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#9614 closed defect (duplicate)

MatchMaker: KeyError with domain matching

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

Description

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

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  

> ui tool show AlphaFold

> alphafold predict
> MDFNSLAYDQKFFNFTAAQLSAEREHIVQDIIKKGIGQIIDKIKTPATAELLEAEKETVERRFQASASKGLKALRELDSKVFHVPPHVLHPEHMFVENQYTSEEEEQKTARLEELKAKYRENMAMLAHLKIEEEKYAAMEDLIQKEIEMQDRVQRSCSSLNITKLKQFWNQVPLQIKKETD,MEDSEAAFKRHEGVGPKVKQAYEEAIKQIFADLSCADLQAWDAIYQEHEQSALDTESIVDRTRSLMTKVVLEMNRCFFASNDVPNKLQTLEMLKEHFAAYEGKKWNVNTAAPDKLTRPLRMRFLDFSVEFMEQQLASQAKELEIAMAKSNANRERLQHVHDKRLKLTVQMEQQLSQYEKVKTELIKLGEALNDF,MEPAESPEKLMKFVRRSDVLEYVGNTSAVDLSSGDLSDIDLKDVPAQLEATLKPRRYEASTLFNIDLDDIWDPSCQEDEVQQYKERAQKEQQKFFDFVMHAALDTDNRKVSFKPNKEQQRYLDQGPNLQNFVRSSLAFTNAAIRFQAEHEDMMELQCNMDDHYLFMRNTMINNAIHQNMANQR,MSKPQNNDTLELDDILSQPVKDKERFAAFMMRKLAENKPAQNDNLFGNFKLDFDLDFEVPLIKKSQAKPKSKLPEVQPLGELVSKNSAATEKVN

Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.  
Running AlphaFold prediction  
AlphaFold prediction finished  
Results in /Users/fpelisch/Downloads/ChimeraX/AlphaFold/prediction_2  

> open
> /Users/fpelisch/Downloads/ChimeraX/AlphaFold/prediction_2/best_model.pdb

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  

> set bgColor white

> sequence chain #1/A

Alignment identifier is 1/A  

> select /A:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A

1485 atoms, 1509 bonds, 181 residues, 1 model selected  

> color sel forest green

> sequence chain #1/B

Alignment identifier is 1/B  

> color sel dark gray

> sequence chain #1/C

Alignment identifier is 1/C  

> color sel cyan

> sequence chain #1/D

Alignment identifier is 1/D  

> select /B:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /B

1576 atoms, 1601 bonds, 194 residues, 1 model selected  

> color sel dark gray

> select /C:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /C

1498 atoms, 1525 bonds, 183 residues, 1 model selected  

> color sel cyan

> select /A:1-2

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select /A

1485 atoms, 1509 bonds, 181 residues, 1 model selected  

> color sel forest green

> select /D:1-2

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select /D

746 atoms, 758 bonds, 94 residues, 1 model selected  

> color sel magenta

> select /A:129

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:129

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> select /A:126

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:126

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> select /A:3-13,17-43,49-54,56-81,91-97,102-138,140-159,162-180

