KeyError matching selected regions

[kamalendu-pal@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Unable to align at specific selected residues 
error sms
matchmaker #2/A & sel to #1/A & sel pairing ss
Traceback (most recent call last):   File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\match_maker\tool.py", line 169, in <lambda>     bbox.button(qbbox.Apply).clicked.connect(lambda *args: self.run_matchmaker(apply=True))   File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\match_maker\tool.py", line 288, in run_matchmaker     run(self.session, cmd)   File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\commands\run.py", line 38, in run     results = command.run(text, log=log, return_json=return_json)   File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2897, in run     result = ci.function(session, **kw_args)   File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\match_maker\match.py", line 730, in cmd_match     ret_vals = match(session, pairing, match_items, matrix, alg, gap_open, gap_extend,   File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\match_maker\match.py", line 314, in match     score, s1, s2 = align(session, ref, match, final_matrix_name[match], alg, KeyError: <chimerax.atomic.molobject.StructureSeq object at 0x000001423B9EC070> KeyError:

File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\match_maker\match.py", line 314, in match
score, s1, s2 = align(session, ref, match, final_matrix_name[match], alg,

See log for complete Python traceback.


Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "E:/9C1_prelim_models/Final Refined
> model/R399A-pH6/R399A-pH6-compresssed/R399A-pH6-compressed_RSR026_A-
> coot-36.pdb"

Chain information for R399A-pH6-compressed_RSR026_A-coot-36.pdb #1  
---  
Chain | Description  
A B | No description available  
  

> open "E:/9C1_prelim_models/Final Refined
> model/R399A-pH8/EDITED_R399A-RSR043_AB-coot-61.pdb"

Chain information for EDITED_R399A-RSR043_AB-coot-61.pdb #2  
---  
Chain | Description  
A B | No description available  
  

> select :487-535,571-652,815-946

8436 atoms, 8548 bonds, 2 pseudobonds, 1052 residues, 3 models selected  

> save "E:/9C1_prelim_models/Final Refined
> model/R399A-pH6/R399A-pH6-compresssed/R399A-pH8_ARD_2.pdb" models #2
> selectedOnly true

> save "E:/9C1_prelim_models/Final Refined
> model/R399A-pH6/R399A-pH6-compresssed/R399A-pH6-compress_ARD_2.pdb" models
> #1 selectedOnly true

> close #1

> close #2

> open "E:/9C1_prelim_models/Final Refined
> model/R399A-pH6/R399A-pH6-compresssed/R399A-pH6-compress_ARD_2.pdb"
> "E:/9C1_prelim_models/Final Refined
> model/R399A-pH6/R399A-pH6-compresssed/R399A-pH8_ARD_2.pdb"

Summary of feedback from opening E:/9C1_prelim_models/Final Refined
model/R399A-pH6/R399A-pH6-compresssed/R399A-pH6-compress_ARD_2.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ILE A 78
LEU A 94 1 17  
Start residue of secondary structure not found: HELIX 2 2 THR A 103 ASN A 119
1 17  
Start residue of secondary structure not found: HELIX 3 3 PRO A 121 ALA A 131
1 11  
Start residue of secondary structure not found: HELIX 4 4 PRO A 135 GLN A 140
1 6  
Start residue of secondary structure not found: HELIX 5 5 PHE A 142 PHE A 152
1 11  
70 messages similar to the above omitted  
  
Summary of feedback from opening E:/9C1_prelim_models/Final Refined
model/R399A-pH6/R399A-pH6-compresssed/R399A-pH8_ARD_2.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ILE A 78
LEU A 94 1 17  
Start residue of secondary structure not found: HELIX 2 2 THR A 103 ASN A 119
1 17  
Start residue of secondary structure not found: HELIX 3 3 PRO A 121 ALA A 131
1 11  
Start residue of secondary structure not found: HELIX 4 4 PRO A 135 GLN A 140
1 6  
Start residue of secondary structure not found: HELIX 5 5 PHE A 142 ALA A 153
1 12  
73 messages similar to the above omitted  
  
Chain information for R399A-pH6-compress_ARD_2.pdb #1  
---  
Chain | Description  
A B | No description available  
  
Chain information for R399A-pH8_ARD_2.pdb #2  
---  
Chain | Description  
A B | No description available  
  

> close #1

> close #2

> open "E:/9C1_prelim_models/Final Refined
> model/R399A-pH6/R399A-pH6-compresssed/R399A-pH8_ARD_1.pdb"

Chain information for R399A-pH8_ARD_1.pdb #1  
---  
Chain | Description  
A B | No description available  
  

> open "E:/9C1_prelim_models/Final Refined
> model/R399A-pH6/R399A-pH6-compresssed/R399A-pH6-compress_ARD_1.pdb"

Chain information for R399A-pH6-compress_ARD_1.pdb #2  
---  
Chain | Description  
A B | No description available  
  

> select /A:488-535

744 atoms, 754 bonds, 96 residues, 2 models selected  

> ui tool show Matchmaker

> matchmaker #2/A & sel to #1/A & sel pairing ss

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\tool.py", line 169, in <lambda>  
bbox.button(qbbox.Apply).clicked.connect(lambda *args:
self.run_matchmaker(apply=True))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\tool.py", line 288, in run_matchmaker  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\match.py", line 730, in cmd_match  
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\match.py", line 314, in match  
score, s1, s2 = align(session, ref, match, final_matrix_name[match], alg,  
KeyError: <chimerax.atomic.molobject.StructureSeq object at
0x000001423B962DF0>  
  
KeyError:  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\match.py", line 314, in match  
score, s1, s2 = align(session, ref, match, final_matrix_name[match], alg,  
  
See log for complete Python traceback.  
  

> matchmaker #2/A & sel to #1/A & sel pairing ss

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\tool.py", line 169, in <lambda>  
bbox.button(qbbox.Apply).clicked.connect(lambda *args:
self.run_matchmaker(apply=True))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\tool.py", line 288, in run_matchmaker  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\match.py", line 730, in cmd_match  
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\match.py", line 314, in match  
score, s1, s2 = align(session, ref, match, final_matrix_name[match], alg,  
KeyError: <chimerax.atomic.molobject.StructureSeq object at
0x000001423B9EC070>  
  
KeyError:  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\match.py", line 314, in match  
score, s1, s2 = align(session, ref, match, final_matrix_name[match], alg,  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 27.20.100.9664
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel

Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: Dell Inc.
Model: OptiPlex 7090
OS: Microsoft Windows 10 Enterprise (Build 19044)
Memory: 16,898,920,448
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i5-10500 CPU @ 3.10GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
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    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
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    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
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    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    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: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    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: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
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    ChimeraX-SelInspector: 1.0
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    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
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    html2text: 2020.1.16
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    imagecodecs: 2022.9.26
    imagesize: 1.4.1
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    ipykernel: 6.21.1
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    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
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    typing-extensions: 4.5.0
    tzdata: 2023.3
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    wcwidth: 0.2.6
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    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    WMI: 1.5.1
    zipp: 3.15.0

[Eric Pettersen]

Repeat with:

open 1gpq 1uuz
sel /A:90-110
matchmaker #2/A & sel to #1/A & sel pairing ss

[Eric Pettersen]

Fix will be in tomorrow's daily build