Allow Uniprot identifiers with isoform specifier in AlphaFold tool

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-12.3.1-arm64-arm-64bit
ChimeraX Version: 1.4.dev202203271748 (2022-03-27 17:48:18 UTC)
Description
The 7mn5 mmCIF file lists uniprot id Q02297-6 in the _struct_ref_seq table and alphafold match does not recognize that as a valid Uniprot id.  The "-6" suffix means isoform 6.  The AlphaFold database does not have isoform predictions so it does not change the result where alphafold match searches the database for a close sequence (and surprisingly finds a sequence different than Q02297).

Might want our code that accepts uniprot ids, such as the AlphaFold tool to accept isoform uniprot ids when specifying a sequence.

Log:
UCSF ChimeraX version: 1.4.dev202203271748 (2022-03-27)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7mn5 format mmcif fromDatabase pdb

7mn5 title:  
Structure of the HER2/HER3/NRG1b Heterodimer Extracellular Domain [more
info...]  
  
Chain information for 7mn5 #1  
---  
Chain | Description | UniProt  
A | Receptor tyrosine-protein kinase erbB-3 | ERBB3_HUMAN  
B | Receptor tyrosine-protein kinase erbB-2,Maltose/maltodextrin-binding
periplasmic protein | MALE_ECOLI  
H | Isoform 6 of Pro-neuregulin-1, membrane-bound isoform | NRG1-6_HUMAN  
  
Non-standard residues in 7mn5 #1  
---  
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)  
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)  
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)  
  

> alphafold match #1

UniProt identifiers must be 6 or 10 characters long, got "Q02297-6"  

1 UniProt id does not have an AlphaFold database model: Q02297-6 (chain H)  

3 AlphaFold models found using UniProt identifiers: P21860 (chain A), P04626
(chain B), P0AEX9 (chain B)  
1 AlphaFold model found using sequence similarity searches: A0A140LHZ9 (chain
H)  
AlphaFold chains matching 7mn5  
---  
Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id  
H | A0A140LHZ9_MOUSE | A0A140LHZ9 | 1.34 | 87 | 49 | 86  
B | ERBB2_HUMAN | P04626 | 3.12 | 1029 | 579 | 100  
A | ERBB3_HUMAN | P21860 | 31.80 | 1021 | 585 | 100  
B | MALE_ECOLI | P0AEX9 | 3.91 | 366 | 579 | 1  
  
Opened 4 AlphaFold models  




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

Locale: en_US.UTF-8
Qt version: PyQt6 6.2.3, Qt 6.2.3
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: 7459.101.3
      OS Loader Version: 7459.101.3

Software:

    System Software Overview:

      System Version: macOS 12.3.1 (21E258)
      Kernel Version: Darwin 21.4.0
      Time since boot: 15 days 9:25

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
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          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
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          Connection Type: Internal


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[Tom Goddard]

The open command handles the isoform fetches, for example, command "open Q02297-6 from uniprot" works.