1254 atoms, 1262 bonds, 153 residues, 1 model selected  

> select /A:112

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:112

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:112,115

16 atoms, 14 bonds, 2 residues, 1 model selected  

> show sel atoms

> select /A:12

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select /A:12-13

22 atoms, 23 bonds, 2 residues, 1 model selected  

> select /A:12-13,15-16

40 atoms, 41 bonds, 4 residues, 1 model selected  

> show sel atoms

> select /B:41

14 atoms, 15 bonds, 1 residue, 1 model selected  

> select /B:41

14 atoms, 15 bonds, 1 residue, 1 model selected  

> select /A:3-13,17-43,49-54,56-81,91-97,102-138,140-159,162-180

1254 atoms, 1262 bonds, 153 residues, 1 model selected  

> select /B:41

14 atoms, 15 bonds, 1 residue, 1 model selected  

> select /B:41

14 atoms, 15 bonds, 1 residue, 1 model selected  

> select /B:41,45

26 atoms, 27 bonds, 2 residues, 1 model selected  

> select /B:41,45-46

35 atoms, 36 bonds, 3 residues, 1 model selected  

> select /B:44

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /B:44-45

20 atoms, 20 bonds, 2 residues, 1 model selected  

> select /B:41,44-45

34 atoms, 35 bonds, 3 residues, 1 model selected  

> show sel atoms

> select /D:26

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel atoms

> select /D:29

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select /D:29

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel atoms

> select /D:29

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select /D:29

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select /D:26-27,29

27 atoms, 27 bonds, 3 residues, 1 model selected  

> select /D:26

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select /D:26

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select /D:26,29

22 atoms, 22 bonds, 2 residues, 1 model selected  

> ui tool show Contacts

> contacts sel interModel false intraMol false ignoreHiddenModels true select
> true color #000000 reveal true

16 contacts  

> select /D:38-39

16 atoms, 16 bonds, 2 residues, 1 model selected  

> select /D:38-94

446 atoms, 454 bonds, 57 residues, 1 model selected  
Drag select of 113 atoms, 390 residues, 106 bonds, 16 pseudobonds  

> hide sel atoms

> open "/Users/fpelisch/OneDrive - University of Dundee/C. elegans centromere
> kinetochore project/MIS12/MIS-12C_HCP-4 model/MIS12C_HCP-4.pdb"

Chain information for MIS12C_HCP-4.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> select

9236 atoms, 9366 bonds, 16 pseudobonds, 1138 residues, 3 models selected  

> show sel cartoons

> hide sel atoms

> sequence chain #2/A

Alignment identifier is 2/A  

> select #2/A

1028 atoms, 1046 bonds, 127 residues, 1 model selected  

> color sel lime

> select #2/B

1064 atoms, 1072 bonds, 132 residues, 1 model selected  

> color sel light gray

> select #2/C

507 atoms, 510 bonds, 64 residues, 1 model selected  

> color sel blue

> select #2/E

856 atoms, 865 bonds, 105 residues, 1 model selected  

> color sel hot pink

> ui tool show Matchmaker

> matchmaker #2/E to #1/D 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 best_model.pdb, chain D (#1) with MIS12C_HCP-4.pdb, chain E (#2),
sequence alignment score = 39.7  
RMSD between 6 pruned atom pairs is 1.019 angstroms; (across all 30 pairs:
9.556)  
  

> ui tool show Matchmaker

> 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 best_model.pdb, chain A (#1) with MIS12C_HCP-4.pdb, chain A (#2),
sequence alignment score = 156.4  
RMSD between 26 pruned atom pairs is 0.842 angstroms; (across all 116 pairs:
5.832)  
  

> select #2/D

476 atoms, 480 bonds, 58 residues, 1 model selected  

> color sel orange

Drag select of 32 residues  

> hide sel cartoons

Drag select of 1 residues  

> hide sel cartoons

Drag select of 5 residues  

> hide sel cartoons

Drag select of 181 residues  

> hide sel cartoons

> ui tool show "Show Sequence Viewer"

> sequence chain #2/A

Destroying pre-existing alignment with identifier 2/A  
Alignment identifier is 2/A  

> sequence chain #2/B

Alignment identifier is 2/B  

> sequence chain #2/C

Alignment identifier is 2/C  

> sequence chain #2/D

Alignment identifier is 2/D  

> sequence chain #2/E

Alignment identifier is 2/E  

> select #2/E:33

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #2/E:33

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #2/E:33,36

23 atoms, 22 bonds, 2 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 23 atom styles  

> select #1/D:26

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select #1/D:26

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select #1/D:26,29

22 atoms, 22 bonds, 2 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 22 atom styles  

> hide #!1 models

> select #2/E:1-2

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #2/E

856 atoms, 865 bonds, 105 residues, 1 model selected  

> hide sel cartoons

Drag select of 23 atoms, 381 residues, 22 bonds  

> hide sel atoms

> open "/Users/fpelisch/OneDrive - University of Dundee/C. elegans centromere
> kinetochore project/MIS12/elegans MIS-12C
> (rank_2_model_2_ptm_seed_0_unrelaxed).pdb"

