KeyError matching selected regions

[francesco.musiani@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Matchmaker done selecting some portions of the proteins to match.

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 2v53 format mmcif fromDatabase pdb

2v53 title:  
Crystal structure of a SPARC-collagen complex [more info...]  
  
Chain information for 2v53 #1  
---  
Chain | Description | UniProt  
A | SPARC | SPRC_HUMAN 53-195 204-286  
B C D | COLLAGEN ALPHA-1(III) CHAIN | CO3A1_HUMAN 7-27  
  
Non-standard residues in 2v53 #1  
---  
CA — calcium ion  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
SO4 — sulfate ion  
  

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> open 1sra format mmcif fromDatabase pdb

1sra title:  
Structure of A novel extracellular CA2+-binding module In
BM-40(slash)sparc(slash)osteonectin [more info...]  
  
Chain information for 1sra #2  
---  
Chain | Description | UniProt  
A | SPARC | SPRC_HUMAN 136-286  
  
Non-standard residues in 1sra #2  
---  
CA — calcium ion  
  

> open 1bmo format mmcif fromDatabase pdb

1bmo title:  
BM-40, FS/ec domain pair [more info...]  
  
Chain information for 1bmo #3  
---  
Chain | Description | UniProt  
A B | BM-40 | SPRC_HUMAN 54-286  
  
Non-standard residues in 1bmo #3  
---  
CA — calcium ion  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  

> open 1nub format mmcif fromDatabase pdb

1nub title:  
Helix C deletion mutant of BM-40 FS-ec domain pair [more info...]  
  
Chain information for 1nub #4  
---  
Chain | Description | UniProt  
A B | BASEMENT MEMBRANE PROTEIN BM-40 | SPRC_HUMAN 54-286  
  
Non-standard residues in 1nub #4  
---  
CA — calcium ion  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
  
1nub mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> ui tool show Matchmaker

> matchmaker #3/A to #1/A pairing ss

Parameters  
---  
Chain pairing | ss  
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 2v53, chain A (#1) with 1bmo, chain A (#3), sequence alignment
score = 1065.2  
RMSD between 81 pruned atom pairs is 0.873 angstroms; (across all 214 pairs:
7.941)  
  

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

Parameters  
---  
Chain pairing | ss  
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 2v53, chain A (#1) with 1sra, chain A (#2), sequence alignment
score = 660.1  
RMSD between 109 pruned atom pairs is 0.888 angstroms; (across all 132 pairs:
1.744)  
  

> matchmaker #4/A to #1/A pairing ss

Parameters  
---  
Chain pairing | ss  
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 2v53, chain A (#1) with 1nub, chain A (#4), sequence alignment
score = 1055.5  
RMSD between 74 pruned atom pairs is 1.134 angstroms; (across all 214 pairs:
5.087)  
  

> select #1/B#1/C#1/D

632 atoms, 673 bonds, 100 residues, 1 model selected  

> hide sel cartoons

> show sel cartoons

> hide sel cartoons

> hide sel atoms

> select #3/B

1899 atoms, 1954 bonds, 12 pseudobonds, 235 residues, 2 models selected  

> hide sel cartoons

> hide sel atoms

[Repeated 1 time(s)]

> select #4/B

1838 atoms, 1891 bonds, 15 pseudobonds, 229 residues, 2 models selected  

> hide sel cartoons

> hide sel atoms

Drag select of 29 atoms, 30 bonds  

> select up

32 atoms, 31 bonds, 4 residues, 2 models selected  

> select up

56 atoms, 58 bonds, 4 residues, 2 models selected  

> select up

7586 atoms, 7810 bonds, 936 residues, 2 models selected  

> select down

56 atoms, 58 bonds, 4 residues, 2 models selected  

> hide sel atoms

Drag select of 283 residues  

> select up

3100 atoms, 3165 bonds, 368 residues, 4 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
0x0000028C090DD970>  
  
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
0x0000028C093438E0>  
  
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.  
  

> select clear

Drag select of 21 residues  
Drag select of 8 residues  
Drag select of 22 residues  

> select up

2171 atoms, 2215 bonds, 251 residues, 4 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
0x0000028C09382D60>  
  
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
0x0000028C09397F70>  
  
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 NVIDIA 529.08
OpenGL renderer: NVIDIA GeForce MX250/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

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

Manufacturer: HP
Model: HP ProBook 450 G7
OS: Microsoft Windows 10 Pro (Build 19045)
Memory: 16,539,754,496
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-10510U CPU @ 1.80GHz
OSLanguage: it-IT

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
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
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    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
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    ChimeraX-ColorGlobe: 1.0
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    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
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    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
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    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
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    ChimeraX-MapFit: 2.0
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    ChimeraX-MDcrds: 2.6
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    ChimeraX-Meeting: 1.0.1
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    ChimeraX-PDB: 2.7.2
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    ChimeraX-ReadPbonds: 1.0.1
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    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
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    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    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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    ipython: 8.10.0
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    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    WMI: 1.5.1
    zipp: 3.15.0

[pett]

Hi Francesco,

Thanks for reporting this problem. It is fixed in the 1.7 release candidate, so if you use that then things will work.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab