Make matchmaker command use nucleic matrix by default for RNA/DNA

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-12.5.1-arm64-arm-64bit
ChimeraX Version: 1.5.dev202208221824 (2022-08-22 18:24:03 UTC)
Description
I was surprised matchmaker "mm #2 to #1" refused to align two RNA models "No chains in match structure model1.pdb #2 compatible with BLOSUM-62 similarity matrix".  Model #2 is a single RNA chain and ChimeraX knows that so I expected it would use "matrix Nucleic" automatically when the molecule being matched is nucleic and no matrix is specified.  It took about 5 minutes of digging through documentation find I needed that option.

Log:
UCSF ChimeraX version: 1.5.dev202208221824 (2022-08-22)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7mlx format mmcif fromDatabase pdb

7mlx title:  
SARS-CoV-2 programmed -1 frameshifting element three stem H-type pseudoknot
[more info...]  
  
Chain information for 7mlx #1  
---  
Chain | Description  
H | BL3-6 Fab Heavy Chain  
L | BL3-6 Fab Light Chain  
R | RNA (65-mer)  
  

> open /Users/goddard/ucsf/data/deepfoldrna/results/model1.pdb

Chain information for model1.pdb #2  
---  
Chain | Description  
A | No description available  
  

> mmaker #2 to #1

No chains in match structure model1.pdb #2 compatible with BLOSUM-62
similarity matrix  

> mmaker #2 to #1 matrix Nucleic

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
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 7mlx, chain R (#1) with model1.pdb, chain A (#2), sequence
alignment score = 260  
RMSD between 51 pruned atom pairs is 1.198 angstroms; (across all 65 pairs:
2.007)  
  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.1
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,2
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 7459.141.1
      OS Loader Version: 7459.141.1

Software:

    System Software Overview:

      System Version: macOS 12.5.1 (21G83)
      Kernel Version: Darwin 21.6.0
      Time since boot: 1 day 12:44

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
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    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.0.5
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    build: 0.7.0
    certifi: 2021.10.8
    cftime: 1.6.1
    charset-normalizer: 2.1.0
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.5.2
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    ChimeraX-ArtiaX: 0.1
    ChimeraX-Atomic: 1.40
    ChimeraX-AtomicLibrary: 7.0.2
    ChimeraX-AtomSearch: 2.0.1
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    ChimeraX-Centroids: 1.2
    ChimeraX-ChangeChains: 1.0
    ChimeraX-CheckWaters: 1.1
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    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5.dev202208221824
    ChimeraX-CoreFormats: 1.1
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    ChimeraX-SwapAA: 2.0.1
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    ChimeraX-TapeMeasure: 1.0
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[Eric Pettersen]

Change in daily build, not 1.5 branch.