Chain information for elegans MIS-12C
(rank_2_model_2_ptm_seed_0_unrelaxed).pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  

> hide #2 models

> select #1/A#2/A#3/A

3722 atoms, 3775 bonds, 457 residues, 3 models selected  

> color (#3 & sel) forest green

> select #1/D#2/D#3/D

2636 atoms, 2675 bonds, 327 residues, 3 models selected  

> color (#3 & sel) orange

> select #1/C#2/C#3/C

4691 atoms, 4760 bonds, 590 residues, 3 models selected  

> color (#3 & sel) orange

> select ~sel

11173 atoms, 11315 bonds, 16 pseudobonds, 1378 residues, 4 models selected  

> hide sel & #3 cartoons

> hide #3 models

> show #2 models

> select #2/C:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/C

507 atoms, 510 bonds, 64 residues, 1 model selected  

> color sel orange

> select #2/D:1

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

> select #2/D

476 atoms, 480 bonds, 58 residues, 1 model selected  

> color sel cyan

> select #2/C:53

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #2/C:53-55

25 atoms, 24 bonds, 3 residues, 1 model selected  

> select #2/C:10-11

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select #2/C:1-11

84 atoms, 83 bonds, 11 residues, 1 model selected  

> ui tool show Contacts

> contacts sel interModel false intraMol false ignoreHiddenModels true select
> true color #000000 reveal true

6 contacts  

> hide sel atoms

Drag select of 6 atoms, 54 residues  

> hide sel atoms

> show #3 models

> hide #!2 models

> select

15864 atoms, 16075 bonds, 22 pseudobonds, 1968 residues, 5 models selected  

> show sel & #3 cartoons

> hide sel & #3 atoms

> select #1/A:3

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select #1/A:3-139

1116 atoms, 1136 bonds, 137 residues, 1 model selected  

> select #1/A:181

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:156-181

213 atoms, 216 bonds, 26 residues, 1 model selected  

> select add #3

6841 atoms, 6925 bonds, 856 residues, 2 models selected  

> select subtract #3

213 atoms, 216 bonds, 26 residues, 1 model selected  

> close #1-2

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 3/A  

> select /A:149

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A

1209 atoms, 1220 bonds, 149 residues, 1 model selected  

> close

> ui tool show AlphaFold

> alphafold predict
> MTTPSPQEISTVTLNSLSKEERKKAILALQTKKNEIKLVIDEHQKKLAEFRQSIPDGCCEMFENEKKIRLKHSSTAELLPHLQKVGSSSVDKEKMINNIRQRVEVQVADQETFKSIEERNELLRRENENLKKEVNTVAAELLQEFESYE,DDSTQLELLMAKIPQEMSGYMKKLATDIKEMSQYDAQLARNIDDMEAVFKSRETKLKSAIEIAKDSFISSALPLRLETLDMTLRKEESPNDIVARLHGSFLDKTQDAGNVNTAQKENQQLEDERGMLEEKLESLNKIKREKDEFLAKMRKEEEEALARREEIKQGFERIDALMSKIKPIPIFEF,DPAVVNVVYLTSEDPSTEQHPEALKFQRIVENEKMKVQHEIDSLNSTNQLSAEKIDMLKTKELLKFSHDEREAIMIARKDAEIKFLELRLKFALEKKIESDQEIAELEQGNSKMAEQLRGLDKMAVVQKELEKLRSLPPSREESGKIRKEWMEMKQWEFDQKMKALRNVRSNMIALRSEKNALEMKVAEEHEKFAQRNDLKKSRMLVFSKAVKKIVNF

