 atoms, 4376 bonds, 7 pseudobonds, 770 residues, 3 models selected  

> select subtract #1

Nothing selected  

> select clear

[Repeated 1 time(s)]

> select /A:86-88/B,D:31-35,86-88,102-112

194 atoms, 186 bonds, 2 pseudobonds, 26 residues, 2 models selected  

> ui tool show "Modeller Comparative"

> ui tool show "Model Loops"

[Repeated 2 time(s)]

> select clear

[Repeated 2 time(s)]

> select add #1

4500 atoms, 4376 bonds, 7 pseudobonds, 770 residues, 3 models selected  

> select subtract #1

Nothing selected  

> hide #!1 models

> show #!1 models

> modeller refine "rcsb_pdb_2AZ5 (1).fasta:1:all-missing" numModels 3 fast
> false adjacentFlexible 1 protocol DOPE executableLocation
> C:/WINDOWS/system32/cmd.exe directory "C:/Users/ASM/Desktop/MD/BET vs TNFa
> Docking/BET vs TNFa Docking/TNFa (Receptor)/Modelling Messing Structures"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.11.dev202506120207\bin\Lib\site-
packages\chimerax\modeller\tool.py", line 311, in launch_modeller  
run(  
File "C:\Program Files\ChimeraX 1.11.dev202506120207\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.dev202506120207\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3246, in run  
result = ci.function(  
^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.dev202506120207\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3882, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.dev202506120207\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3225, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.dev202506120207\bin\Lib\site-
packages\chimerax\modeller\cmd.py", line 138, in model_loops  
loops.model(session, targets, adjacent_flexible=adjacent_flexible,
block=block, chains=chains,  
File "C:\Program Files\ChimeraX 1.11.dev202506120207\bin\Lib\site-
packages\chimerax\modeller\loops.py", line 142, in model  
find_affixes(r.chain, {r.chain: (seq, None, match_map)})]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.dev202506120207\bin\Lib\site-
packages\chimerax\modeller\loops.py", line 306, in find_affixes  
match_map = aseq.match_maps[chain]  
^^^^^^^^^^^^^^^  
AttributeError: 'Sequence' object has no attribute 'match_maps'  
  
AttributeError: 'Sequence' object has no attribute 'match_maps'  
  
File "C:\Program Files\ChimeraX 1.11.dev202506120207\bin\Lib\site-
packages\chimerax\modeller\loops.py", line 306, in find_affixes  
match_map = aseq.match_maps[chain]  
^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> modeller refine "rcsb_pdb_2AZ5 (1).fasta:1:all-missing" numModels 3 fast
> false adjacentFlexible 1 protocol DOPE executableLocation
> C:/WINDOWS/system32/cmd.exe directory "C:/Users/ASM/Desktop/MD/BET vs TNFa
> Docking/BET vs TNFa Docking/TNFa (Receptor)/Modelling Messing Structures"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.11.dev202506120207\bin\Lib\site-
packages\chimerax\modeller\tool.py", line 311, in launch_modeller  
run(  
File "C:\Program Files\ChimeraX 1.11.dev202506120207\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.dev202506120207\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3246, in run  
result = ci.function(  
^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.dev202506120207\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3882, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.dev202506120207\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3225, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.dev202506120207\bin\Lib\site-
packages\chimerax\modeller\cmd.py", line 138, in model_loops  
loops.model(session, targets, adjacent_flexible=adjacent_flexible,
block=block, chains=chains,  
File "C:\Program Files\ChimeraX 1.11.dev202506120207\bin\Lib\site-
packages\chimerax\modeller\loops.py", line 142, in model  
find_affixes(r.chain, {r.chain: (seq, None, match_map)})]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.dev202506120207\bin\Lib\site-
packages\chimerax\modeller\loops.py", line 306, in find_affixes  
match_map = aseq.match_maps[chain]  
^^^^^^^^^^^^^^^  
AttributeError: 'Sequence' object has no attribute 'match_maps'  
  
AttributeError: 'Sequence' object has no attribute 'match_maps'  
  
File "C:\Program Files\ChimeraX 1.11.dev202506120207\bin\Lib\site-
packages\chimerax\modeller\loops.py", line 306, in find_affixes  
match_map = aseq.match_maps[chain]  
^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 31.0.101.2125
OpenGL renderer: Intel(R) UHD Graphics
OpenGL vendor: Intel

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

Manufacturer: Microsoft Corporation
Model: Surface Laptop Go
OS: Microsoft Windows 11 Pro (Build 22631)
Memory: 8,155,983,872
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-1035G1 CPU @ 1.00GHz
OSLanguage: en-US

Installed Packages:
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    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.3.4
    build: 1.2.2.post1
    certifi: 2025.4.26
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.0
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.3.1
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.9
    ChimeraX-AtomicLibrary: 14.1.19
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
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    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
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    ChimeraX-ChangeChains: 1.1
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    ChimeraX-ChemGroup: 2.0.2
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    ChimeraX-CommandLine: 1.3.0
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.11.dev202506120207
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
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    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    ChimeraX-Dssp: 2.0
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    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5.1
    ChimeraX-Help: 1.3
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    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
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    ChimeraX-Meeting: 1.0.1
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    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
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    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.15.1
    ChimeraX-OrthoPick: 1.0.1
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    ChimeraX-PubChem: 2.2
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    ChimeraX-RotamerLibsRichardson: 2.0
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    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
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    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.2
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    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
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    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
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    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.46.1
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 0.1
    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: 1.1.5
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    colorama: 0.4.6
    comm: 0.2.2
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    cycler: 0.12.1
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    executing: 2.2.0
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    imagesize: 1.4.1
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    sphinxcontrib-serializinghtml: 2.0.0
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    tables: 3.10.2
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    tifffile: 2025.3.13
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    webcolors: 24.11.1
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    widgetsnbextension: 4.0.14
    WMI: 1.5.1

Change History (2)

comment:1 by pett, 4 months ago

Component: Unassigned → Sequence
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Modeller: 'Sequence' object has no attribute 'match_maps'
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