MatchMaker: KeyError matching chains

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-13.3.1-arm64-arm-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:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
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 figureS.3.C.potabc-nanodisc-com.cxc

> open ../pdb/EcPotABC-apo-final.pdb

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

> open ../pdb/EcPotABC-nanodisc-final.pdb

Chain information for EcPotABC-nanodisc-final.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  

> color /A pink

> color /D violet

> color /B wheat

> color /C lime

> dssp

> color #2 #808080

> cartoon style width 2 thickness .4

> set bgColor white

> select #1/B:301/E:9

Nothing selected  

> color sel salmon

> color sel byhetero

> ~select

Nothing selected  

> matchmaker #2 to #1 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 EcPotABC-apo-final.pdb, chain A (#1) with EcPotABC-nanodisc-
final.pdb, chain A (#2), sequence alignment score = 1824.8  
Matchmaker EcPotABC-apo-final.pdb, chain B (#1) with EcPotABC-nanodisc-
final.pdb, chain B (#2), sequence alignment score = 1409.4  
Matchmaker EcPotABC-apo-final.pdb, chain C (#1) with EcPotABC-nanodisc-
final.pdb, chain C (#2), sequence alignment score = 1249.2  
Matchmaker EcPotABC-apo-final.pdb, chain D (#1) with EcPotABC-nanodisc-
final.pdb, chain D (#2), sequence alignment score = 1787.2  
RMSD between 1239 pruned atom pairs is 0.595 angstroms; (across all 1240
pairs: 0.598)  
  

> lighting soft depthCue true depthCueStart 0.4 depthCueEnd 0.8 shadows false

> view matrix camera
> -0.46886,0.0091658,0.88322,389.6,-0.87646,0.11913,-0.46651,-57.953,-0.10949,-0.99284,-0.047822,95.148

> view matrix models #1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0

executed figureS.3.C.potabc-nanodisc-com.cxc  

> matchmaker #2 to #1 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 EcPotABC-apo-final.pdb, chain A (#1) with EcPotABC-nanodisc-
final.pdb, chain A (#2), sequence alignment score = 1824.8  
Matchmaker EcPotABC-apo-final.pdb, chain B (#1) with EcPotABC-nanodisc-
final.pdb, chain B (#2), sequence alignment score = 1409.4  
Matchmaker EcPotABC-apo-final.pdb, chain C (#1) with EcPotABC-nanodisc-
final.pdb, chain C (#2), sequence alignment score = 1249.2  
Matchmaker EcPotABC-apo-final.pdb, chain D (#1) with EcPotABC-nanodisc-
final.pdb, chain D (#2), sequence alignment score = 1787.2  
RMSD between 1239 pruned atom pairs is 0.595 angstroms; (across all 1240
pairs: 0.598)  
  

> view matrix

view matrix camera
0.85583,0.13304,-0.49985,-44.962,-0.50439,0.00044941,-0.86348,-169.66,-0.11466,0.99111,0.067489,129.53  
view matrix models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.62778,0.77377,-0.084691,-7.2244,0.77462,-0.63173,-0.029746,109.8,-0.076519,-0.046929,-0.99596,226.27  
  

> save ../figure/figureS.3.C-nanodisc.png supersample 3 transparentBackground
> true

> hide #2 models

> view matrix

view matrix camera
0.86508,0.19473,-0.46228,-32.361,-0.48194,0.067034,-0.87364,-172.99,-0.13913,0.97857,0.15184,157.67  
view matrix models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.62778,0.77377,-0.084691,-7.2244,0.77462,-0.63173,-0.029746,109.8,-0.076519,-0.046929,-0.99596,226.27  
  

> close session

> open /Users/qiaozhu/Dropbox/PotABCD/figure/cxc/figureS.3.C.potabc-
> compare.cxc

> open ../pdb/EcPotABC-apo-final.pdb

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

> open ../pdb/EcPotABC-with-2SPD.pdb

Summary of feedback from opening ../pdb/EcPotABC-with-2SPD.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 14 14 ILE B 2
PHE B 25 1 24  
Start residue of secondary structure not found: HELIX 15 15 ASP B 41 LEU B 47
1 7  
Start residue of secondary structure not found: HELIX 16 16 PRO B 49 LYS B 82
1 34  
Start residue of secondary structure not found: HELIX 17 17 ARG B 88 TRP B 100
1 13  
Start residue of secondary structure not found: HELIX 18 18 SER B 103 LEU B
114 1 12  
9 messages similar to the above omitted  
  
Chain information for EcPotABC-with-2SPD.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  

> color /A pink

> color /D violet

> color /B wheat

> color /C lime

> dssp

> color #2 #808080

> cartoon style width 2 thickness .4

> set bgColor white

> select #1/B:301/E:9

Nothing selected  

> color sel salmon

> color sel byhetero

> ~select

Nothing selected  

> matchmaker #2 to #1 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 EcPotABC-apo-final.pdb, chain A (#1) with EcPotABC-with-2SPD.pdb,
chain A (#2), sequence alignment score = 1771.1  
Matchmaker EcPotABC-apo-final.pdb, chain B (#1) with EcPotABC-with-2SPD.pdb,
chain B (#2), sequence alignment score = 1381.8  
Matchmaker EcPotABC-apo-final.pdb, chain C (#1) with EcPotABC-with-2SPD.pdb,
chain C (#2), sequence alignment score = 1236.6  
Matchmaker EcPotABC-apo-final.pdb, chain D (#1) with EcPotABC-with-2SPD.pdb,
chain D (#2), sequence alignment score = 1774.9  
RMSD between 989 pruned atom pairs is 0.939 angstroms; (across all 1240 pairs:
2.515)  
  

> lighting soft depthCue true depthCueStart 0.4 depthCueEnd 0.8 shadows false

> view matrix camera
> 0.86508,0.19473,-0.46228,-32.361,-0.48194,0.067034,-0.87364,-172.99,-0.13913,0.97857,0.15184,157.67

> view matrix models
> #1,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.62778,0.77377,-0.084691,-7.2244,0.77462,-0.63173,-0.029746,109.8,-0.076519,-0.046929,-0.99596,226.27

executed figureS.3.C.potabc-compare.cxc  

> hide #2 models

> matchmaker #2:A-D to #1/A-D 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/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
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 0x137bca520>  
  
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 Metal - 83.1
OpenGL renderer: Apple M1
OpenGL vendor: Apple

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: iMac21,2
      Model Number: Z14M0000VZP/A
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 8422.100.650
      OS Loader Version: 8422.100.650

Software:

    System Software Overview:

      System Version: macOS 13.3.1 (a) (22E772610a)
      Kernel Version: Darwin 22.4.0
      Time since boot: 5 hours, 51 minutes

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 7
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 4.5K (4480 x 2520)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
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    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
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    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
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    ChimeraX-BasicActions: 1.1.2
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    ChimeraX-CageBuilder: 1.0.1
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    ChimeraX-ChemGroup: 2.0.1
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    ChimeraX-ColorActions: 1.0.3
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    ChimeraX-ColorKey: 1.5.3
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    ChimeraX-Contacts: 1.0.1
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    ChimeraX-ESMFold: 1.0
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    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
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