Running AlphaFold prediction  

> alphafold predict
> MTTPSPQEISTVTLNSLSKEERKKAILALQTKKNEIKLVIDEHQKKLAEFRQSIPDGCCEMFENEKKIRLKHSSTAELLPHLQKVGSSSVDKEKMINNIRQRVEVQVADQETFKSIEERNELLRRENENLKKEVNTVAAELLQEFESYE,DDSTQLELLMAKIPQEMSGYMKKLATDIKEMSQYDAQLARNIDDMEAVFKSRETKLKSAIEIAKDSFISSALPLRLETLDMTLRKEESPNDIVARLHGSFLDKTQDAGNVNTAQKENQQLEDERGMLEEKLESLNKIKREKDEFLAKMRKEEEEALARREEIKQGFERIDALMSKIKPIPIFEF,DPAVVNVVYLTSEDPSTEQHPEALKFQRIVENEKMKVQHEIDSLNSTNQLSAEKIDMLKTKELLKFSHDEREAIMIARKDAEIKFLELRLKFALEKKIESDQEIAELEQGNSKMAEQLRGLDKMAVVQKELEKLRSLPPSREESGKIRKEWMEMKQWEFDQKMKALRNVRSNMIALRSEKNALEMKVAEEHEKFAQRNDLKKSRMLVFSKAVKKIVNF

Running AlphaFold prediction  
AlphaFold prediction finished  
Results in /Users/fpelisch/Downloads/ChimeraX/AlphaFold/prediction_2  

> open
> /Users/fpelisch/Downloads/ChimeraX/AlphaFold/prediction_2/best_model.pdb

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> sequence chain #1/A

Alignment identifier is 1/A  

> sequence chain #1/B

Alignment identifier is 1/B  

> sequence chain #1/C

Alignment identifier is 1/C  

> select /A:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A

1209 atoms, 1220 bonds, 149 residues, 1 model selected  

> color sel cyan

> select /B:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /B

1486 atoms, 1500 bonds, 184 residues, 1 model selected  

> color sel orange

> select /C:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /C

1789 atoms, 1810 bonds, 218 residues, 1 model selected  

> color sel purple

> open "/Users/fpelisch/OneDrive - University of Dundee/C. elegans centromere
> kinetochore project/MIS12/elegans MIS-12C
> (rank_2_model_2_ptm_seed_0_unrelaxed).pdb"

Chain information for elegans MIS-12C
(rank_2_model_2_ptm_seed_0_unrelaxed).pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  

> hide #1 models

Drag select of 830 residues  

> hide sel cartoons

> select #2/C

2686 atoms, 2725 bonds, 343 residues, 1 model selected  

> show sel cartoons

> ui tool show "Show Sequence Viewer"

> sequence chain #2/C

Alignment identifier is 2/C  

> select #2/C:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/C:1-157

1186 atoms, 1210 bonds, 157 residues, 1 model selected  

> hide sel cartoons

> select #2/C:268

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/C:268-343

637 atoms, 642 bonds, 76 residues, 1 model selected  

> show #1 models

> ui tool show Matchmaker

> matchmaker #2/C & sel to #1/B pairing ss

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 288, in run_matchmaker  
run(self.session, cmd)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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 0x7fdfb3066b50>  
  
KeyError:  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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: 4.1 ATI-4.5.14
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac18,3
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 4.2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      System Firmware Version: 429.120.4.0.0
      SMC Version (system): 2.41f2

Software:

    System Software Overview:

      System Version: macOS 11.4 (20F71)
      Kernel Version: Darwin 20.5.0
      Time since boot: 8 days 20:24

Graphics/Displays:

    Radeon Pro 580:

      Chipset Model: Radeon Pro 580
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c0
      ROM Revision: 113-D000AA-931
      VBIOS Version: 113-D0001A1X-025
      EFI Driver Version: 01.00.931
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    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: 2021.10.8
    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
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    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
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    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
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    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
    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
    zipp: 3.15.0

Attachments (1)

test.cxs (582.2 KB ) - added by pett 2 years ago.

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Change History (4)

comment:1 by pett, 2 years ago

Component:	Unassigned → Structure Comparison
Owner:	set to pett
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → MatchMaker: KeyError with domain matching

by pett, 2 years ago

Attachment:	test.cxs added

comment:2 by pett, 2 years ago

Repeat with attached session and: matchmaker #1/C & sel to #2/B pairing ss

comment:3 by pett, 2 years ago

Resolution:	→ duplicate
Status:	accepted → closed

duplicate of #9586

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